1
|
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.
Collapse
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
| |
Collapse
|
2
|
Velasco M, Eduard J, Lago IBA, Netto WBG, Dias LDNS, Sindeaux-Neto JL. Histopathological and phylogenetic description of an Amazonian cