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Velasco M, Neto JLS, Eduard J, Gonçalves EC, Videira M, Oliveira E, Matos E. New species of Myxobolus in potamodromous catfish from the eastern Amazon, Brazil. Parasitol Int 2024; 103:102939. [PMID: 39074632 DOI: 10.1016/j.parint.2024.102939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 07/31/2024]
Abstract
The mapará (Hypophthalmus marginatus) is a commercially important fish in the Brazilian Amazon and has been described as a host for numerous myxosporid species. The integrated taxonomy of a new species, Myxobolus mickeyii n. sp., discovered in the urinary bladder of H. marginatus, is undertaken in this study. In 105 specimens of H. marginatus, plasmodia and myxospores were observed in the urinary bladder fluid, the myxospores measuring 20.5 (19.6-21.3) μm in length and 14.0 (13.2-14.9) μm in width. The posterior valves of the spore body were thick, with valvulogenic nuclei, endoplasmic reticulum, and the presence of secretory vesicles. Two elliptical, rounded appendages attached to the valve, containing tubular filaments. The two polar capsules, symmetry, measuring 6.1 (5.9-6.3) μm in length and 4.4 (3.6-6.2) μm in width, with polar tubules of 3 to 5 turns. Phylogenetic analyses of the small subunit ribosomal RNA gene (SSU rDNA) sequencing revealed that M. mickeyii n. sp. is part of a Myxobolidae family clade with freshwater fish of the Siluriformes order, with a genetic distance of 19% to the nearest species. This work contributes to the wide diversity of myxozoans in this host, as other taxa have previously been reported infecting different tissues.
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Affiliation(s)
- Michele Velasco
- Morpho-Molecular Integration Laboratory and Technologies (LIMT), Federal Rural University of the Amazon (UFRA), Belém, Pará, Brazil.
| | - José Ledamir Sindeaux Neto
- Morpho-Molecular Integration Laboratory and Technologies (LIMT), Federal Rural University of the Amazon (UFRA), Belém, Pará, Brazil
| | - Jhonata Eduard
- Morpho-Molecular Integration Laboratory and Technologies (LIMT), Federal Rural University of the Amazon (UFRA), Belém, Pará, Brazil; Biology of Infectious and Parasitic Agents (BAIP), Federal University of Pará (UFPA), Belem, Brazil
| | - Evonnildo Costa Gonçalves
- Biology of Infectious and Parasitic Agents (BAIP), Federal University of Pará (UFPA), Belem, Brazil; Laboratory of Biomolecular Technology, Federal University of Pará (UFPA), Belem, Pará, Brazil
| | - Marcela Videira
- Laboratory of Morphophysiology and Animal Health, Amapá State University (UEAP), Macapá, Amapá, Brazil
| | - Elsa Oliveira
- Laboratory of Cell Biology, Institute of Biomedical Sciences, University of Porto, Porto, Portugal
| | - Edilson Matos
- Morpho-Molecular Integration Laboratory and Technologies (LIMT), Federal Rural University of the Amazon (UFRA), Belém, Pará, Brazil
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Fabbri C, Giovanetti M, Luppo V, Fonseca V, Garcia J, Barulli C, Feroci M, Perrone S, Casoni D, Giamperetti S, Alvarez Lopez MC, Foussal MD, Figueredo M, Salvatierra K, Lejona S, Ruiz Diaz N, Castro G, Bravo G, Jackel N, Sen C, Poklepovich Caride T, Franco L, Giovachini C, Mendez Rico J, Alcantara LCJ, Morales MA. Tracing the evolution of the chikungunya virus in Argentina, 2016-2023: independent introductions and prominence of Latin American lineages. Emerg Microbes Infect 2024; 13:2362941. [PMID: 38813649 PMCID: PMC11168220 DOI: 10.1080/22221751.2024.2362941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/29/2024] [Indexed: 05/31/2024]
Abstract
Chikungunya virus (CHIKV) has emerged as a significant public health concern due to its rapid spread and potential for causing debilitating epidemics. In Argentina, the virus has garnered attention since its introduction to the Americas in 2013, due to its growing incidence and impact in neighbouring countries. Here we present a comprehensive analysis of the spatiotemporal dynamics of CHIKV in Argentina, focusing on the evolutionary trajectory of its genetic variants. Through a combination of active surveillance, screening of historical and recent samples, and whole-genome sequencing, we traced the evolutionary history of CHIKV lineages circulating within the country. Our results reveal that two distinct genotypes circulated in Argentina: The Asian lineage during the 2016 epidemic and the ECSA lineage in 2023. This distribution reflects the dominance of particular variants across Latin America. Since 2023, the ECSA lineage has led to a surge in cases throughout the Americas, marking a significant shift. The replacement of lineages in the American region constitutes a major epidemiological event, potentially affecting the dynamics of virus transmission and the clinical outcomes in impacted populations. The spatiotemporal analysis highlights CHIKV's distribution across Argentina and underscores the significant role of human mobility, especially when considering recent epidemics in neighbouring countries such as Paraguay and Uruguay, which have facilitated the spread and introduction of the viral strain into different districts. By integrating epidemiological data with genomic insights, we elucidate the patterns of virus dissemination, highlighting key areas of transmission and potential factors contributing to its spread.
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Affiliation(s)
- Cintia Fabbri
- Instituto Nacional de Enfermedaes Virales Humanas “Dr. Maiztegui”, ANLIS, Pergamino, Argentina
| | - Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Universita Campus Bio-Medico di Roma, Rome, Italy
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Minas Gerais, Brazil
| | - Victoria Luppo
- Instituto Nacional de Enfermedaes Virales Humanas “Dr. Maiztegui”, ANLIS, Pergamino, Argentina
| | - Vagner Fonseca
- Climate Amplified Diseases and Epidemics (CLIMADE), Minas Gerais, Brazil
- Departamento de Ciências Exatas e da Terra, Universidade do Estado da Bahia, Salvador, Brazil
| | - Jorge Garcia
- Instituto Nacional de Enfermedaes Virales Humanas “Dr. Maiztegui”, ANLIS, Pergamino, Argentina
| | - Cintia Barulli
- Instituto Nacional de Enfermedaes Virales Humanas “Dr. Maiztegui”, ANLIS, Pergamino, Argentina
| | - Mariel Feroci
- Instituto Nacional de Enfermedaes Virales Humanas “Dr. Maiztegui”, ANLIS, Pergamino, Argentina
| | - Sofia Perrone
- Instituto Nacional de Enfermedaes Virales Humanas “Dr. Maiztegui”, ANLIS, Pergamino, Argentina
| | - Doraldina Casoni
- Instituto Nacional de Enfermedaes Virales Humanas “Dr. Maiztegui”, ANLIS, Pergamino, Argentina
| | - Sergio Giamperetti
- Hospital de Infecciosas Francisco Javier Muñiz, CABA, Buenos Aires, Argentina
| | | | | | - Mauricio Figueredo
- Hospital de Alta Complejidad “Pte. Juan Domingo Perón”, Formosa, Argentina
| | | | - Sergio Lejona
- CEMAR – Secretaria de Salud – Municipalidad de Rosario, Santa Fe, Argentina
| | - Natalia Ruiz Diaz
- Laboratorio Central de Redes y Programas de Corrientes, Corrientes, Argentina
| | - Gonzalo Castro
- Laboratorio Central de la Provincia de Cordoba, Córdoba, Argentina
| | | | - Noelia Jackel
- Instituto Nacional de Enfermedaes Virales Humanas “Dr. Maiztegui”, ANLIS, Pergamino, Argentina
| | - Carina Sen
- Instituto Nacional de Enfermedaes Virales Humanas “Dr. Maiztegui”, ANLIS, Pergamino, Argentina
| | | | - Leticia Franco
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organi-zation/World Health Organization (PAHO/WHO), Washington, DC, USA
| | - Carlos Giovachini
- Direccion de Epidemiologia, Minsiterio de Salud de la Nacion, Buenos Aires, Argentina
| | - Jairo Mendez Rico
- Infectious Hazards Management, Health Emergencies Department (PHE), Pan American Health Organi-zation/World Health Organization (PAHO/WHO), Washington, DC, USA
| | - Luiz Carlos Junior Alcantara
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
- Climate Amplified Diseases and Epidemics (CLIMADE), Minas Gerais, Brazil
| | - Maria Alejandra Morales
- Instituto Nacional de Enfermedaes Virales Humanas “Dr. Maiztegui”, ANLIS, Pergamino, Argentina
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de La Bourdonnaye G, Ghazalova T, Fojtik P, Kutalkova K, Bednar D, Damborsky J, Rotrekl V, Stepankova V, Chaloupkova R. Computer-aided engineering of stabilized fibroblast growth factor 21. Comput Struct Biotechnol J 2024; 23:942-951. [PMID: 38379823 PMCID: PMC10877085 DOI: 10.1016/j.csbj.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/03/2024] [Accepted: 02/03/2024] [Indexed: 02/22/2024] Open
Abstract
FGF21 is an endocrine signaling protein belonging to the family of fibroblast growth factors (FGFs). It has emerged as a molecule of interest for treating various metabolic diseases due to its role in regulating glucogenesis and ketogenesis in the liver. However, FGF21 is prone to heat, proteolytic, and acid-mediated degradation, and its low molecular weight makes it susceptible to kidney clearance, significantly reducing its therapeutic potential. Protein engineering studies addressing these challenges have generally shown that increasing the thermostability of FGF21 led to improved pharmacokinetics. Here, we describe the computer-aided design and experimental characterization of FGF21 variants with enhanced melting temperature up to 15 °C, uncompromised efficacy at activation of MAPK/ERK signaling in Hep G2 cell culture, and ability to stimulate proliferation of Hep G2 and NIH 3T3 fibroblasts cells comparable with FGF21-WT. We propose that stabilizing the FGF21 molecule by rational design should be combined with other reported stabilization strategies to maximize the pharmaceutical potential of FGF21.
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Affiliation(s)
- Gabin de La Bourdonnaye
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Enantis Ltd., Biotechnology Incubator INBIT, Brno, Czech Republic
| | - Tereza Ghazalova
- Enantis Ltd., Biotechnology Incubator INBIT, Brno, Czech Republic
| | - Petr Fojtik
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | - David Bednar
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Jiri Damborsky
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Loschmidt Laboratories, Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Vladimir Rotrekl
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | | | - Radka Chaloupkova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Enantis Ltd., Biotechnology Incubator INBIT, Brno, Czech Republic
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Tolman ER, Beatty CD, Kohli MK, Abbott J, Bybee SM, Frandsen PB, Stephen Gosnell J, Guralnick R, Kalkman VJ, Newton LG, Suvorov A, Ware JL. A molecular phylogeny of the Petaluridae (Odonata: Anisoptera): A 160-Million-Year-Old story of drift and extinction. Mol Phylogenet Evol 2024; 200:108185. [PMID: 39209047 DOI: 10.1016/j.ympev.2024.108185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 08/12/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Petaluridae (Odonata: Anisoptera) is a relict dragonfly family, having diverged from its sister family in the Jurassic, of eleven species that are notable among odonates (dragonflies and damselflies) for their exclusive use of fen and bog habitats, their burrowing behavior as nymphs, large body size as adults, and extended lifespans. To date, several nodes within this family remain unresolved, limiting the study of the evolution of this peculiar family. Using an anchored hybrid enrichment dataset of over 900 loci we reconstructed the species tree of Petaluridae. To estimate the temporal origin of the genera within this family, we used a set of well-vetted fossils and a relaxed molecular clock model in a divergence time estimation analysis. We estimate that Petaluridae originated in the early Cretaceous and confirm the existence of monophyletic Gondwanan and Laurasian clades within the family. Our relaxed molecular clock analysis estimated that these clades diverged from their MRCA approximately 160 mya. Extant lineages within this family were identified to have persisted from 6 (Uropetala) to 120 million years (Phenes). Our biogeographical analyses focusing on a set of key regions suggest that divergence within Petaluridae is largely correlated with continental drift, the exposure of land bridges, and the development of mountain ranges. Our results support the hypothesis that species within Petaluridae have persisted for tens of millions of years, with little fossil evidence to suggest widespread extinction in the family, despite optimal conditions for the fossilization of nymphs. Petaluridae appear to be a rare example of habitat specialists that have persisted for tens of millions of years.
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Affiliation(s)
- Ethan R Tolman
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024; Department of Biological Sciences, Virginia Tech, Blacksburg, VA; Conservation Connection Foundation, Boise, ID.
| | - Christopher D Beatty
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024; Program for Conservation Genomics, Department of Biology, Stanford University
| | - Manpreet K Kohli
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024; Conservation Connection Foundation, Boise, ID; Department of Natural Sciences, Baruch College, New York
| | - John Abbott
- Alabama Museum of Natural History and Department of Research and Collections, The University of Alabama
| | - Seth M Bybee
- Department of Biology and Monte L. Bean Museum, Brigham Young University, Provo, UT
| | - Paul B Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT
| | - J Stephen Gosnell
- Department of Natural Sciences, Baruch College, New York; PhD Program in Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, Room 4315, New York, 10016
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL
| | - V J Kalkman
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden
| | - Lacie G Newton
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024
| | - Anton Suvorov
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA
| | - Jessica L Ware
- American Museum of Natural History, Department of Invertebrate Zoology, New York, 10024
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Bang WJ, Seol A, Shin S. Insights from multigene analysis: first report of a Southeast Asian Mosquito, Aedes (Mucidus) laniger (Diptera: Culicidae) on Jeju Island from Korea. Parasit Vectors 2024; 17:386. [PMID: 39267122 PMCID: PMC11395179 DOI: 10.1186/s13071-024-06373-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/24/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND Certain mosquitoes are known as dominant vectors worldwide, and transmit infectious diseases. The expansion of mosquito habitats due to climate change and increased human activities poses a significant health threat by facilitating the spread of various non-native infectious diseases. This study focused on the detection of the Southeast Asian mosquito species, Aedes (Mucidus) laniger (Wiedemann, 1820) on Jeju Island, the southernmost region of the Republic of Korea (ROK), highlighting the potential risks associated with the spread of vector-borne diseases, particularly emphasizing the elevated likelihood of invasion by Southeast Asian mosquitoes. METHODS Field surveys were conducted in August 2023 on Jeju Island. Adult mosquitoes were collected using BG-sentinel traps and identified to the species level using taxonomic keys. Morphological and molecular analyses were employed to confirm species designations. Molecular data, including mitochondrial and nuclear genes, were used for phylogenetic analysis, which was performed to compare and identify among recorded subgenera in ROK. Species distribution modeling for Ae. laniger was performed to predict potential habitats using R package 'BIOMOD2'. RESULTS The two specimens of Ae. laniger were collected for the first time on Jeju Island. Morphological and molecular analyses confirmed the identity of this species within the subgenus Mucidus and validated the first record of this species in the ROK. We employed a simple multigene phylogenetic analysis to confirm a new mosquito record at the genus and subgenus levels, finally validating the consistency between morphological identification and molecular phylogenetic outcomes. Furthermore, we have updated the taxonomic keys for the genus Aedes in the ROK, and revised mosquito lists for Jeju Island, incorporating the inclusion of Ae. laniger. On the basis of species distribution modeling, the area of suitable habitat for Ae. laniger is expected to expand due to climate change, but this change did not appear to be meaningful in East Asia. CONCLUSIONS This case offers the first report of the Southeast Asian mosquito, Ae. laniger, in the ROK. The detection of this species on Jeju Island suggests the potential establishment of a breeding population their habitat and raises concerns about further expansion into the Korean Peninsula. Considering the annual occurrence of mosquito-borne disease cases in the Southeast Asia, it is essential to conduct monitoring not only in Jeju Island, where Ae. laniger has been identified, but also across the entire Korean Peninsula.
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Affiliation(s)
- Woo Jun Bang
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ara Seol
- Warm Temperate and Subtropical Forest Research Center, National Institute of Forest Science, Jeju, 63582, Republic of Korea
| | - Seunggwan Shin
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
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Yoshinaga TT, Giovanella P, de Farias GS, Dos Santos JA, Pellizzer EP, Sette LD. Fungi from Antarctic marine sediment: characterization and assessment for textile dye decolorization and detoxification. Braz J Microbiol 2024:10.1007/s42770-024-01485-w. [PMID: 39259479 DOI: 10.1007/s42770-024-01485-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/25/2024] [Indexed: 09/13/2024] Open
Abstract
Cold-adapted microorganisms can produce enzymes with activity at low and mild temperatures, which can be applied to environmental biotechnology. This study aimed to characterize 20 Antarctic fungi to identify their genus (ITS rDNA marker) and growth temperatures and evaluate their ability to decolorize and detoxify the textile dye indigo carmine (IC). An individual screening was performed to assess the decolorization and detoxification of IC by the isolates, as well as in consortia with other fungi. The isolates were affiliated with seven ascomycete genera: Aspergillus (n = 4), Cosmospora (n = 2), Leuconeurospora (n = 2), Penicillium (n = 3), Pseudogymnoascus (n = 6), Thelebolus (n = 2), and Trichoderma (n = 1). The two isolates from the genus Leuconeurospora were characterized as psychrophilic, while the others were psychrotolerant. The Penicillium isolates were able to decolorize between 60 and 82% of IC. The isolates identified as Pseudogymnoascus showed the best detoxification capacity, with results varying from 49 to 74%. The consortium using only Antarctic ascomycetes (C1) showed 45% of decolorization, while the consortia with the addition of basidiomycetes (C1 + Peniophora and C1 + Pholiota) showed 40% and 50%, respectively. The consortia C1 with the addition of the basidiomycetes presented a lower toxicity after the treatments. In addition, a higher fungal biomass was produced in the presence of dye when compared with the experiment without the dye, which can be indicative of dye metabolization. The results highlight the potential of marine-derived Antarctic fungi in the process of textile dye degradation. The findings encourage further studies to elucidate the degradation and detoxification pathways of the dye IC by these fungal isolates.
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Affiliation(s)
- Thaís Tiemi Yoshinaga
- Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), 24A, 1515, Rio Claro, CEP 13506-900, SP, Brazil
| | - Patrícia Giovanella
- Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), 24A, 1515, Rio Claro, CEP 13506-900, SP, Brazil
- Centro de Estudos Ambientais, Universidade Estadual Paulista (UNESP), Rio Claro, CEP 13506-900, SP, Brazil
| | - Gabriele Santana de Farias
- Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), 24A, 1515, Rio Claro, CEP 13506-900, SP, Brazil
| | - Juliana Aparecida Dos Santos
- Universidade do Vale do Sapucaí (Univás), Av. Prefeito Tuany Toledo, 470 - Fatima, Pouso Alegre, 37550-000, MG, Brazil
| | - Elisa Pais Pellizzer
- Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), 24A, 1515, Rio Claro, CEP 13506-900, SP, Brazil
| | - Lara Durães Sette
- Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), 24A, 1515, Rio Claro, CEP 13506-900, SP, Brazil.
- Centro de Estudos Ambientais, Universidade Estadual Paulista (UNESP), Rio Claro, CEP 13506-900, SP, Brazil.
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Götz M, Sommerfeld K, Gärber U, Braun U, Ashrafi S. Rhexocercosporidium matricariae sp. nov.: A New Pathogen on the Medicinal Plant Matricaria recutita. PLANT DISEASE 2024:PDIS01240085SR. [PMID: 38764342 DOI: 10.1094/pdis-01-24-0085-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
A new disease was observed on chamomile plants (Matricaria recutita) in various commercially cultivated fields in 2016 and 2017 in Germany. From symptomatic stems and leaves, the fungal species described here was isolated repeatedly. Koch's postulates using in planta experiments were fulfilled by inoculation of chamomile plants proving the fungus to be the causal agent of the disease. Morphological studies and phylogenetic analyses using internal transcribed spacer, large subunit, and translation elongation factor-1α sequences suggested that the fungus represents a new species within the genus Rhexocercosporidium (Helotiales). The data are presented together with a description of the growth parameters and comprehensive illustrations of the new species, Rhexocercosporidium matricariae. All species so far assigned to Rhexocercosporidium are compared and discussed. The combination Rhexocercosporidium microsporum is validated.
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Affiliation(s)
- Monika Götz
- Institute for Plant Protection in Horticulture and Urban Green, Julius Kühn-Institute (JKI) - Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
| | - Katja Sommerfeld
- Institute for Plant Protection in Horticulture and Urban Green, Julius Kühn-Institute (JKI) - Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
| | - Ute Gärber
- Institute for Plant Protection in Horticulture and Urban Green, Julius Kühn-Institute (JKI) - Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
| | - Uwe Braun
- Herbarium, Department of Geobotany and Botanical Garden, Institute of Biology, Martin Luther University, 06108 Halle (Saale), Germany
| | - Samad Ashrafi
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institute (JKI) - Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
- Institute for Crop and Soil Science, Julius Kühn-Institute (JKI) - Federal Research Centre for Cultivated Plants, 38116 Braunschweig, Germany
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8
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Rødsgaard-Jørgensen A, Leal-Dutra CA, de Santana SF, Jensen AR, Marques RE, Aguiar ERGR, Shik JZ. Two +ssRNA mycoviruses cohabiting the fungal cultivar of leafcutter ants. Virol J 2024; 21:211. [PMID: 39232804 PMCID: PMC11373429 DOI: 10.1186/s12985-024-02465-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024] Open
Abstract
Leafcutter ants are dominant herbivores in the Neotropics and rely on a fungus (Leucoagaricus gongylophorus) to transform freshly gathered leaves into a source of nourishment rather than consuming the vegetation directly. Here we report two virus-like particles that were isolated from L. gongylophorus and observed using transmission electron microscopy. RNA sequencing identified two +ssRNA mycovirus strains, Leucoagaricus gongylophorus tymo-like virus 1 (LgTlV1) and Leucoagaricus gongylophorus magoulivirus 1 (LgMV1). Genome annotation of LgTlV1 (7401 nt) showed conserved domains for methyltransferase, endopeptidase, viral RNA helicase, and RNA-dependent RNA polymerase (RdRp). The smaller genome of LgMV1 (2636 nt) contains one open reading frame encoding an RdRp. While we hypothesize these mycoviruses function as symbionts in leafcutter farming systems, further study will be needed to test whether they are mutualists, commensals, or parasites.
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Affiliation(s)
- Asta Rødsgaard-Jørgensen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Caio Ambrosio Leal-Dutra
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark.
| | - Sabrina Ferreira de Santana
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Asger Roland Jensen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | | | - Jonathan Zvi Shik
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
- Smithsonian Tropical Research Institute, Apartado Postal, 0843-03092, Balboa, Ancon, Panama
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Banyard AC, Bennison A, Byrne AMP, Reid SM, Lynton-Jenkins JG, Mollett B, De Silva D, Peers-Dent J, Finlayson K, Hall R, Blockley F, Blyth M, Falchieri M, Fowler Z, Fitzcharles EM, Brown IH, James J. Detection and spread of high pathogenicity avian influenza virus H5N1 in the Antarctic Region. Nat Commun 2024; 15:7433. [PMID: 39227574 PMCID: PMC11372179 DOI: 10.1038/s41467-024-51490-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 08/08/2024] [Indexed: 09/05/2024] Open
Abstract
Until recent events, the Antarctic was the only major geographical region in which high pathogenicity avian influenza virus (HPAIV) had never previously been detected. Here we report on the detection of clade 2.3.4.4b H5N1 HPAIV in the Antarctic and sub-Antarctic regions of South Georgia and the Falkland Islands, respectively. We initially detected H5N1 HPAIV in samples collected from brown skuas at Bird Island, South Georgia on 8th October 2023. Since this detection, mortalities were observed in several avian and mammalian species at multiple sites across South Georgia. Subsequent testing confirmed H5N1 HPAIV across several sampling locations in multiple avian species and two seal species. Simultaneously, we also confirmed H5N1 HPAIV in southern fulmar and black-browed albatross in the Falkland Islands. Genetic assessment of the virus indicates spread from South America, likely through movement of migratory birds. Critically, genetic assessment of sequences from mammalian species demonstrates no increased risk to human populations above that observed in other instances of mammalian infections globally. Here we describe the detection, species impact and genetic composition of the virus and propose both introductory routes and potential long-term impact on avian and mammalian species across the Antarctic region. We also speculate on the threat to specific populations following recent reports in the area.
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Affiliation(s)
- Ashley C Banyard
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK.
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK.
| | - Ashley Bennison
- British Antarctic Survey, Madingley Road, Cambridge, CB3 0ET, UK
| | - Alexander M P Byrne
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
- Worldwide Influenza Centre, The Francis Crick Institute, Midland Road, London, NW1 1AT, UK
| | - Scott M Reid
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Joshua G Lynton-Jenkins
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Benjamin Mollett
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Dilhani De Silva
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Jacob Peers-Dent
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Kim Finlayson
- KEMH Pathology and Food, Water & Environmental Laboratory, St Mary's Walk, Stanley, FIQQ 1ZZ, Falkland Islands
| | - Rosamund Hall
- British Antarctic Survey, Madingley Road, Cambridge, CB3 0ET, UK
| | - Freya Blockley
- British Antarctic Survey, Madingley Road, Cambridge, CB3 0ET, UK
| | - Marcia Blyth
- British Antarctic Survey, Madingley Road, Cambridge, CB3 0ET, UK
| | - Marco Falchieri
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Zoe Fowler
- Department of Agriculture, Bypass Road, Stanley, FIQQ 1ZZ, Falkland Islands
| | | | - Ian H Brown
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK
| | - Joe James
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK.
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK.
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10
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Valerio F, Martel C, Stefanescu C, van Nouhuys S, Kankare M, Duplouy A. Wolbachia strain diversity in a complex group of sympatric cryptic parasitoid wasp species. BMC Microbiol 2024; 24:319. [PMID: 39223450 PMCID: PMC11368008 DOI: 10.1186/s12866-024-03470-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Maternally-inherited symbionts can induce pre-mating and/or post-mating reproductive isolation between sympatric host lineages, and speciation, by modifying host reproductive phenotypes. The large parasitoid wasp genus Cotesia (Braconidae) includes a diversity of cryptic species, each specialized in parasitizing one to few related Lepidoptera host species. Here, we characterized the infection status of an assemblage of 21 Cotesia species from 15 countries by several microbial symbionts, as a first step toward investigating whether symbionts may provide a barrier to gene flow between these parasitoid host lineages. RESULTS The symbiotic microbes Arsenophonus, Cardinium, Microsporidium and Spiroplasma were not detected in the Cotesia wasps. However, the endosymbiotic bacterium Wolbachia was present in at least eight Cotesia species, and hence we concentrated on it upon screening additional DNA extracts and SRAs from NCBI. Some of the closely related Cotesia species carry similar Wolbachia strains, but most Wolbachia strains showed patterns of horizontal transfer between phylogenetically distant host lineages. CONCLUSIONS The lack of co-phylogenetic signal between Wolbachia and Cotesia suggests that the symbiont and hosts have not coevolved to an extent that would drive species divergence between the Cotesia host lineages. However, as the most common facultative symbiont of Cotesia species, Wolbachia may still function as a key-player in the biology of the parasitoid wasps. Its precise role in the evolution of this complex clade of cryptic species remains to be experimentally investigated.
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Affiliation(s)
- Federica Valerio
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | | | | | - Saskya van Nouhuys
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, India
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anne Duplouy
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.
- Department of Biology, Lund University, Lund, Sweden.
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11
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Farias de Farias N, Gunski RJ, Del Valle Garnero A, Cañedo AD, Herculano Correa de Oliveira E, Oliveira Silva FA, Torres FP. Chromosome mapping of retrotransposon AviRTE in a neotropical bird species: Trogon surrucura (Trogoniformes; Trogonidae). Genome 2024; 67:307-315. [PMID: 38722237 DOI: 10.1139/gen-2023-0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Avian genomes are characterized as being more compact than other amniotes, with less diversity and density of transposable elements (TEs). In addition, birds usually show bimodal karyotypes, exhibiting a great variation in diploid numbers. Some species present unusually large sex chromosomes, possibly due to the accumulation of repetitive sequences. Avian retrotransposon-like element (AviRTE) is a long interspersed nuclear element (LINE) recently discovered in the genomes of birds and nematodes, and it is still poorly characterized in terms of chromosomal mapping and phylogenetic relationships. In this study, we mapped AviRTE isolated from the Trogon surrucura genome into the T. surrucura (TSU) karyotype. Furthermore, we analyzed the phylogenetic relationships of this LINE in birds and other vertebrates. Our results showed that the distribution pattern of AviRTE is not restricted to heterochromatic regions, with accumulation on the W chromosome of TSU, yet another species with an atypical sex chromosome and TE hybridization. The phylogenetic analysis of AviRTE sequences in birds agreed with the proposed phylogeny of species in most clades, and allowed the detection of this sequence in other species, expanding the distribution of the element.
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Affiliation(s)
- Nairo Farias de Farias
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, Campus São Gabriel, RS, Brazil
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, Campus São Gabriel, RS, Brazil
| | - Ricardo José Gunski
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, Campus São Gabriel, RS, Brazil
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, Campus São Gabriel, RS, Brazil
| | - Analía Del Valle Garnero
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, Campus São Gabriel, RS, Brazil
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, Campus São Gabriel, RS, Brazil
| | - Andrés Delgado Cañedo
- Programa de Pós-graduação em Ciências Biológicas, Universidade Federal do Pampa, Campus São Gabriel, RS, Brazil
| | - Edivaldo Herculano Correa de Oliveira
- Laboratório de Citogenômica e Mutagênese ambiental, SEAMB, Instituto Evandro Chagas, Ananindeua, PA, Brazil
- Faculdade de Ciências Naturais, ICEN, Universidade Federal do Pará, Belém, PA, Brazil
| | - Fábio Augusto Oliveira Silva
- Programa de Pós-Graduação em Neurociências e Biologia Celular, ICB, Universidade Federal do Pará, Belém, PA, Brazil
| | - Fabiano Pimentel Torres
- Laboratório de Diversidade Genética Animal, Universidade Federal do Pampa, Campus São Gabriel, RS, Brazil
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12
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Coelho-Nascimento C, Zabin DA, E Silva-Filho AGDS, Drewinski MP, Alves-Silva G, Kossmann T, Titton M, Drechsler-Santos ER, Menolli N. Unroughing the cat's tongue mushrooms: Four new species of Pseudohydnum from Brazil based on morphological and molecular phylogenetic evidence. Mycologia 2024; 116:792-820. [PMID: 39121366 DOI: 10.1080/00275514.2024.2363141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/30/2024] [Indexed: 08/11/2024]
Abstract
Pseudohydnum, commonly known as cat's tongue mushrooms, is a monophyletic assemblage within Auriculariales, which encompasses species with gelatinous basidiomata, spathulate, flabellate, or shell-shaped pileus, hydnoid hymenophore, globose to ellipsoidal basidiospores, and longitudinally cruciate-septate basidia. According to the available literature, 16 species have been described in Pseudohydnum, mostly represented in temperate-boreal forests of the Northern Hemisphere. However, the limited morphological, molecular, and ecological information, especially from the Southern Hemisphere ecosystems, does not presently allow a reliable assessment of its taxonomic boundaries nor provide a complete picture of the species diversity in the genus. In an ongoing effort to examine specimens collected in dense and mixed ombrophilous forest fragments (Atlantic Rainforest domain) from Southeastern and Southern Brazil, additional taxa assigned to Pseudohydnum were identified. Four new species are recognized based mostly on characters of the pileus surface, stipe, hymenium, and basidiospores. Molecular phylogenetic analyses based on nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS barcode), partial nuc rDNA 28S, and partial RNA polymerase II largest subunit (RPB1) sequences supported the description of these new taxa. Here, we propose Pseudohydnum brasiliense, P. brunneovelutinum, P. cupulisnymphae, and P. viridimontanum as new species. Morphological descriptions, line drawings, habitat photos, and comparisons with closely related taxa are provided. A dichotomous key for identification of currently known Southern Hemisphere Pseudohydnum species is presented.
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Affiliation(s)
- Cristiano Coelho-Nascimento
- Departamento de Micologia, Núcleo de Pós-graduação Stricto Sensu, Pós-graduação em Biodiversidade Vegetal e Meio Ambiente, Instituto de Pesquisas Ambientais (IPA), Av. Miguel Estefano 3687, Água Funda, São Paulo, São Paulo 04301-012, Brazil
- IFungiLab, Subárea de Biologia, Departamento de Ciências da Natureza e Matemática, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo (SPO), Rua Pedro Vicente 625, São Paulo, São Paulo 01109-010, Brazil
- Departamento de Ciências da Natureza, Laboratório de Biologia, Instituto Federal de Educação, Ciência e Tecnologia do Piauí (IFPI), Câmpus Piripiri (CAPIR), Av. Rio dos Matos s/n, Piripiri, Piauí 74260-000, Brazil
| | - Denis A Zabin
- Departamento de Micologia, Núcleo de Pós-graduação Stricto Sensu, Pós-graduação em Biodiversidade Vegetal e Meio Ambiente, Instituto de Pesquisas Ambientais (IPA), Av. Miguel Estefano 3687, Água Funda, São Paulo, São Paulo 04301-012, Brazil
- IFungiLab, Subárea de Biologia, Departamento de Ciências da Natureza e Matemática, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo (SPO), Rua Pedro Vicente 625, São Paulo, São Paulo 01109-010, Brazil
| | - Alexandre G Dos Santos E Silva-Filho
- IFungiLab, Subárea de Biologia, Departamento de Ciências da Natureza e Matemática, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo (SPO), Rua Pedro Vicente 625, São Paulo, São Paulo 01109-010, Brazil
| | - Mariana P Drewinski
- Departamento de Micologia, Núcleo de Pós-graduação Stricto Sensu, Pós-graduação em Biodiversidade Vegetal e Meio Ambiente, Instituto de Pesquisas Ambientais (IPA), Av. Miguel Estefano 3687, Água Funda, São Paulo, São Paulo 04301-012, Brazil
- IFungiLab, Subárea de Biologia, Departamento de Ciências da Natureza e Matemática, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo (SPO), Rua Pedro Vicente 625, São Paulo, São Paulo 01109-010, Brazil
| | - Genivaldo Alves-Silva
- Programa de Pós-graduação em Biologia de Fungos, Algas e Plantas, Laboratório de Micologia (MICOLAB-UFSC), Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Câmpus Universitário Reitor João David Ferreira Lima s/n, Florianópolis, Santa Catarina 88040-900, Brazil
- MIND.Funga (Monitoring and Inventorying Neotropical Diversity of Fungi), Laboratório de Micologia (MICOLAB-UFSC), Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Câmpus Universitário Reitor João David Ferreira Lima s/n, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Thiago Kossmann
- MIND.Funga (Monitoring and Inventorying Neotropical Diversity of Fungi), Laboratório de Micologia (MICOLAB-UFSC), Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Câmpus Universitário Reitor João David Ferreira Lima s/n, Florianópolis, Santa Catarina 88040-900, Brazil
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, 1900 Pleasant Street, Boulder, Colorado 80304
| | - Mahatma Titton
- Programa de Pós-graduação em Biologia de Fungos, Algas e Plantas, Laboratório de Micologia (MICOLAB-UFSC), Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Câmpus Universitário Reitor João David Ferreira Lima s/n, Florianópolis, Santa Catarina 88040-900, Brazil
- MIND.Funga (Monitoring and Inventorying Neotropical Diversity of Fungi), Laboratório de Micologia (MICOLAB-UFSC), Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Câmpus Universitário Reitor João David Ferreira Lima s/n, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Elisandro R Drechsler-Santos
- Programa de Pós-graduação em Biologia de Fungos, Algas e Plantas, Laboratório de Micologia (MICOLAB-UFSC), Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Câmpus Universitário Reitor João David Ferreira Lima s/n, Florianópolis, Santa Catarina 88040-900, Brazil
- MIND.Funga (Monitoring and Inventorying Neotropical Diversity of Fungi), Laboratório de Micologia (MICOLAB-UFSC), Departamento de Botânica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, Câmpus Universitário Reitor João David Ferreira Lima s/n, Florianópolis, Santa Catarina 88040-900, Brazil
| | - Nelson Menolli
- Departamento de Micologia, Núcleo de Pós-graduação Stricto Sensu, Pós-graduação em Biodiversidade Vegetal e Meio Ambiente, Instituto de Pesquisas Ambientais (IPA), Av. Miguel Estefano 3687, Água Funda, São Paulo, São Paulo 04301-012, Brazil
- IFungiLab, Subárea de Biologia, Departamento de Ciências da Natureza e Matemática, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo (SPO), Rua Pedro Vicente 625, São Paulo, São Paulo 01109-010, Brazil
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13
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Taylor DJ, Barnhart MH. Genomic transfers help to decipher the ancient evolution of filoviruses and interactions with vertebrate hosts. PLoS Pathog 2024; 20:e1011864. [PMID: 39226335 PMCID: PMC11398700 DOI: 10.1371/journal.ppat.1011864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 09/13/2024] [Accepted: 08/21/2024] [Indexed: 09/05/2024] Open
Abstract
Although several filoviruses are dangerous human pathogens, there is conflicting evidence regarding their origins and interactions with animal hosts. Here we attempt to improve this understanding using the paleoviral record over a geological time scale, protein structure predictions, tests for evolutionary maintenance, and phylogenetic methods that alleviate sources of bias and error. We found evidence for long branch attraction bias in the L gene tree for filoviruses, and that using codon-specific models and protein structural comparisons of paleoviruses ameliorated conflict and bias. We found evidence for four ancient filoviral groups, each with extant viruses and paleoviruses with open reading frames. Furthermore, we found evidence of repeated transfers of filovirus-like elements to mouse-like rodents. A filovirus-like nucleoprotein ortholog with an open reading frame was detected in three subfamilies of spalacid rodents (present since the Miocene). We provide evidence that purifying selection is acting to maintain amino acids, protein structure and open reading frames in these elements. Our finding of extant viruses nested within phylogenetic clades of paleoviruses informs virus discovery methods and reveals the existence of Lazarus taxa among RNA viruses. Our results resolve a deep conflict in the evolutionary framework for filoviruses and reveal that genomic transfers to vertebrate hosts with potentially functional co-options have been more widespread than previously appreciated.
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Affiliation(s)
- Derek J Taylor
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Max H Barnhart
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
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14
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Roulet ME, Ceriotti LF, Gatica-Soria L, Sanchez-Puerta MV. Horizontally transferred mitochondrial DNA tracts become circular by microhomology-mediated repair pathways. THE NEW PHYTOLOGIST 2024; 243:2442-2456. [PMID: 39044460 DOI: 10.1111/nph.19984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Accepted: 07/02/2024] [Indexed: 07/25/2024]
Abstract
The holoparasitic plant Lophophytum mirabile exhibits remarkable levels of mitochondrial horizontal gene transfer (HGT). Gathering comparative data from other individuals and host plants can provide insights into the HGT process. We sequenced the mitochondrial genome (mtDNA) from individuals of two species of Lophophytum and from mimosoid hosts. We applied a stringent phylogenomic approach to elucidate the origin of the whole mtDNAs, estimate the timing of the transfers, and understand the molecular mechanisms involved. Ancestral and recent HGT events replaced and enlarged the multichromosomal mtDNA of Lophophytum spp., with the foreign DNA ascending to 74%. A total of 14 foreign mitochondrial chromosomes originated from continuous regions in the host mtDNA flanked by short direct repeats. These foreign tracts are circularized by microhomology-mediated repair pathways and replicate independently until they are lost or they eventually recombine with other chromosomes. The foreign noncoding chromosomes are variably present in the population and likely evolve by genetic drift. We present the 'circle-mediated HGT' model in which foreign mitochondrial DNA tracts become circular and are maintained as plasmid-like molecules. This model challenges the conventional belief that foreign DNA must be integrated into the recipient genome for successful HGT.
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Affiliation(s)
- M Emilia Roulet
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
| | - Luis Federico Ceriotti
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - Leonardo Gatica-Soria
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
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15
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Esteban-Collado J, Fernández-Mañas M, Fernández-Moreno M, Maeso I, Corominas M, Serras F. Reactive oxygen species activate the Drosophila TNF receptor Wengen for damage-induced regeneration. EMBO J 2024; 43:3604-3626. [PMID: 39020149 PMCID: PMC11377715 DOI: 10.1038/s44318-024-00155-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/05/2024] [Accepted: 06/12/2024] [Indexed: 07/19/2024] Open
Abstract
Tumor necrosis factor receptors (TNFRs) control pleiotropic pro-inflammatory functions that range from apoptosis to cell survival. The ability to trigger a particular function will depend on the upstream cues, association with regulatory complexes, and downstream pathways. In Drosophila melanogaster, two TNFRs have been identified, Wengen (Wgn) and Grindelwald (Grnd). Although several reports associate these receptors with JNK-dependent apoptosis, it has recently been found that Wgn activates a variety of other functions. We demonstrate that Wgn is required for survival by protecting cells from apoptosis. This is mediated by dTRAF1 and results in the activation of p38 MAP kinase. Remarkably, Wgn is required for apoptosis-induced regeneration and is activated by the reactive oxygen species (ROS) produced following apoptosis. This ROS activation is exclusive for Wgn, but not for Grnd, and can occur after knocking down Eiger/TNFα. The extracellular cysteine-rich domain of Grnd is much more divergent than that of Wgn, which is more similar to TNFRs from other animals, including humans. Our results show a novel TNFR function that responds to stressors by ensuring p38-dependent regeneration.
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Affiliation(s)
- José Esteban-Collado
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Mar Fernández-Mañas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Manuel Fernández-Moreno
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute for Biodiversity Research (IRBio), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Ignacio Maeso
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institute for Biodiversity Research (IRBio), Barcelona, Spain
| | - Montserrat Corominas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Florenci Serras
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain.
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16
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Dong J, Zhu Y, Qian C, Zhao C. Taxonomy and phylogeny of Auriculariales (Agaricomycetes, Basidiomycota) with descriptions of four new species from south-western China. MycoKeys 2024; 108:115-146. [PMID: 39246551 PMCID: PMC11380053 DOI: 10.3897/mycokeys.108.128659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 08/04/2024] [Indexed: 09/10/2024] Open
Abstract
The wood-inhabiting fungi play an integral role in wood degradation and the cycle of matter in the ecological system. They are considered as the "key player" in wood decomposition, because of their ability to produce lignocellulosic enzymes that break down woody lignin, cellulose and hemicellulose. In the present study, four new wood-inhabiting fungal species, Adustochaetealbomarginata, Ad.punctata, Alloexidiopsisgrandinea and Al.xantha collected from southern China, are proposed, based on a combination of morphological features and molecular evidence. Adustochaetealbomarginata is characterised by resupinate basidiomata with cream to buff, a smooth, cracked, hymenial surface, a monomitic hyphal system with clamped generative hyphae and subcylindrical to allantoid basidiospores (12-17.5 × 6.5-9 µm). Adustochaetepunctata is characterised by resupinate basidiomata with cream, a smooth, punctate hymenial surface, a monomitic hyphal system with clamped generative hyphae and subcylindrical to allantoid basidiospores (13.5-18 × 6-8.2 µm). Alloexidiopsisgrandinea is characterised by resupinate basidiomata with buff to slightly yellowish, a grandinioid hymenial surface, a monomitic hyphal system with clamped generative hyphae and allantoid basidiospores (10-12.3 × 5-5.8 µm). Additionally, Alloexidiopsisxantha is characterised by resupinate basidiomata with cream to slightly buff, a smooth hymenial surface, a monomitic hyphal system with clamped generative hyphae and subcylindrical to allantoid basidiospores measuring 20-24 × 5-6.2 µm. Sequences of the internal transcribed spacers (ITS) and the large subunit (nrLSU) of the nuclear ribosomal DNA (rDNA) markers of the studied samples were generated. Phylogenetic analyses were performed with the Maximum Likelihood, Maximum Parsimony and Bayesian Inference methods. The phylogram, based on the ITS+nLSU rDNA gene regions, revealed that four new species were assigned to the genera Adustochaete and Alloexidiopsis within the order Auriculariales, individually. The phylogenetic tree inferred from the ITS sequences highlighted that Ad.albomarginata was retrieved as a sister to Ad.yunnanensis and the species Ad.punctata was sister to Ad.rava. The topology, based on the ITS sequences, showed that Al.grandinea was retrieved as a sister to Al.schistacea and the taxon Al.xantha formed a monophyletic lineage. Furthermore, two identification keys to Adustochaete and Alloexidiopsis worldwide are provided.
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Affiliation(s)
- Junhong Dong
- The Key Laboratory of Forest Resources Conservation and Utilization in the South-west Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Re-source, Southwest Forestry University, Kunming 650224, China Southwest Forestry University Kunming China
| | - Yonggao Zhu
- The Key Laboratory of Forest Resources Conservation and Utilization in the South-west Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Re-source, Southwest Forestry University, Kunming 650224, China Southwest Forestry University Kunming China
| | - Chengbin Qian
- The Key Laboratory of Forest Resources Conservation and Utilization in the South-west Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Re-source, Southwest Forestry University, Kunming 650224, China Southwest Forestry University Kunming China
| | - Changlin Zhao
- The Key Laboratory of Forest Resources Conservation and Utilization in the South-west Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Re-source, Southwest Forestry University, Kunming 650224, China Southwest Forestry University Kunming China
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17
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Sebastião CS, Pingarilho M, Bathy J, Bonfim E, Toancha K, Miranda MNS, Martins MRO, Gomes P, Lázaro L, Pina-Araujo I, Nhampossa T, Leal S, Abecasis AB, Pimentel V. MARVEL-minimising the emergence and dissemination of HIV-1 drug resistance in Portuguese-speaking African Countries (PALOP): low-cost portable NGS platform for HIV-1 surveillance in Africa. BMC Infect Dis 2024; 24:884. [PMID: 39210296 PMCID: PMC11360575 DOI: 10.1186/s12879-024-09803-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND HIV-1 infections remain a global public health concern. Scaled-up antiretroviral treatment (ART) is crucial for reducing morbidity and mortality related to HIV/AIDS. The emergence of drug-resistance mutations (DRMs) compromises viral suppression and contributes to the continued HIV-1 transmission. Several reports indicate a recent increase in acquired (ADR) and transmitted (TDR) drug resistance in Africa, probably linked to the lack of implementation of HIV drug resistance (HIVDR) testing and suboptimal treatment adherence. Herein, we will develop a low-cost protocol using third-generation sequencing (Oxford Nanopore Technology) for HIV-1 surveillance in Portuguese-speaking African Countries - PALOP [Angola (AO), Cape Verde (CV), Mozambique (MZ), and Sao Tome & Principe (STP)]. METHODS This is a multicentric cross-sectional study that includes around 600 adult patients newly diagnosed with HIV-1 in the PALOP. An epidemiological questionnaire previously validated by our research team will be used to collect sociodemographic and clinical data. Also, whole blood samples will be collected and the plasma samples will be subjected to drug resistance testing using an in-house low-cost NGS protocol. Data analysis will involve bioinformatics, biostatistics and machine learning techniques to generate accurate and up-to-date information about HIV-1 genetic diversity, ADR and TDR. DISCUSSION The implementation of this low-cost NGS platform for HIV-1 surveillance in the PALOP will allow: (i) to increase DRM surveillance capacity in resource-limited settings; (ii) to understand the pattern and determinants of dissemination of resistant HIV-1 strains; and (iii) to promote the development of technical and scientific skills of African researchers for genomic surveillance of viral pathogens and bioinformatics analysis. These objectives will contribute to reinforcing the capacity to combat HIV infection in Africa by optimizing the selection of ART regimens, improving viral suppression, and reducing ADR or TDR prevalence in PALOPs, with relevant implications for public health.
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Affiliation(s)
- Cruz S Sebastião
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, GHTM, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, Lisboa, 1349-008, Portugal
- Centro de Investigação em Saúde de Angola (CISA), Caxito, Angola
- Instituto Nacional de Investigação em Saúde (INIS), Luanda, Angola
| | - Marta Pingarilho
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, GHTM, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, Lisboa, 1349-008, Portugal
| | - Jamila Bathy
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Elizângela Bonfim
- Centro de Endemias de São Tome & Principe, Sao Tome, Sao Tome and Principe
| | - Katia Toancha
- Laboratório Central de Tuberculose e HIV de São Tome & Principe, Sao Tome, Sao Tome and Principe
| | - Mafalda N S Miranda
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, GHTM, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, Lisboa, 1349-008, Portugal
| | - M Rosário O Martins
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, GHTM, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, Lisboa, 1349-008, Portugal
| | - Perpetua Gomes
- Laboratório de Biologia Molecular (LMCBM, SPC, ULSLO), Lisbon, 1349-019, Portugal
- Egas Moniz School of Health & Sicence, Egas Moniz Center for Interdisciplinary Research (CiiEM), Caparica, Almada, 2829-511, Portugal
| | - Lazismino Lázaro
- Laboratório Central de Tuberculose e HIV de São Tome & Principe, Sao Tome, Sao Tome and Principe
| | | | - Tacilta Nhampossa
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Silvania Leal
- Instituto de Saúde Pública, Praia, Cape Verde, Cabo Verde
| | - Ana B Abecasis
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, GHTM, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, Lisboa, 1349-008, Portugal
| | - Victor Pimentel
- Global Health and Tropical Medicine, Associate Laboratory in Translation and Innovation Towards Global Health, GHTM, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, Lisboa, 1349-008, Portugal.
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18
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da Silva FG, Moura DR, de Oliveira PM, de Souza Cardoso Quintão T, Cassemiro ÉM, de Campos GM, da Silva AS, Bezerra RDS, de Noronha LAG, Ramalho WM, de Araújo WN, Pereira AL, Slavov SN, Haddad R. Molecular characterization and frequency of human pegivirus type 1 (HPgV-1) in kidney transplant recipients from Central-West Brazil. Braz J Microbiol 2024:10.1007/s42770-024-01490-z. [PMID: 39164460 DOI: 10.1007/s42770-024-01490-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 08/09/2024] [Indexed: 08/22/2024] Open
Abstract
Human Pegivirus Type 1 (HPgV-1), a ubiquitous commensal virus, has been recently suggested as a marker of immunologic function. There is scarce data for the presence, genotypes, and molecular characteristics of HPgV-1 among kidney transplant recipients. Therefore, the objective of this study was to examine the prevalence and the molecular characteristics (cycle threshold, genotypes) of this viral infection among kidney transplant recipients from the Brasília, Federal District of Brazil. HPgV-1 RNA detection in the plasma was assessed by RT-qPCR. Positive samples were submitted to sequencing and phylogenetic analysis of the 5´-UTR portion of the viral genome. The estimated HPgV-1 prevalence among renal-transplant recipients was 20%. The performed phylogenetic inference revealed that the most frequent genotype among these patients was HPgV-1 genotype 2 (78.9%) presented by its two subgenotypes (2 A and 2B), followed by genotypes 1 and 3 (10.5% each). This study presents new data about the HPgV-1 circulation and molecular characteristics among kidney transplant recipients from the Federal District of Brazil. Further work is fundamental to examine the effect of HPgV-1 among patients with immunological suppression, including kidney transplant recipients.
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Affiliation(s)
| | | | - Pâmela Maria de Oliveira
- Center for Tropical Medicine, University of Brasília, Federal District, Brasília, Brazil
- Molecular Diagnostics Laboratory, University Hospital of Brasília/EBSERH, Federal District, Brasília, Brazil
| | - Tatyane de Souza Cardoso Quintão
- Center for Tropical Medicine, University of Brasília, Federal District, Brasília, Brazil
- Molecular Diagnostics Laboratory, University Hospital of Brasília/EBSERH, Federal District, Brasília, Brazil
| | - Évelin Mota Cassemiro
- Center for Tropical Medicine, University of Brasília, Federal District, Brasília, Brazil
- Molecular Diagnostics Laboratory, University Hospital of Brasília/EBSERH, Federal District, Brasília, Brazil
| | - Gabriel Montenegro de Campos
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Anielly Sarana da Silva
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rafael Dos Santos Bezerra
- Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Walter Massa Ramalho
- Center for Tropical Medicine, University of Brasília, Federal District, Brasília, Brazil
- Campus of Ceilândia, University of Brasília, Federal District, Brasília, Brazil
| | - Wildo Navegantes de Araújo
- Center for Tropical Medicine, University of Brasília, Federal District, Brasília, Brazil
- Campus of Ceilândia, University of Brasília, Federal District, Brasília, Brazil
- National Institute for Science and Technology for Health Technology Assessment, Porto Alegre, RS, Brazil
| | - Alex Leite Pereira
- Center for Tropical Medicine, University of Brasília, Federal District, Brasília, Brazil
- Campus of Ceilândia, University of Brasília, Federal District, Brasília, Brazil
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Butantan Institute, São Paulo, Brazil
| | - Rodrigo Haddad
- Center for Tropical Medicine, University of Brasília, Federal District, Brasília, Brazil.
- Molecular Diagnostics Laboratory, University Hospital of Brasília/EBSERH, Federal District, Brasília, Brazil.
- Campus of Ceilândia, University of Brasília, Federal District, Brasília, Brazil.
- Campus Universitário - Centro Metropolitano- DF, Ceilândia Sul, Brasília, DF, CEP: 72220-275, Brazil.
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19
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Li Y, Moritz C, Brennan IG, Zwick A, Nicholls J, Grealy A, Slipinski A. Evolution across the adaptive landscape in a hyperdiverse beetle radiation. Curr Biol 2024; 34:3685-3697.e6. [PMID: 39067451 DOI: 10.1016/j.cub.2024.06.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
The extraordinary diversification of beetles on Earth is a textbook example of adaptive evolution. Yet, the tempo and drivers of this super-radiation remain largely unclear. Here, we address this problem by investigating macroevolutionary dynamics in darkling beetles (Coleoptera: Tenebrionidae), one of the most ecomorphologically diverse beetle families (with over 30,000 species). Using multiple genomic datasets and analytical approaches, we resolve the long-standing inconsistency over deep relationships in the family. In conjunction with a landmark-based dataset of body shape morphology, we show that the evolutionary history of darkling beetles is marked by ancient rapid radiations, frequent ecological transitions, and rapid bursts of morphological diversification. On a global scale, our analyses uncovered a significant pulse of phenotypic diversification proximal to the Cretaceous-Palaeogene (K/Pg) mass extinction and convergence of body shape associated with recurrent ecological specializations. On a regional scale, two major Australasian radiations, the Adeliini and the Heleine clade, exhibited contrasting patterns of ecomorphological diversification, representing phylogenetic niche conservatism versus adaptive radiation. Our findings align with the Simpsonian model of adaptive evolution across the macroevolutionary landscape and highlight a significant role of ecological opportunity in driving the immense ecomorphological diversity in a hyperdiverse beetle group.
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Affiliation(s)
- Yun Li
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia.
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - James Nicholls
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - Alicia Grealy
- Australian National Herbarium, CSIRO, Canberra, ACT 2601, Australia
| | - Adam Slipinski
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
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20
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Poon AFY. Prospects for a sequence-based taxonomy of influenza A virus subtypes. Virus Evol 2024; 10:veae064. [PMID: 39247559 PMCID: PMC11378807 DOI: 10.1093/ve/veae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 05/03/2024] [Accepted: 08/09/2024] [Indexed: 09/10/2024] Open
Abstract
Hemagglutinin (HA) and neuraminidase (NA) proteins are the primary antigenic targets of influenza A virus (IAV) infections. IAV infections are generally classified into subtypes of HA and NA proteins, e.g. H3N2. Most of the known subtypes were originally defined by a lack of antibody cross-reactivity. However, genetic sequencing has played an increasingly important role in characterizing the evolving diversity of IAV. Novel subtypes have recently been described solely by their genetic sequences, and IAV infections are routinely subtyped by molecular assays, or the comparison of sequences to references. In this study, I carry out a comparative analysis of all available IAV protein sequences in the Genbank database (over 1.1 million, reduced to 272,292 unique sequences prior to phylogenetic reconstruction) to determine whether the serologically defined subtypes can be reproduced with sequence-based criteria. I show that a robust genetic taxonomy of HA and NA subtypes can be obtained using a simple clustering method, namely, by progressively partitioning the phylogeny on its longest internal branches. However, this taxonomy also requires some amendments to the current nomenclature. For example, two IAV isolates from bats previously characterized as a divergent lineage of H9N2 should be separated into their own subtype. With the exception of these small and highly divergent lineages, the phylogenies relating each of the other six genomic segments do not support partitions into major subtypes.
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Affiliation(s)
- Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, Dental Sciences Building, Rm. 4044, London, Ontario N6A 5C1, Canada
- Department of Microbiology & Immunology, Western University, 1151 Richmond Street, London, Ontario N6A 3K7, Canada
- Department of Computer Science, Western University, Room 355, Middlesex College, London N6A 5B7, Canada
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21
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Demura M. New species and species diversity of Desmodesmus (Chlorophyceae, Chlorophyta) in Saga City, Japan. Sci Rep 2024; 14:18980. [PMID: 39152251 PMCID: PMC11329507 DOI: 10.1038/s41598-024-69941-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/12/2024] [Indexed: 08/19/2024] Open
Abstract
Desmodesmus spp. are one of the most dominant components of phytoplankton, which are present in most water bodies. However, identification of the species based only on morphological data is challenging. The aim of the present study was to provide a comprehensive understanding of the actual distribution of the Desmodesmus species in Saga City, Saga Prefecture, Japan. In the present study, 38 water bodies were surveyed between June 2017 and March 2023. A total of 86 culture strains were established from the samples collected from the 21 sites, and identified by molecular phylogenetic analysis, comparison of ITS2 rRNA secondary structures, and observation of surface microstructure. In total, four new species, including D. notatus Demura sp. nov., D. lamellatus Demura sp. nov., D. fragilis Demura sp. nov., and D. reticulatus Demura sp. nov. were proposed and 17 Desmodesmus species were identified as described species. The present study revealed > 20 Desmodesmus species, exhibiting high genetic diversity in a small area.
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Affiliation(s)
- Mikihide Demura
- Faculty of Agriculture, College of Natural Sciences, Institute of Education and Research, Saga University, 1 Honjo, Saga, 840-8502, Japan.
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22
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Gao Y, Li J, He J, Yu Y, Qian Z, Geng Z, Yang L, Zhang Y, Ke Y, Lin Q, Wang J, Chen S, Chen F, Yuan YW, Ding B. BLADE-ON-PETIOLE interacts with CYCLOIDEA to fine-tune CYCLOIDEA-mediated flower symmetry in monkeyflowers ( Mimulus). SCIENCE ADVANCES 2024; 10:eado4571. [PMID: 39141743 PMCID: PMC11323955 DOI: 10.1126/sciadv.ado4571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/08/2024] [Indexed: 08/16/2024]
Abstract
Morphological novelties, or key innovations, are instrumental to the diversification of the organisms. In plants, one such innovation is the evolution of zygomorphic flowers, which is thought to promote outcrossing and increase flower morphological diversity. We isolated three allelic mutants from two Mimulus species displaying altered floral symmetry and identified the causal gene as the ortholog of Arabidopsis BLADE-ON-PETIOLE. We found that MlBOP and MlCYC2A physically interact and this BOP-CYC interaction module is highly conserved across the angiosperms. Furthermore, MlBOP self-ubiquitinates and suppresses MlCYC2A self-activation. MlCYC2A, in turn, impedes MlBOP ubiquitination. Thus, this molecular tug-of-war between MlBOP and MlCYC2A fine-tunes the expression of MlCYC2A, contributing to the formation of bilateral symmetry in flowers, a key trait in angiosperm evolution.
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Affiliation(s)
- Yuan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Jingjian Li
- College of Pharmacy, Guilin Medical University, Guilin 541199, P. R. China
| | - Jiayue He
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Yaqi Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Zexin Qian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Zhiqiang Geng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Liuhui Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Yumin Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Yujie Ke
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Qiaoshan Lin
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Jing Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, P. R. China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, P. R. China
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Baoqing Ding
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization; Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs; Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P. R. China
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing 210014, P. R. China
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23
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Owuor DC, de Laurent ZR, Oketch JW, Murunga N, Otieno JR, Nabakooza G, Chaves SS, Nokes DJ, Agoti CN. Phylogeography and reassortment patterns of human influenza A viruses in sub-Saharan Africa. Sci Rep 2024; 14:18987. [PMID: 39152215 PMCID: PMC11329769 DOI: 10.1038/s41598-024-70023-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 08/12/2024] [Indexed: 08/19/2024] Open
Abstract
The role of sub-Saharan Africa in the global spread of influenza viruses remains unclear due to insufficient spatiotemporal sequence data. Here, we analyzed 222 codon-complete sequences of influenza A viruses (IAVs) sampled between 2011 and 2013 from five countries across sub-Saharan Africa (Kenya, Zambia, Mali, Gambia, and South Africa); these genomes were compared with 1209 contemporaneous global genomes using phylogeographical approaches. The spread of influenza in sub-Saharan Africa was characterized by (i) multiple introductions of IAVs into the region over consecutive influenza seasons, with viral importations originating from multiple global geographical regions, some of which persisted in circulation as intra-subtype reassortants for multiple seasons, (ii) virus transfer between sub-Saharan African countries, and (iii) virus export from sub-Saharan Africa to other geographical regions. Despite sparse data from influenza surveillance in sub-Saharan Africa, our findings support the notion that influenza viruses persist as temporally structured migrating metapopulations in which new virus strains can emerge in any geographical region, including in sub-Saharan Africa; these lineages may have been capable of dissemination to other continents through a globally migrating virus population. Further knowledge of the viral lineages that circulate within understudied sub-Saharan Africa regions is required to inform vaccination strategies in those regions.
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Affiliation(s)
- D Collins Owuor
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - John W Oketch
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - James R Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Grace Nabakooza
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Sandra S Chaves
- Influenza Division, Centers for Disease Control and Prevention (CDC), Nairobi, Kenya
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), CDC, Atlanta, GA, USA
| | - D James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Public Health and Human Sciences, Pwani University, Kilifi, Kenya
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Su H, Hao T, Yu M, Zhou W, Wu L, Sheng Y, Yi Z. Complex evolutionary patterns within the tubulin gene family of ciliates, unicellular eukaryotes with diverse microtubular structures. BMC Biol 2024; 22:170. [PMID: 39135200 PMCID: PMC11321004 DOI: 10.1186/s12915-024-01969-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Tubulins are major components of the eukaryotic cytoskeletons that are crucial in many cellular processes. Ciliated protists comprise one of the oldest eukaryotic lineages possessing cilia over their cell surface and assembling many diverse microtubular structures. As such, ciliates are excellent model organisms to clarify the origin and evolution of tubulins in the early stages of eukaryote evolution. Nonetheless, the evolutionary history of the tubulin subfamilies within and among ciliate classes is unclear. RESULTS We analyzed the evolutionary pattern of ciliate tubulin gene family based on genomes/transcriptomes of 60 species covering 10 ciliate classes. Results showed: (1) Six tubulin subfamilies (α_Tub, β_Tub, γ_Tub, δ_Tub, ε_Tub, and ζ_Tub) originated from the last eukaryotic common ancestor (LECA) were observed within ciliates. Among them, α_Tub, β_Tub, and γ_Tub were present in all ciliate species, while δ_Tub, ε_Tub, and ζ_Tub might be independently lost in some species. (2) The evolutionary history of the tubulin subfamilies varied. Evolutionary history of ciliate γ_Tub, δ_Tub, ε_Tub, and ζ_Tub showed a certain degree of consistency with the phylogeny of species after the divergence of ciliate classes, while the evolutionary history of ciliate α_Tub and β_Tub varied among different classes. (3) Ciliate α- and β-tubulin isoforms could be classified into an "ancestral group" present in LECA and a "divergent group" containing only ciliate sequences. Alveolata-specific expansion events probably occurred within the "ancestral group" of α_Tub and β_Tub. The "divergent group" might be important for ciliate morphological differentiation and wide environmental adaptability. (4) Expansion events of the tubulin gene family appeared to be consistent with whole genome duplication (WGD) events in some degree. More Paramecium-specific tubulin expansions were detected than Tetrahymena-specific ones. Compared to other Paramecium species, the Paramecium aurelia complex underwent a more recent WGD which might have experienced more tubulin expansion events. CONCLUSIONS Evolutionary history among different tubulin gene subfamilies seemed to vary within ciliated protists. And the complex evolutionary patterns of tubulins among different ciliate classes might drive functional diversification. Our investigation provided meaningful information for understanding the evolution of tubulin gene family in the early stages of eukaryote evolution.
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Affiliation(s)
- Hua Su
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Tingting Hao
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Minjie Yu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Wuyu Zhou
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Lei Wu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China
- School of Marine and Fisheries, Guangdong Eco-engineering Polytechnic, Guangzhou, 510320, China
| | - Yalan Sheng
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China.
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Tedersoo L, Magurno F, Alkahtani S, Mikryukov V. Phylogenetic classification of arbuscular mycorrhizal fungi: new species and higher-ranking taxa in Glomeromycota and Mucoromycota (class Endogonomycetes). MycoKeys 2024; 107:273-325. [PMID: 39169987 PMCID: PMC11336396 DOI: 10.3897/mycokeys.107.125549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/20/2024] [Indexed: 08/23/2024] Open
Abstract
Arbuscular mycorrhizal (AM) fungi - Glomeromycota and Endogonomycetes - comprise multiple species and higher-level taxa that have remained undescribed. We propose a mixed morphology- and DNA-based classification framework to promote taxonomic communication and shed light into the phylogenetic structure of these ecologically essential fungi. Based on eDNA samples and long reads as type materials, we describe 15 new species and corresponding genera (Pseudoentrophosporakesseensis, Hoforsarebekkae, Kahvenarebeccae, Kelottijaerviashannonae, Kungsaengenashadiae, Langduoadianae, Lehetuaindrekii, Lokrumastenii, Moosteastephanieae, Nikkaluoktamahdiehiae, Parniguacraigii, Riederbergasylviae, Ruuacoralieae, Tammsaareavivikae and Unemaeeanathalieae), the genus Parvocarpum as well as 19 families (Pseudoentrophosporaceae, Hoforsaceae, Kahvenaceae, Kelottijaerviaceae, Kungsaengenaceae, Langduoaceae, Lehetuaceae, Lokrumaceae, Moosteaceae, Nikkaluoktaceae, Parniguaceae, Riederbergaceae, Ruuaceae, Tammsaareaceae, Unemaeeaceae, Bifigurataceae, Planticonsortiaceae, Jimgerdemanniaceae and Vinositunicaceae) and 17 orders (Hoforsales, Kahvenales, Kelottijaerviales, Kungsaengenales, Langduoales, Lehetuales, Lokrumales, Moosteales, Nikkaluoktales, Parniguales, Riederbergales, Ruuales, Tammsaareales, Unemaeeales, Bifiguratales and Densosporales), and propose six combinations (Diversisporabareae, Diversisporanevadensis, Fuscutatacerradensis, Fuscutatareticulata, Viscosporadeserticola and Parvocarpumbadium) based on phylogenetic evidence. We highlight further knowledge gaps in the phylogenetic structure of AM fungi and propose an alphanumeric coding system for preliminary communication and reference-based eDNA quality-filtering of the remaining undescribed genus- and family-level groups. Using AM fungi as examples, we hope to offer a sound, mixed framework for classification to boost research in the alpha taxonomy of fungi, especially the "dark matter fungi".
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Affiliation(s)
- Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, 2 Liivi, 50409 Tartu, Estonia
- Department of Zoology, College of Science, King Saud University, 12371 Riyadh, Saudi Arabia
| | - Franco Magurno
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
| | - Saad Alkahtani
- Department of Zoology, College of Science, King Saud University, 12371 Riyadh, Saudi Arabia
| | - Vladimir Mikryukov
- Mycology and Microbiology Center, University of Tartu, 2 Liivi, 50409 Tartu, Estonia
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Yuan Q, Zhao C. Morphology and multigene phylogeny revealed four new species of Xylodon (Schizoporaceae, Basidiomycota) from southern China. MycoKeys 2024; 107:161-187. [PMID: 39169988 PMCID: PMC11336394 DOI: 10.3897/mycokeys.107.128223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/23/2024] [Indexed: 08/23/2024] Open
Abstract
Fungi are one of the most diverse groups of organisms on Earth, amongst which wood-inhabiting fungi play a crucial role in ecosystem processes and functions. Four new wood-inhabiting fungi, Xylodoncremeoparinaceus, X.luteodontioides, X.poroides and X.wumengshanensis are proposed, based on morphological features and molecular evidence. Xylodoncremeoparinaceus is distinguished by a cream hymenial surface with a pruinose hymenophore, a monomitic hyphal system with clamped generative hyphae and ellipsoid basidiospores. Xylodonluteodontioides is characterised by flavescens hymenophore surface with odontioid hymenophore, monomitic hyphal system with clamped generative hyphae and ellipsoid basidiospores. Xylodonporoides bears coriaceous basidiomata with a poroid hymenophore surface, monomitic hyphal system with clamped generative hyphae and ellipsoid basidiospores. Xylodonwumengshanensis is a distinct taxon by its grandinoid hymenophore surface, monomitic hyphal system with clamped generative hyphae and ellipsoid basidiospores. Sequences of ITS and nLSU rRNA markers of the studied samples were generated and phylogenetic analyses were performed using the Maximum Likelihood, Maximum Parsimony, and Bayesian Inference methods. The phylogram, based on the ITS+nLSU rDNA gene regions, included three genera within the Schizoporaceae as Fasciodontia, Lyomyces and Xylodon. The four new species were grouped into the genus Xylodon. The topology, based on the ITS sequences, revealed that Xylodoncremeoparinaceus was grouped closely with X.pruinosus, X.detriticus and X.ussuriensis. The taxon X.luteodontioides was sister to X.nesporii. The species X.poroides separated from X.pseudotropicus, while X.wumengshanensis was grouped with four taxa: X.patagonicus, X.radula, X.subtropicus and X.taiwanianus.
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Affiliation(s)
- Qi Yuan
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
| | - Changlin Zhao
- The Key Laboratory of Forest Resources Conservation and Utilization in the Southwest Mountains of China Ministry of Education, Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Southwest China, Yunnan Provincial Key Laboratory for Conservation and Utilization of In-forest Resource, Southwest Forestry University, Kunming 650224, ChinaSouthwest Forestry UniversityKunmingChina
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Gravey F, Michel A, Langlois B, Gérard M, Galopin S, Gakuba C, Du Cheyron D, Fazilleau L, Brossier D, Guérin F, Giard JC, Le Hello S. Central role of the ramAR locus in the multidrug resistance in ESBL -Enterobacterales. Microbiol Spectr 2024; 12:e0354823. [PMID: 38916360 PMCID: PMC11302662 DOI: 10.1128/spectrum.03548-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
The aim of this study was to evaluate the proportion of resistance to a temocillin, tigecycline, ciprofloxacin, and chloramphenicol phenotype called t2c2 that resulted from mutations within the ramAR locus among extended-spectrum β-lactamases-Enterobacterales (ESBL-E) isolated in three intensive care units for 3 years in a French university hospital. Two parallel approaches were performed on all 443 ESBL-E included: (i) the minimal inhibitory concentrations of temocillin, tigecycline, ciprofloxacin, and chloramphenicol were determined and (ii) the genomes obtained from the Illumina sequencing platform were analyzed to determine multilocus sequence types, resistomes, and diversity of several tetR-associated genes including ramAR operon. Among the 443 ESBL-E strains included, isolates of Escherichia coli (n = 194), Klebsiella pneumoniae (n = 122), and Enterobacter cloacae complex (Ecc) (n = 127) were found. Thirty-one ESBL-E strains (7%), 16 K. pneumoniae (13.1%), and 15 Ecc (11.8%) presented the t2c2 phenotype in addition to their ESBL profile, whereas no E. coli presented these resistances. The t2c2 phenotype was invariably reversible by the addition of Phe-Arg-β-naphthylamide, indicating a role of resistance-nodulation-division pumps in these observations. Mutations associated with the t2c2 phenotype were restricted to RamR, the ramAR intergenic region (IR), and AcrR. Mutations in RamR consisted of C- or N-terminal deletions and amino acid substitutions inside its DNA-binding domain or within key sites of protein-substrate interactions. The ramAR IR showed nucleotide substitutions involved in the RamR DNA-binding domain. This diversity of sequences suggested that RamR and the ramAR IR represent major genetic events for bacterial antimicrobial resistance.IMPORTANCEMorbimortality caused by infectious diseases is very high among patients hospitalized in intensive care units (ICUs). A part of these outcomes can be explained by antibiotic resistance, which delays the appropriate therapy. The transferable antibiotic resistance gene is a well-known mechanism to explain the high rate of multidrug resistance (MDR) bacteria in ICUs. This study describes the prevalence of chromosomal mutations, which led to additional antibiotic resistance among MDR bacteria. More than 12% of Klebsiella pneumoniae and Enterobacter cloacae complex strains presented mutations within the ramAR locus associated with a dysregulation of an efflux pump called AcrAB-TolC and a porin: OmpF. These dysregulations led to an increase in antibiotic output notably tigecycline, ciprofloxacin, and chloramphenicol associated with a decrease of input for beta-lactam, especially temocillin. Mutations within transcriptional regulators such as ramAR locus played a major role in antibiotic resistance dissemination and need to be further explored.
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Affiliation(s)
- François Gravey
- Department of Infectious Agents, Bacteriology, Université de Caen Normandie, Univ Rouen Normandie, INSERM, Normandie Univ, DYNAMICURE UMR 1311, CHU Caen Normandie, Caen, France
| | - Alice Michel
- Univ de Caen Normandie, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, France
| | - Bénédicte Langlois
- Department of Infectious Agents, Bacteriology, Université de Caen Normandie, Univ Rouen Normandie, INSERM, Normandie Univ, DYNAMICURE UMR 1311, CHU Caen Normandie, Caen, France
| | - Mattéo Gérard
- Univ de Caen Normandie, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, France
| | - Sébastien Galopin
- Univ de Caen Normandie, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, France
| | - Clément Gakuba
- Service de Réanimation Chirurgicale, Univ de Caen Normandie, CHU de Caen Normandie, Caen, France
| | - Damien Du Cheyron
- Service de Réanimation Médicale, Univ de Caen Normandie, CHU de Caen Normandie, Caen, France
| | - Laura Fazilleau
- Service de Réanimation Néonatale, Univ de Caen Normandie, CHU de Caen Normandie, Caen, France
| | - David Brossier
- Service de Réanimation Pédiatrique, Univ de Caen Normandie, CHU de Caen Normandie, Caen, France
| | - François Guérin
- Service de Bactériologie, CHU de Rennes Pontchaillou, Rennes, France
| | - Jean-Christophe Giard
- Univ de Caen Normandie, Univ Rouen Normandie, INSERM, DYNAMICURE UMR 1311, Caen, France
| | - Simon Le Hello
- Department of Infectious Agents, Bacteriology, Université de Caen Normandie, Univ Rouen Normandie, INSERM, Normandie Univ, DYNAMICURE UMR 1311, CHU Caen Normandie, Caen, France
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28
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Mapalo MA, Wolfe JM, Ortega-Hernández J. Cretaceous amber inclusions illuminate the evolutionary origin of tardigrades. Commun Biol 2024; 7:953. [PMID: 39107512 PMCID: PMC11303527 DOI: 10.1038/s42003-024-06643-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/28/2024] [Indexed: 08/10/2024] Open
Abstract
Tardigrades are a diverse phylum of microscopic invertebrates widely known for their extreme survival capabilities. Molecular clocks suggest that tardigrades diverged from other panarthropods before the Cambrian, but their fossil record is extremely sparse. Only the fossil tardigrades Milnesium swolenskyi (Late Cretaceous) and Paradoryphoribius chronocaribbeus (Miocene) have resolved taxonomic positions, restricting the availability of calibration points for estimating for the origin of this phylum. Here, we revise two crown-group tardigrades from Canadian Cretaceous-aged amber using confocal fluorescence microscopy, revealing critical morphological characters that resolve their taxonomic positions. Formal morphological redescription of Beorn leggi reveals that it features Hypsibius-type claws. We also describe Aerobius dactylus gen. et sp. nov. based on its unique combination of claw characters. Phylogenetic analyses indicate that Beo. leggi and Aer. dactylus belong to the eutardigrade superfamily Hypsibioidea, adding a critical fossil calibration point to investigate tardigrade origins. Our molecular clock estimates suggest an early Paleozoic diversification of crown-group Tardigrada and highlight the importance of Beo. leggi as a calibration point that directly impacts estimates of shallow nodes. Our results suggest that independent terrestrialization of eutardigrades and heterotardigrades occurred around the end-Carboniferous and Lower Jurassic, respectively. These estimates also provide minimum ages for convergent acquisition of cryptobiosis.
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Affiliation(s)
- Marc A Mapalo
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Joanna M Wolfe
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Javier Ortega-Hernández
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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Kobayashi G, Abe H. Cost-efficient PCR based DNA barcoding of marine invertebrate specimens with NovaSeq amplicon sequencing. Mol Biol Rep 2024; 51:887. [PMID: 39105821 DOI: 10.1007/s11033-024-09811-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/19/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND The marine environment harbors high biodiversity; however, it is poorly understood. Nucleotide sequence data of all marine organisms should be accumulated before natural and/or anthropogenic environmental changes jeopardize the marine environment. In this study, we report a cost-effective and easy DNA barcoding method. This method can be readily adopted without using library preparation kits. It includes multiplex PCR of short targets, indexing PCR, and outsourcing to a sequencing service using the NovaSeq system. METHODS AND RESULTS We targeted four mitochondrial genes [cytochrome c oxidase subunit I (COI), COIII, 16S rRNA (16S), and 12S rRNA (12S)] and three nuclear genes [18S rRNA (18S), 28S rRNA (28S), internal transcribed spacer 2 (ITS2)] in 95 marine invertebrate specimens, which were primarily annelids. The primers, including adapters and indices for NovaSeq sequencing, were newly designed. Two PCR runs were conducted. The 1st PCR amplified specific loci with universal primers and the 2nd added sequencing adapters and indices to the 1st PCR products. The gene sequences obtained from the FASTQ files were subjected to BLAST search and phylogenetic analyses. One run using 95 specimens yielded sequences averaging 2816 bp per specimen for a total length of six loci. Nuclear genes were more successfully assembled compared with mitochondrial genes. A weak but significantly negative correlation was observed between the average length of each locus and success rate of the assembly. Some of the sequences were almost identical to the sequences obtained from specimens collected far from Japan, indicating the presence of potentially invasive species identified for the first time. CONCLUSIONS We obtained gene sequences efficiently using next-generation sequencing rather than Sanger sequencing. Although this method requires further optimization to increase the success rate for some loci, it is used as a first step to select specimens for further analyses by determining the specific loci of the targets.
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Affiliation(s)
- Genki Kobayashi
- Research Center for Creative Partnerships, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan.
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan.
| | - Hirokazu Abe
- Faculty of Science and Engineering, Ishinomaki Senshu University, Ishinomaki, Miyagi, Japan
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Coomber A, Saville A, Ristaino JB. Evolution of Phytophthora infestans on its potato host since the Irish potato famine. Nat Commun 2024; 15:6488. [PMID: 39103347 DOI: 10.1038/s41467-024-50749-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 07/18/2024] [Indexed: 08/07/2024] Open
Abstract
Phytophthora infestans is a major oomycete plant pathogen, responsible for potato late blight, which led to the Irish Potato Famine from 1845-1852. Since then, potatoes resistant to this disease have been bred and deployed worldwide. Their resistance (R) genes recognize pathogen effectors responsible for virulence and then induce a plant response stopping disease progression. However, most deployed R genes are quickly overcome by the pathogen. We use targeted sequencing of effector and R genes on herbarium specimens to examine the joint evolution in both P. infestans and potato from 1845-1954. Currently relevant effectors are historically present in P. infestans, but with alternative alleles compared to modern reference genomes. The historic FAM-1 lineage has the virulent Avr1 allele and the ability to break the R1 resistance gene before breeders deployed it in potato. The FAM-1 lineage is diploid, but later, triploid US-1 lineages appear. We show that pathogen virulence genes and host resistance genes have undergone significant changes since the Famine, from both natural and artificial selection.
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Affiliation(s)
- Allison Coomber
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA
- Functional Genomics Program, NC State University, Raleigh, NC, USA
| | - Amanda Saville
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA
| | - Jean Beagle Ristaino
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA.
- Emerging Plant Disease and Global Food Security Cluster, NC State University, Raleigh, NC, USA.
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Vargas-Pinilla P, S Oliveira Fam B, Medina Tavares G, Lima T, Landau L, Paré P, de Cássia Aleixo Tostes R, Pissinatti A, Falótico T, Costa-Neto C, Maestri R, Bortolini MC. From molecular variations to behavioral adaptations: Unveiling adaptive epistasis in primate oxytocin system. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 184:e24947. [PMID: 38783700 DOI: 10.1002/ajpa.24947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
OBJECTIVE Our primary objective was to investigate the variability of oxytocin (OT) and the GAMEN binding motif within the LNPEP oxytocinase in primates. MATERIALS AND METHODS We sequenced the LNPEP segment encompassing the GAMEN motif in 34 Platyrrhini species, with 21 of them also sequenced for the OT gene. Our dataset was supplemented with primate sequences of LNPEP, OT, and the oxytocin receptor (OTR) sourced from public databases. Evolutionary analysis and coevolution predictions were made followed by the macroevolution analysis of relevant amino acids associated with phenotypic traits, such as mating systems, parental care, and litter size. To account for phylogenetic structure, we utilized two distinct statistical tests. Additionally, we calculated binding energies focusing on the interaction between Callithtrix jacchus VAMEN and Pro8OT. RESULTS We identified two novel motifs (AAMEN and VAMEN), challenging the current knowledge of motif conservation in placental mammals. Coevolution analysis demonstrated a correlation between GAMEN, AAMEN, and VAMEN and their corresponding OTs and OTRs. Callithrix jacchus exhibited a higher binding energy between VAMEN and Pro8OT than orthologous molecules found in humans (GAMEN and Leu8OT). DISCUSSION The coevolution of AAMEN and VAMEN with their corresponding OTs and OTRs suggests a functional relationship that could have contributed to specific reproductive and adaptive behaviors, including paternal care, social monogamy, and twin births, prominent traits in Cebidae species, such as marmosets and tamarins. Our findings underscore the coevolution of taxon-specific amino acids among the three studied molecules, shedding light on the oxytocinergic system as an adaptive epistatic repertoire in primates.
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Affiliation(s)
- Pedro Vargas-Pinilla
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Departamento de Farmacologia, Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Bibiana S Oliveira Fam
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental (CPE), Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Gustavo Medina Tavares
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thaynara Lima
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luane Landau
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Pâmela Paré
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | | | - Tiago Falótico
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, Brazil
| | - Cláudio Costa-Neto
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Renan Maestri
- Laboratório de Ecomorfologia e Macroevolução, Departamento de Ecologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Maria Cátira Bortolini
- Laboratory of Human and Molecular Evolution, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Vieira C, Brooks CM, Akita S, Kim MS, Saunders GW. Of sea, rivers and symbiosis: Diversity, systematics, biogeography and evolution of the deeply diverging florideophycean order Hildenbrandiales (Rhodophyta). Mol Phylogenet Evol 2024; 197:108106. [PMID: 38750675 DOI: 10.1016/j.ympev.2024.108106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 05/03/2024] [Accepted: 05/12/2024] [Indexed: 05/27/2024]
Abstract
The Hildenbrandiales, a typically saxicolous red algal order, is an early diverging florideophycean group with global significance in marine and freshwater ecosystems across diverse temperature zones. To comprehensively elucidate the diversity, phylogeny, biogeography, and evolution of this order, we conducted a thorough re-examination employing molecular data derived from nearly 700 specimens. Employing a species delimitation method, we identified Evolutionary Species Units (ESUs) within the Hildenbrandiales aiming to enhance our understanding of species diversity and generate the first time-calibrated tree and ancestral area reconstruction for this order. Mitochondrial cox1 and chloroplast rbcL markers were used to infer species boundaries, and subsequent phylogenetic reconstructions involved concatenated sequences of cox1, rbcL, and 18S rDNA. Time calibration of the resulting phylogenetic tree used a fossil record from a Triassic purportedly freshwater Hildenbrandia species and three secondary time points from the literature. Our species delimitation analysis revealed an astounding 97 distinct ESUs, quintupling the known diversity within this order. Our time-calibration analysis placed the origin of Hildenbrandiales (crown age) in the Ediacaran period, with freshwater species emerging as a monophyletic group during the later Permian to early Triassic. Phylogenetic reconstructions identified seven major clades, experiencing early diversification during the Silurian to Carboniferous period. Two major evolutionary events-colonization of freshwater habitats and obligate systemic symbiosis with a marine fungus-marked this order, leading to significant morphological alterations without a commensurate increase in species diversification. Despite the remarkable newly discovered diversity, the extant taxon diversity appears relatively constrained when viewed against an evolutionary timeline spanning over 800 million years. This limitation may stem from restricted geographic sampling or the prevalence of asexual reproduction. However, species richness estimation and rarefaction analyses suggest a substantially larger diversity yet to be uncovered-potentially four times greater. These findings drastically reshape our understanding of the deeply diverging florideophycean order Hildenbrandiales species diversity, and contribute valuable insights into this order's evolutionary history and ecological adaptations. Supported by phylogenetic, ecological and morphological evidence, we established the genus Riverina gen. nov. to accommodate freshwater species of Hildenbrandiales, which form a monophyletic clade in our analyses. This marks the first step toward refining the taxonomy of the Hildenbrandiales, an order demanding thorough revisions, notably with the creation of several genera to address the polyphyletic status of Hildenbrandia. However, the limited diagnostic features pose a challenge, necessitating a fresh approach to defining genera. A potential solution lies in embracing a molecular systematic perspective, which can offer precise delineations of taxonomic boundaries.
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Affiliation(s)
- Christophe Vieira
- Research Institute for Basic Sciences, Jeju National University, Jeju 63243, Korea.
| | - Cody M Brooks
- Bedford Institute of Oceanography, Department of Fisheries and Oceans, Dartmouth, NS, Canada
| | - Shingo Akita
- Faculty of Fisheries Sciences, Hokkaido University, Minato-cho 3-1-1, Hakodate, Hokkaido 041-8611, Japan
| | - Myung Sook Kim
- Research Institute for Basic Sciences, Jeju National University, Jeju 63243, Korea.
| | - Gary W Saunders
- Biology Department, Centre for Environmental and Molecular Algal Research, University of New Brunswick, Fredericton, NB, Canada
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33
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Goya S, Ruis C, Neher RA, Meijer A, Aziz A, Hinrichs AS, von Gottberg A, Roemer C, Amoako DG, Acuña D, McBroome J, Otieno JR, Bhiman JN, Everatt J, Muñoz-Escalante JC, Ramaekers K, Duggan K, Presser LD, Urbanska L, Venter M, Wolter N, Peret TC, Salimi V, Potdar V, Borges V, Viegas M. Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level. Emerg Infect Dis 2024; 30:1631-1641. [PMID: 39043393 PMCID: PMC11286072 DOI: 10.3201/eid3008.240209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
A globally implemented unified phylogenetic classification for human respiratory syncytial virus (HRSV) below the subgroup level remains elusive. We formulated global consensus of HRSV classification on the basis of the challenges and limitations of our previous proposals and the future of genomic surveillance. From a high-quality curated dataset of 1,480 HRSV-A and 1,385 HRSV-B genomes submitted to GenBank and GISAID (https://www.gisaid.org) public sequence databases through March 2023, we categorized HRSV-A/B sequences into lineages based on phylogenetic clades and amino acid markers. We defined 24 lineages within HRSV-A and 16 within HRSV-B and provided guidelines for defining prospective lineages. Our classification demonstrated robustness in its applicability to both complete and partial genomes. We envision that this unified HRSV classification proposal will strengthen HRSV molecular epidemiology on a global scale.
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Affiliation(s)
| | | | | | - Adam Meijer
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Ammar Aziz
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Angie S. Hinrichs
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Anne von Gottberg
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Cornelius Roemer
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | | | - Dolores Acuña
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Jakob McBroome
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - James R. Otieno
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Jinal N. Bhiman
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Josie Everatt
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Juan C. Muñoz-Escalante
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | | | - Kate Duggan
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Lance D. Presser
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Laura Urbanska
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Marietjie Venter
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Nicole Wolter
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Teresa C.T. Peret
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Vahid Salimi
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Varsha Potdar
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Vítor Borges
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
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Setton EVW, Ballesteros JA, Blaszczyk PO, Klementz BC, Sharma PP. A taxon-restricted duplicate of Iroquois3 is required for patterning the spider waist. PLoS Biol 2024; 22:e3002771. [PMID: 39208370 PMCID: PMC11361693 DOI: 10.1371/journal.pbio.3002771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
The chelicerate body plan is distinguished from other arthropod groups by its division of segments into 2 tagmata: the anterior prosoma ("cephalothorax") and the posterior opisthosoma ("abdomen"). Little is understood about the genetic mechanisms that establish the prosomal-opisthosomal (PO) boundary. To discover these mechanisms, we created high-quality genomic resources for the large-bodied spider Aphonopelma hentzi. We sequenced specific territories along the antero-posterior axis of developing embryos and applied differential gene expression analyses to identify putative regulators of regional identity. After bioinformatic screening for candidate genes that were consistently highly expressed in only 1 tagma (either the prosoma or the opisthosoma), we validated the function of highly ranked candidates in the tractable spider model Parasteatoda tepidariorum. Here, we show that an arthropod homolog of the Iroquois complex of homeobox genes is required for proper formation of the boundary between arachnid tagmata. The function of this homolog had not been previously characterized, because it was lost in the common ancestor of Pancrustacea, precluding its investigation in well-studied insect model organisms. Knockdown of the spider copy of this gene, which we designate as waist-less, in P. tepidariorum resulted in embryos with defects in the PO boundary, incurring discontinuous spider germ bands. We show that waist-less is required for proper specification of the segments that span the prosoma-opisthosoma boundary, which in adult spiders corresponds to the narrowed pedicel. Our results demonstrate the requirement of an ancient, taxon-restricted paralog for the establishment of the tagmatic boundary that defines Chelicerata.
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Affiliation(s)
- Emily V. W. Setton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jesús A. Ballesteros
- Department of Biology, Kean University, Union, New Jersey, United States of America
| | - Pola O. Blaszczyk
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Benjamin C. Klementz
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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35
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van Mazijk R, West AG, Verboom GA, Elliott TL, Bureš P, Muasya AM. Genome size variation in Cape schoenoid sedges (Schoeneae) and its ecophysiological consequences. AMERICAN JOURNAL OF BOTANY 2024; 111:e16315. [PMID: 38695147 DOI: 10.1002/ajb2.16315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 08/24/2024]
Abstract
PREMISE Increases in genome size in plants-often associated with larger, low-density stomata and greater water-use efficiency (WUE)-could affect plant ecophysiological and hydraulic function. Variation in plant genome size is often due to polyploidy, having occurred repeatedly in the austral sedge genus Schoenus in the Cape Floristic Region (CFR), while species in the other major schoenoid genus in the region, Tetraria, have smaller genomes. Comparing these genera is useful as they co-occur at the landscape level, under broadly similar bioclimatic conditions. We hypothesized that CFR Schoenus have greater WUE, with lower maximum stomatal conductance (gwmax) imposed by larger, less-dense stomata. METHODS We investigated relationships between genome size and stomatal parameters in a phylogenetic context, reconstructing a phylogeny of CFR-occurring Schoeneae (Cyperaceae). Species' stomatal and functional traits were measured from field-collected and herbarium specimens. Carbon stable isotopes were used as an index of WUE. Genome size was derived from flow-cytometric measurements of leafy shoots. RESULTS Evolutionary regressions demonstrated that stomatal size and density covary with genome size, positively and negatively, respectively, with genome size explaining 72-75% of the variation in stomatal size. Larger-genomed species had lower gwmax and C:N ratios, particularly in culms. CONCLUSIONS We interpret differences in vegetative physiology between the genera as evidence of more-conservative strategies in CFR Schoenus compared to the more-acquisitive Tetraria. Because Schoenus have smaller, reduced leaves, they likely rely more on culm photosynthesis than Tetraria. Across the CFR Schoeneae, ecophysiology correlates with genome size, but confounding sources of trait variation limit inferences about causal relationships between traits.
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Affiliation(s)
- Ruan van Mazijk
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
- Bolus Herbarium, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
- C4 EcoSolutions, Tokai, Cape Town, 7945, South Africa
| | - Adam G West
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
| | - G Anthony Verboom
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
- Bolus Herbarium, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
| | - Tammy L Elliott
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
- Bolus Herbarium, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 611 37, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 611 37, Czech Republic
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
- Bolus Herbarium, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa
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36
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Dvořák P, Skoupý S, Jarošová H, Páleníčková K, Stanojković A. Population genomics resolves cryptic species of the ecologically flexible genus Laspinema (Cyanobacteria). JOURNAL OF PHYCOLOGY 2024; 60:871-885. [PMID: 38922955 DOI: 10.1111/jpy.13475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 06/28/2024]
Abstract
Cyanobacterial taxonomy is entering the genomic era, but only a few taxonomic studies have employed population genomics, which provides a framework and a multitude of tools to understand species boundaries. Phylogenomic and population genomic analyses previously suggested that several cryptic lineages emerged within the genus Laspinema. Here, we apply population genomics to define boundaries between these lineages and propose two new cryptic species, Laspinema olomoucense and L. palackyanum. Moreover, we sampled soil and puddles across Central Europe and sequenced the 16S rRNA gene and 16S-23S ITS region of the isolated Laspinema strains. Together with database mining of 16S rRNA gene sequences, we determined that the genus Laspinema has a cosmopolitan distribution and inhabits a wide variety of habitats, including freshwater, saline water, mangroves, soil crusts, soils, puddles, and the human body.
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Affiliation(s)
- Petr Dvořák
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Svatopluk Skoupý
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Hana Jarošová
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Kateřina Páleníčková
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Aleksandar Stanojković
- Department of Botany, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
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37
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Andrade P, Alves JM, Pereira P, Rubin CJ, Silva E, Sprehn CG, Enbody E, Afonso S, Faria R, Zhang Y, Bonino N, Duckworth JA, Garreau H, Letnic M, Strive T, Thulin CG, Queney G, Villafuerte R, Jiggins FM, Ferrand N, Andersson L, Carneiro M. Selection against domestication alleles in introduced rabbit populations. Nat Ecol Evol 2024; 8:1543-1555. [PMID: 38907020 DOI: 10.1038/s41559-024-02443-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
Humans have moved domestic animals around the globe for thousands of years. These have occasionally established feral populations in nature, often with devastating ecological consequences. To understand how natural selection shapes re-adaptation into the wild, we investigated one of the most successful colonizers in history, the European rabbit. By sequencing the genomes of 297 rabbits across three continents, we show that introduced populations exhibit a mixed wild-domestic ancestry. We show that alleles that increased in frequency during domestication were preferentially selected against in novel natural environments. Interestingly, causative mutations for common domestication traits sometimes segregate at considerable frequencies if associated with less drastic phenotypes (for example, coat colour dilution), whereas mutations that are probably strongly maladaptive in nature are absent. Whereas natural selection largely targeted different genomic regions in each introduced population, some of the strongest signals of parallelism overlap genes associated with neuronal or brain function. This limited parallelism is probably explained by extensive standing genetic variation resulting from domestication together with the complex mixed ancestry of introduced populations. Our findings shed light on the selective and molecular mechanisms that enable domestic animals to re-adapt to the wild and provide important insights for the mitigation and management of invasive populations.
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Affiliation(s)
- Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
| | - Joel M Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Palaeogenomics and Bio-Archaeology Research Network Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Paulo Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Institute of Marine Research, Bergen, Norway
| | - Eugénio Silva
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - C Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Sandra Afonso
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Yexin Zhang
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Never Bonino
- Estación Experimental Bariloche, Instituto Nacional de Tecnología Agropecuaria, Casilla de Correo Bariloche, Argentina
| | - Janine A Duckworth
- Wildlife Ecology and Management Group, Manaaki Whenua - Landcare Research, Lincoln, New Zealand
- Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, Australian Capital Territory, Australia
| | - Hervé Garreau
- GenPhySE, Université de Toulouse, Castanet-Tolosan, France
| | - Mike Letnic
- Centre for Ecosystem Science, School of BEES, University of New South Wales, Sydney, New South Wales, Australia
- Evolution and Ecology Research Centre, School of BEES, University of New South Wales, Sydney, New South Wales, Australia
| | - Tanja Strive
- Centre for Invasive Species Solutions, University of Canberra, Bruce, Australian Capital Territory, Australia
- Commonwealth Scientific and Industrial Research Organisation, Canberra, Australian Capital Territory, Australia
| | - Carl-Gustaf Thulin
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Guillaume Queney
- ANTAGENE, Wildlife Genetics Laboratory, La Tour de Salvagny, France
| | | | | | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, South Africa
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal.
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Alcantara DMC, Dos Santos CM, Torres JM, Stutz C, Vieira CA, Moreira RMDS, Rodrigues R, Marcon GEB, Ferreira EDC, Mendes FML, Sarti ECFB, de Oliveira TF, Lemos EF, Andrade UV, Lichs GGDC, Demarchi LHF, Zardin MCSU, Gonçalves CCM, Guilhermino JDF, Fernandez ZDC. Long-term surveillance of SARS-CoV-2 in the school community from Campo Grande, Brazil. BMC Public Health 2024; 24:2057. [PMID: 39085807 PMCID: PMC11290088 DOI: 10.1186/s12889-024-19555-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic has significantly impacted education systems worldwide, with Brazil being one of the countries with the longest school closures. Over a million children and teenagers have been affected, leading to increased hunger and nutritional deficiencies. This study aimed to implement long-term surveillance of SARS-CoV-2 infections in public and private schools in Campo Grande, Brazil, after returning to in-person classes. METHODS The study involved testing and genomic surveillance at 23 public and private schools in Campo Grande, Mato Grosso do Sul, Brazil, from October 18, 2021 to November 21, 2022. The participants eligible for enrollment were students aged 6-17 years and staff members from school institutions. At the time of collection, participants were asked if they had symptoms in the last two weeks. Whole-genome sequencing of SARS-CoV-2 was conducted to identify circulating variants and to compare them with those detected in the municipality. The demographic data and clinical history of the participants were described, and a logistic regression model was used to understand how the RT-qPCR results could be related to different characteristics. RESULTS The study included 999 participants, most of whom were women. A total of 85 tests were positive, with an overall positivity rate of 3.2%. The dynamics of case frequency were consistent with those observed in the municipality during the study period. The most common symptoms reported were cough, rhinorrhea, headache, and sore throat. Symptoms were significantly associated with SARS-CoV-2 infection. Eleven lineages were identified in school community samples, with a frequency of occurrence per period similar to that found in the sequences available for the municipality. The most prevalent lineages within the sampling period were BA.2 (59.3%) and BA.5 (29.6%). CONCLUSIONS Our findings demonstrate that schools can play a crucial role in epidemiological surveillance, helping trigger rapid responses to pathogens such as SARS-CoV-2. Long-term surveillance can be used to track outbreaks and assess the role of children and adults in transmission. It can also contribute to pandemic preparedness, enabling a rapid response to emergencies, such as COVID-19.
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Affiliation(s)
| | - Camila Maria Dos Santos
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
| | - Jaire Marinho Torres
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
| | - Claudia Stutz
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas, Alimentos e Nutrição (FACFAN), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Camila Aoyama Vieira
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
| | - Raissa Mariele Dos Santos Moreira
- Instituto Integrado de Saúde (INISA), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Rudielle Rodrigues
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Eduardo de Castro Ferreira
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
- Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina (FAMED), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Flavia Maria Lins Mendes
- FIOCRUZ Mato Grosso do Sul, Fundação Oswaldo Cruz (FIOCRUZ), Campo Grande, Mato Grosso do Sul, Brazil
| | | | | | - Everton Ferreira Lemos
- Universidade Estadual de Mato Grosso do Sul (UEMS), Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Gislene Garcia de Castro Lichs
- Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul (LACEN/MS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Luiz Henrique Ferraz Demarchi
- Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina (FAMED), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
- Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul (LACEN/MS), Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Crhistinne Cavalheiro Maymone Gonçalves
- Programa de Pós-graduação em Doenças Infecciosas e Parasitárias, Faculdade de Medicina (FAMED), Fundação Universidade Federal de Mato Grosso do Sul (UFMS), Campo Grande, Mato Grosso do Sul, Brazil
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
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De Sabato L, Monini M, Galuppi R, Dini FM, Ianiro G, Vaccari G, Ostanello F, Di Bartolo I. Investigating the Hepatitis E Virus (HEV) Diversity in Rat Reservoirs from Northern Italy. Pathogens 2024; 13:633. [PMID: 39204234 PMCID: PMC11357196 DOI: 10.3390/pathogens13080633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 07/23/2024] [Accepted: 07/24/2024] [Indexed: 09/03/2024] Open
Abstract
Hepatitis E virus belonging to the Rocahepevirus ratti species, genotype HEV-C1, has been extensively reported in rats in Europe, Asia and North America. Recently, human cases of hepatitis associated with HEV-C1 infection have been reported, but the zoonotic nature of rat-HEV remains controversial. The transmission route of rat-HEV is unidentified and requires further investigation. The HEV strains of the Paslahepevirus balayani species, belonging to the same Hepeviridae family, and including the zoonotic genotype HEV-3 usually found in pigs, have also sporadically been identified in rats. We sampled 115 rats (liver, lung, feces) between 2020 and 2023 in Northeast Italy and the HEV detection was carried out by using Reverse Transcription PCR. HEV RNA was detected in 3/115 (2.6%) rats who tested positive for HEV-C1 strains in paired lung, intestinal contents and liver samples. Overall, none tested positive for the Paslahepevirus balayani strains. In conclusion, our results confirm the presence of HEV-rat in Italy with a prevalence similar to previous studies but show that there is a wide heterogeneity of strains in circulation. The detection of HEV-C1 genotype of Rocahepevirus ratti species in some human cases of acute hepatitis suggests that HEV-C1 may be an underestimated source of human infections. This finding, with the geographically widespread detection of HEV-C1 in rats, raises questions about the role of rats as hosts for both HEV-C1 and HEV-3 and the possibility of zoonotic transmission.
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Affiliation(s)
- Luca De Sabato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy; (L.D.S.); (G.I.); (G.V.); (I.D.B.)
| | - Marina Monini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy; (L.D.S.); (G.I.); (G.V.); (I.D.B.)
| | - Roberta Galuppi
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50, Ozzano dell’Emilia, 40064 Bologna, Italy; (R.G.); (F.M.D.); (F.O.)
| | - Filippo Maria Dini
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50, Ozzano dell’Emilia, 40064 Bologna, Italy; (R.G.); (F.M.D.); (F.O.)
| | - Giovanni Ianiro
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy; (L.D.S.); (G.I.); (G.V.); (I.D.B.)
| | - Gabriele Vaccari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy; (L.D.S.); (G.I.); (G.V.); (I.D.B.)
| | - Fabio Ostanello
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50, Ozzano dell’Emilia, 40064 Bologna, Italy; (R.G.); (F.M.D.); (F.O.)
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy; (L.D.S.); (G.I.); (G.V.); (I.D.B.)
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Barbosa ADO, Gava D, Tochetto C, Ribeiro LC, Bastos APA, Morés MAZ, Schaefer R, de Lima M. Immunogenicity of an Inactivated Senecavirus A Vaccine with a Contemporary Brazilian Strain in Mice. Vaccines (Basel) 2024; 12:845. [PMID: 39203971 PMCID: PMC11358955 DOI: 10.3390/vaccines12080845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 09/03/2024] Open
Abstract
Senecavirus A (SVA) is a picornavirus that is endemic in swine, causing a vesicular disease clinically indistinguishable from other vesicular diseases, like foot-and-mouth disease. The widespread viral circulation, constant evolution, and economic losses caused to the swine industry emphasize the need for measures to control the agent. In this study, we evaluated the immunogenicity of a whole-virus-inactivated vaccine using a representative contemporary Brazilian SVA strain in Balb/ByJ mice. The animals were vaccinated with two doses by an intramuscular route. The humoral response induced by the vaccination was evaluated by an in-house ELISA assay for IgG detection. The cellular response was assessed by flow cytometry after in vitro SVA stimulation in splenocyte cultures from vaccinated and non-vaccinated groups. Protection against SVA was assessed in the experimental groups following an oral challenge with the homologous virus. The vaccination induced high levels of IgG antibodies and the proliferation of CD45R/B220+sIgM+, CD3e+CD69+, and CD3e+CD4+CD44+CD62L- cells. These results indicate the immunogenicity and safety of the vaccine formulation in a murine model and the induction of humoral and cellular response against SVA.
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Affiliation(s)
- Amanda de Oliveira Barbosa
- Laboratório de Virologia e Imunologia, Universidade Federal de Pelotas, Capão do Leão 96160-000, RS, Brazil; (A.d.O.B.); (L.C.R.)
| | - Danielle Gava
- Embrapa Suínos e Aves, BR 153, Km 110, Distrito de Tamanduá, Concordia 89715-899, SC, Brazil; (D.G.); (C.T.); (A.P.A.B.); (M.A.Z.M.); (R.S.)
| | - Caroline Tochetto
- Embrapa Suínos e Aves, BR 153, Km 110, Distrito de Tamanduá, Concordia 89715-899, SC, Brazil; (D.G.); (C.T.); (A.P.A.B.); (M.A.Z.M.); (R.S.)
| | - Leonardo Clasen Ribeiro
- Laboratório de Virologia e Imunologia, Universidade Federal de Pelotas, Capão do Leão 96160-000, RS, Brazil; (A.d.O.B.); (L.C.R.)
| | - Ana Paula Almeida Bastos
- Embrapa Suínos e Aves, BR 153, Km 110, Distrito de Tamanduá, Concordia 89715-899, SC, Brazil; (D.G.); (C.T.); (A.P.A.B.); (M.A.Z.M.); (R.S.)
| | - Marcos Antônio Zanella Morés
- Embrapa Suínos e Aves, BR 153, Km 110, Distrito de Tamanduá, Concordia 89715-899, SC, Brazil; (D.G.); (C.T.); (A.P.A.B.); (M.A.Z.M.); (R.S.)
| | - Rejane Schaefer
- Embrapa Suínos e Aves, BR 153, Km 110, Distrito de Tamanduá, Concordia 89715-899, SC, Brazil; (D.G.); (C.T.); (A.P.A.B.); (M.A.Z.M.); (R.S.)
| | - Marcelo de Lima
- Laboratório de Virologia e Imunologia, Universidade Federal de Pelotas, Capão do Leão 96160-000, RS, Brazil; (A.d.O.B.); (L.C.R.)
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Seth-Smith H, Bommana S, Dean D, Read TD, Marti H. Chlamydia suis undergoes interclade recombination promoting Tet-island exchange. BMC Genomics 2024; 25:724. [PMID: 39060998 PMCID: PMC11282597 DOI: 10.1186/s12864-024-10606-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND The obligate intracellular bacterial family Chlamydiaceae comprises a number of different species that cause disease in various vertebrate hosts including humans. Chlamydia suis, primarily found in the gastrointestinal tract of pigs, is the only species of the Chlamydiaceae family to have naturally gained tetracycline resistance (TetR), through a genomic island (Tet-island), integrated into the middle of chromosomal invasin-like gene inv. Previous studies have hypothesised that the uptake of the Tet-island from a host outside the Chlamydiaceae family was a unique event, followed by spread among C. suis through homologous recombination. In vitro recombination studies have shown that Tet-island exchange between C. suis strains is possible. Our aim in this study was to gain a deeper understanding of the interclade recombination of the Tet-island, among currently circulating C. suis field strains compared to in vitro-generated recombinants, using published whole genome sequences of C. suis field strains (n = 35) and in vitro-generated recombinants (n = 63). RESULTS We found that the phylogeny of inv better reflected the phylogeny of the Tet-island than that of the whole genome, supporting recombination rather than site-specific insertion as the means of transfer. There were considerable differences between the distribution of recombinations within in vitro-generated strains compared to that within the field strains. These differences are likely because in vitro-generated recombinants were selected for a tetracycline and rifamycin/rifampicin resistant background, leading to the largest peak of recombination across the Tet-island. Finally, we found that interclade recombinations across the Tet-island were more variable in length downstream of the Tet-island than upstream. CONCLUSIONS Our study supports the hypothesis that the occurrence of TetR strains in both clades of C. suis came about through interclade recombination after a single ancestral horizontal gene transfer event.
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Affiliation(s)
- Helena Seth-Smith
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Sankhya Bommana
- Division of Infectious Diseases and Global Health, Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Deborah Dean
- Division of Infectious Diseases and Global Health, Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Joint Graduate Program in Bioengineering, University of California Berkeley, University of California San Francisco, Berkeley and San Francisco, CA, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Hanna Marti
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland.
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Baruti K, Choga WT, Phinius BB, Phakedi B, Bhebhe L, Mpebe GGA, Motshosi PC, Ratsoma T, Moyo S, Jongman M, Anderson M, Gaseitsiwe S. Impact of Hepatitis Delta Virus Infection on the Selection of Hepatitis B Surface Antigen Mutations. Genes (Basel) 2024; 15:982. [PMID: 39202343 PMCID: PMC11353884 DOI: 10.3390/genes15080982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 09/03/2024] Open
Abstract
The interaction of multiple viruses in one host is thought to enhance the development of mutations. However, the impact of hepatitis D virus (HDV) positivity on the development of unique hepatitis B virus (HBV) mutations among people living with human immunodeficiency virus (HIV) (PLWH) remains poorly understood in African countries, including Botswana. We used HBV sequences generated from the Botswana Combination Prevention Project (BCPP), which is the largest pair-matched cluster-randomized HIV trial in Botswana. Only participants with available HBV sequences (n = 55) were included in our study ([HIV/HBV-positive (n = 50) and HIV/HBV/HDV-positive (n = 5)]. Geno2pheno was used to determine HBV genotypes, and HBV surface region sequences (all subgenotype A1) were aligned in AliView for mutational analysis, while the impact of mutations was assessed using Phyre2. Our results identified 182 common mutations between the two groups. In the HIV/HBV/HDV cohort, only three mutations (L95W, W156Q, C221Y) were classified as deleterious, with only L95W being the most frequent. In the HIV/HBV cohort, four mutations (W199R, C221A, C221S, W223G) were also classified as deleterious. Our results demonstrate the presence of unique HBV mutations among the HIV/HBV/HDV-positive cohort. Functional characterization of these mutations is recommended to determine their effect on HDV.
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Affiliation(s)
- Kabo Baruti
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone Private Bag 00704, Botswana
| | - Wonderful T. Choga
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone Private Bag 00704, Botswana
| | - Bonolo B. Phinius
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone Private Bag 00704, Botswana
| | - Basetsana Phakedi
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
| | - Lynnette Bhebhe
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
| | - Gorata G. A. Mpebe
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
| | - Patience C. Motshosi
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
| | - Tsholofelo Ratsoma
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
| | - Sikhulile Moyo
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Pathology, Division of Medical Virology, Stellenbosch University, Cape Town 7535, South Africa
| | - Mosimanegape Jongman
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone Private Bag 00704, Botswana
| | - Motswedi Anderson
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
- Africa Health Research Institute (AHRI), Durban 4013, South Africa
- The Francis Crick Institute, London NW1 2BE, UK
| | - Simani Gaseitsiwe
- Research Laboratory, Botswana Harvard Health Partnership, Gaborone Private Bag BO 320, Botswana; (K.B.); (W.T.C.); (B.B.P.); (B.P.); (L.B.); (G.G.A.M.); (P.C.M.); (T.R.); (S.M.); (M.J.); (M.A.)
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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Fletcher J, Smith A, Honan A, Leary W, Dabney T, Branco S. Inter- and intra-specific metal tolerance variation in ectomycorrhizal fungal Suillus species. MYCORRHIZA 2024:10.1007/s00572-024-01162-8. [PMID: 39037611 DOI: 10.1007/s00572-024-01162-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 07/04/2024] [Indexed: 07/23/2024]
Abstract
Soil metal contamination can affect growth, metabolism, and reproduction of organisms, and can lead to death. However, some fungi have evolved metal tolerance and are able to live in contaminated soils. Species in the ectomycorrhizal genus Suillus from Europe and Asia display variation in metal tolerance, yet it is unknown whether this is a widespread trait in the genus and whether it occurs in North America. Here we investigate cadmium (Cd) and zinc (Zn) tolerance in S. brevipes and S. tomentosus isolates collected from sites in the Rocky Mountains of Colorado displaying different metal content. In line with previous findings for other Suillus species, we hypothesized (1) S. brevipes and S. tomentosus to display intra-specific metal tolerance variation, (2) Zn and Cd tolerance to be correlated to soil metal content, and (3) tolerant isolates to show lower metal tissue content compared to sensitive isolates (due to increased metal exclusion). We found ample intra- and inter-specific Zn and Cd tolerance variation in both S. brevipes and S. tomentosus, but no correlation between soil metal content and tolerance. There was a negative correlation between tolerance level and Zn uptake, indicating an exclusion-based Zn tolerance strategy. Sensitive and tolerant isolates showed no difference in Cd accumulation, indicating that Cd tolerance in these species is likely not dependent on exclusion. Our study sets the groundwork for further investigation into the genetic basis of Suillus metal tolerance and whether and how it impacts pine mycorrhizal partners.
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Affiliation(s)
- Jessica Fletcher
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA.
| | - Alexander Smith
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Amy Honan
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, US
| | - William Leary
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Treya Dabney
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
| | - Sara Branco
- Department of Integrative Biology, University of Colorado Denver, Denver, CO, USA
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Angus RB, Maté JF, Angus EM, Král D. Towards a revision of the Palaearctic species of Aphodius Hellwig, 1798, subgenus Liothorax Motschulsky, 1860 (Coleoptera, Scarabaeidae, Aphodiinae). Zookeys 2024; 1207:205-299. [PMID: 39081542 PMCID: PMC11287083 DOI: 10.3897/zookeys.1207.117225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/06/2024] [Indexed: 08/02/2024] Open
Abstract
The Palaearctic species of Aphodius Hellwig, 1798, subgenus Liothorax Motschulsky, 1860 are revised using a combination of chromosome analysis, molecular phylogenetics and morphological statistical analysis. Sixteen species are recognised, one of which is shown to comprise two subspecies. Based mainly on the morphology of the aedeagal endophallus and the phylogenetic analysis, they are placed in two groups: the. niger group, apparently monophyletic, comprising Aphodius (Liothorax) niger Illiger, 1798, A. (L.) muscorum (Ádám, 1994), stat. rest., A. (L.) felixsp. nov., A. (L.) bellumgerenssp. nov., A. (L.) bameulisp. nov., A. (L.) krellisp. nov., A. (L.) isikdagensis (Balthasar, 1953), A. (L.) albertisp. nov. and A. (L.) wilsonae Maté et Angus, 2005, stat. rest.; and the plagiatus group, almost certainly paraphyletic, comprising A. (L.) plagiatus (Linnaeus, 1767), including A. (L.) p. plagiatus and A. (L.) p. sinoplagiatussubsp. nov., A. (L.) rodrigoisp. nov., A. (L.) discoidesA. Schmidt, 1916, stat. rest., A. (L.) rutilipennis (Baudi di Selve, 1870), stat. rest., A. (L.) chellalasp. nov., A. (L.) kraatzi Harold, 1868, and A. (L.) rusakovi Gusakov, 2004. A key to the species is given as well as details of their morphology, distributions, and habitats.
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Affiliation(s)
- Robert B. Angus
- Department of Life Sciences (Insects), The Natural History Museum, Cromwell Road, London SW7 5BD, UKThe Natural History MuseumLondonUnited Kingdom
| | - Jason F. Maté
- c/Henares 16, Velilla de San Antonio, Madrid, 28891, SpainUnaffiliatedMadridSpain
| | - Elizabeth M. Angus
- Biomedical Imaging Unit, Level B South Block, Mail point 12, General Hospital, Southampton SO16 6YD, UKMail point 12, General HospitalSouthamptonUnited Kingdom
| | - David Král
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, CZ-128 00, Praha 2, Czech RepublicCharles UniversityPrahaCzech Republic
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45
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Petersen RH, Hughes KW. Two new species of Collybiopsis (Agaricales, Omphalotaceae) from Eastern North America. MycoKeys 2024; 107:95-124. [PMID: 39081830 PMCID: PMC11287082 DOI: 10.3897/mycokeys.107.122634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/05/2024] [Indexed: 08/02/2024] Open
Abstract
Two small gymnopoid fungi from the southern Appalachian Mountains and Massachusetts, Collybiopsiscomplicata sp. nov. and C.prolapsis sp. nov., are identified and described. A new generic nrITS-LSU phylogeny of Collybiopsis places C.complicata and C.prolapsis in a small clade together with C.minor, and an unknown taxon from Arkansas. This clade adds to the growing circumscription of Collybiopsis (= Marasmiellus).
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Affiliation(s)
- Ronald H. Petersen
- Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN 37996-1100, USAUniversity of TennesseeKnoxvilleUnited States of America
| | - Karen W. Hughes
- Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN 37996-1100, USAUniversity of TennesseeKnoxvilleUnited States of America
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Gonzalez FN, Raticelli F, Ferrufino C, Fagúndez G, Rodriguez G, Miño S, Dus Santos MJ. Detection and characterization of Deformed Wing Virus (DWV) in apiaries with stationary and migratory management in the province of Entre Ríos, Argentina. Sci Rep 2024; 14:16747. [PMID: 39033233 PMCID: PMC11271310 DOI: 10.1038/s41598-024-67264-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Abstract
In Argentina, migratory activity in search of floral diversity has become a common approach to maximizing honey production. The Entre Ríos province possesses a floral diversity that allows beekeepers to perform migratory or stationary management. Beyond the impact caused by transhumance, migratory colonies in this province start and end the season in monoculture areas. To study the effect of these practices on viral infection, we assayed for the presence, abundance and genetic characterization of the Deformed Wing Virus (DWV) in honey bees from apiaries with both types of management. In migratory apiaries, DWV was detectable in 86.2% of the colonies at the beginning of the season (September 2018), and 66% at the end of the season (March 2019). On the other hand, DWV was detected in 44.11% and 53.12% of stationary samples, at the beginning and the end of the season, respectively. Sequence analysis from migratory and stationary colonies revealed that all samples belonged to DWV-A type. The highest viral loads were detected in migratory samples collected in September. Higher DWV presence and abundance were associated with migratory management and the sampling time. Based on our findings we propose that the benefit of migration to wild flowering areas can be dissipated when the bee colonies end the season with monoculture.
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Affiliation(s)
- F N Gonzalez
- Instituto de Virología e Innovaciones Tecnológicas (IVIT), CICVyA, Instituto Nacional de Tecnología Agropecuaria. De las Cabañas y De los Reseros s/n, Hurlingham, Buenos Aires, Argentina
| | - F Raticelli
- Laboratorio de Especialidades Productivas de Maciá (LEPMA), Ecología y Medio Ambiente, Secretaría de Producción, Municipio de Gobernador Maciá, Entre Ríos, Argentina
| | - C Ferrufino
- Instituto de Virología e Innovaciones Tecnológicas (IVIT), CICVyA, Instituto Nacional de Tecnología Agropecuaria. De las Cabañas y De los Reseros s/n, Hurlingham, Buenos Aires, Argentina
| | - G Fagúndez
- Laboratorio de Actuopalinología, CICYTTP (CONICET - UADER), Diamante, Entre Ríos, Argentina
| | - G Rodriguez
- EEA Hilario Ascasubi, Instituto Nacional de Tecnología Agropecuaria, Ruta Nacional 3, Km 794, Hilario Ascasubi, Buenos Aires, Argentina
| | - S Miño
- EEA Cerro Azul, Instituto Nacional de Tecnología Agropecuaria, Ruta Nacional 14, Km 836, Cerro Azul, Misiones, Argentina
| | - M J Dus Santos
- Instituto de Virología e Innovaciones Tecnológicas (IVIT), CICVyA, Instituto Nacional de Tecnología Agropecuaria. De las Cabañas y De los Reseros s/n, Hurlingham, Buenos Aires, Argentina.
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Yamamoto H, Tamura T, Ichikawa T, Taguchi Y, Mori K, Oguri S, Suzuki R, Suzuki S, Teshima T, Fukuhara T. Generation of recombinant viruses directly from clinical specimens of COVID-19 patients. J Clin Microbiol 2024; 62:e0004224. [PMID: 38874339 PMCID: PMC11250110 DOI: 10.1128/jcm.00042-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024] Open
Abstract
Rapid characterization of the causative agent(s) during a disease outbreak can aid in the implementation of effective control measures. However, isolation of the agent(s) from crude clinical samples can be challenging and time-consuming, hindering the establishment of countermeasures. In the present study, we used saliva specimens collected for the diagnosis of SARS-CoV-2-a good example of a practical target-and attempted to characterize the virus within the specimens without virus isolation. Thirty-four saliva samples from coronavirus disease 2019 patients were used to extract RNA and synthesize DNA amplicons by PCR. New primer sets were designed to generate DNA amplicons of the full-length spike (S) gene for subsequent use in a circular polymerase extension reaction (CPER), a simple method for deriving recombinant viral genomes. According to the S sequence, four clinical specimens were classified as BA. 1, BA.2, BA.5, and XBB.1 and were used for the de novo generation of recombinant viruses carrying the entire S gene. Additionally, chimeric viruses carrying the gene encoding GFP were generated to evaluate viral propagation using a plate reader. We successfully used the RNA purified directly from clinical saliva samples to generate chimeric viruses carrying the entire S gene by our updated CPER method. The chimeric viruses exhibited robust replication in cell cultures with similar properties. Using the recombinant GFP viruses, we also successfully characterized the efficacy of the licensed antiviral AZD7442. Our proof-of-concept demonstrates the novel utility of CPER to allow rapid characterization of viruses from clinical specimens. IMPORTANCE Characterization of the causative agent(s) for infectious diseases helps in implementing effective control measurements, especially in outbreaks. However, the isolation of the agent(s) from clinical specimens is often challenging and time-consuming. In this study, saliva samples from coronavirus disease 2019 patients were directly subjected to purifying viral RNA, synthesizing DNA amplicons for sequencing, and generating recombinant viruses. Utilizing an updated circular polymerase extension reaction method, we successfully generated chimeric SARS-CoV-2 viruses with sufficient in vitro replication capacity and antigenicity. Thus, the recombinant viruses generated in this study were applicable for evaluating the antivirals. Collectively, our developed method facilitates rapid characterization of specimens circulating in hosts, aiding in the establishment of control measurements. Additionally, this approach offers an advanced strategy for controlling other (re-)emerging viral infectious diseases.
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Affiliation(s)
- Hirotaka Yamamoto
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Takaya Ichikawa
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Department of Hematology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Department of Hematology, Sapporo City General Hospital, Sapporo, Japan
| | - Yudai Taguchi
- Department of Clinical Laboratory Testing, Sapporo City General Hospital, Sapporo, Japan
| | - Kento Mori
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Satoshi Oguri
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Takanori Teshima
- Department of Hematology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
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Moreno KMF, de Andrade VA, de Melo Iani FC, Fonseca V, Lima MT, de Castro Barbosa E, Tomé LMR, Guimarães NR, Fritsch HM, Adelino T, Oliveira Fereguetti T, Aspahan MC, Gamarano Barros T, Alcantara LCJ, Giovanetti M. Exploring Microorganisms Associated to Acute Febrile Illness and Severe Neurological Disorders of Unknown Origin: A Nanopore Metagenomics Approach. Genes (Basel) 2024; 15:922. [PMID: 39062701 PMCID: PMC11276239 DOI: 10.3390/genes15070922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Acute febrile illness (AFI) and severe neurological disorders (SNDs) often present diagnostic challenges due to their potential origins from a wide range of infectious agents. Nanopore metagenomics is emerging as a powerful tool for identifying the microorganisms potentially responsible for these undiagnosed clinical cases. In this study, we aim to shed light on the etiological agents underlying AFI and SND cases that conventional diagnostic methods have not been able to fully elucidate. Our approach involved analyzing samples from fourteen hospitalized patients using a comprehensive nanopore metagenomic approach. This process included RNA extraction and enrichment using the SMART-9N protocol, followed by nanopore sequencing. Subsequent steps involved quality control, host DNA/cDNA removal, de novo genome assembly, and taxonomic classification. Our findings in AFI cases revealed a spectrum of disease-associated microbes, including Escherichia coli, Streptococcus sp., Human Immunodeficiency Virus 1 (Subtype B), and Human Pegivirus. Similarly, SND cases revealed the presence of pathogens such as Escherichia coli, Clostridium sp., and Dengue virus type 2 (Genotype-II lineage). This study employed a metagenomic analysis method, demonstrating its efficiency and adaptability in pathogen identification. Our investigation successfully identified pathogens likely associated with AFI and SNDs, underscoring the feasibility of retrieving near-complete genomes from RNA viruses. These findings offer promising prospects for advancing our understanding and control of infectious diseases, by facilitating detailed genomic analysis which is critical for developing targeted interventions and therapeutic strategies.
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Affiliation(s)
- Keldenn Melo Farias Moreno
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (K.M.F.M.); (M.T.L.); (H.M.F.)
| | | | - Felipe Campos de Melo Iani
- Central Public Health Laboratory of the State of Minas Gerais, Ezequiel Dias Foundation, Belo Horizonte 30510-010, Brazil; (F.C.d.M.I.); (T.A.)
| | - Vagner Fonseca
- Department of Exact and Earth Sciences, University of the State of Bahia, Salvador 41150-000, Brazil;
| | - Maurício Teixeira Lima
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (K.M.F.M.); (M.T.L.); (H.M.F.)
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil; (E.d.C.B.); (L.M.R.T.); (N.R.G.); (L.C.J.A.)
| | - Emerson de Castro Barbosa
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil; (E.d.C.B.); (L.M.R.T.); (N.R.G.); (L.C.J.A.)
| | - Luiz Marcelo Ribeiro Tomé
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil; (E.d.C.B.); (L.M.R.T.); (N.R.G.); (L.C.J.A.)
| | - Natália Rocha Guimarães
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil; (E.d.C.B.); (L.M.R.T.); (N.R.G.); (L.C.J.A.)
| | - Hegger Machado Fritsch
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (K.M.F.M.); (M.T.L.); (H.M.F.)
- Morphogenesis and Antigenicity of HIV and Hepatitis Viruses, University of Tours, 37032 Tours, France
| | - Talita Adelino
- Central Public Health Laboratory of the State of Minas Gerais, Ezequiel Dias Foundation, Belo Horizonte 30510-010, Brazil; (F.C.d.M.I.); (T.A.)
| | | | - Maíra Cardoso Aspahan
- Eduardo de Menezes Hospital, Belo Horizonte 30622-020, Brazil; (V.A.d.A.); (T.O.F.); (M.C.A.); (T.G.B.)
| | - Tereza Gamarano Barros
- Eduardo de Menezes Hospital, Belo Horizonte 30622-020, Brazil; (V.A.d.A.); (T.O.F.); (M.C.A.); (T.G.B.)
| | - Luiz Carlos Junior Alcantara
- René Rachou Institute, Oswaldo Cruz Foundation, Belo Horizonte 30190-002, Brazil; (E.d.C.B.); (L.M.R.T.); (N.R.G.); (L.C.J.A.)
| | - Marta Giovanetti
- Department of Sciences and Technologies for Sustainable Development and One Health, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
- Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil
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Tiwary BK. A positive selection at binding site 501 in the B.1 lineage might have triggered the highly infectious sub-lineages of SARS-CoV-2. Gene 2024; 915:148427. [PMID: 38575097 DOI: 10.1016/j.gene.2024.148427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
The descendants of the B lineage are the most predominant variants among the SARS-CoV-2 virus due to the incorporation of new mutations augmenting the infectivity of the virus. There is a substantial increase in the transition transversion bias, nucleotide diversity and purifying selection on the spike protein in the descendants of the B lineage of the SARS-CoV-2 virus on a temporal scale. A strong bias for C-to-U substitutions is found in the genes encoding spike protein in this lineage. The positive selection has operated on the spike gene of B lineages and its sub-lineages. The B.1 lineage has undergone positive selection on site 501 of the receptor binding domain ultimately reflected in a key substitution N501Y in its three descendant lineages namely B.1.1.7, B.1.351 and P.1. The intensity of purifying selection on the multiple sites of the spike gene has increased substantially in the sub-lineages of B.1 in a timescale. The binding site 501 on the spike protein in B lineage is found to coevolve with other amino acid sites. This study sheds light on the evolutionary trajectory of the B lineage into highly infectious descendants in the recent past under the influence of positive and purifying selection exerted by natural immunity and vaccination of the host.
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Affiliation(s)
- Basant K Tiwary
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry 605 014, India.
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50
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Phinius BB, Choga WT, Anderson M, Mokomane M, Gobe I, Ratsoma T, Phakedi B, Mpebe G, Bhebhe L, Gaolathe T, Mosepele M, Makhema J, Shapiro R, Lockman S, Musonda R, Moyo S, Gaseitsiwe S. Molecular Characterization of Hepatitis B Virus in People Living with HIV in Rural and Peri-Urban Communities in Botswana. Biomedicines 2024; 12:1561. [PMID: 39062134 PMCID: PMC11275055 DOI: 10.3390/biomedicines12071561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
(1) Background: Hepatitis B virus (HBV) sequencing data are important for monitoring HBV evolution. We aimed to molecularly characterize HBV sequences from participants with HBV surface antigen-positive (HBsAg+) serology and occult hepatitis B infection (OBI+). (2) Methods: We utilized archived plasma samples from people living with human immunodeficiency virus (PLWH) in Botswana. HBV DNA was sequenced, genotyped and analyzed for mutations. We compared mutations from study sequences to those from previously generated HBV sequences in Botswana. The impact of OBI-associated mutations on protein function was assessed using the Protein Variation Effect Analyzer. (3) Results: Sequencing success was higher in HBsAg+ than in OBI+ samples [86/128 (67.2%) vs. 21/71 (29.2%)]. Overall, 93.5% (100/107) of sequences were genotype A1, 2.8% (3/107) were D3 and 3.7% (4/107) were E. We identified 13 escape mutations in 18/90 (20%) sequences with HBsAg coverage, with K122R having the highest frequency. The mutational profile of current sequences differed from previous Botswana HBV sequences, suggesting possible mutational changes over time. Mutations deemed to have an impact on protein function were tpQ6H, surfaceV194A and preCW28L. (4) Conclusions: We characterized HBV sequences from PLWH in Botswana. Escape mutations were prevalent and were not associated with OBI. Longitudinal HBV studies are needed to investigate HBV natural evolution.
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Affiliation(s)
- Bonolo B. Phinius
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone Private Bag UB0022, Botswana; (M.M.); (I.G.)
| | - Wonderful T. Choga
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone Private Bag UB0022, Botswana; (M.M.); (I.G.)
| | - Motswedi Anderson
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
- Africa Health Research Institute (AHRI), Private Bag X7, Congella, Durban 4013, South Africa
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Margaret Mokomane
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone Private Bag UB0022, Botswana; (M.M.); (I.G.)
| | - Irene Gobe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone Private Bag UB0022, Botswana; (M.M.); (I.G.)
| | - Tsholofelo Ratsoma
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
| | - Basetsana Phakedi
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
| | - Gorata Mpebe
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
| | - Lynnette Bhebhe
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
| | - Tendani Gaolathe
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
- Faculty of Medicine, University of Botswana, Gaborone Private Bag UB0022, Botswana
| | - Mosepele Mosepele
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
- Faculty of Medicine, University of Botswana, Gaborone Private Bag UB0022, Botswana
| | - Joseph Makhema
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Roger Shapiro
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Shahin Lockman
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Rosemary Musonda
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Sikhulile Moyo
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone Private Bag UB0022, Botswana; (M.M.); (I.G.)
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Private Bag X1, Matieland, Cape Town 7602, South Africa
- School of Health Systems and Public Health, University of Pretoria, Private Bag X20, Pretoria 0028, South Africa
| | - Simani Gaseitsiwe
- Botswana Harvard Health Partnership, Gaborone Private Bag BO320, Botswana; (B.B.P.); (S.M.)
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
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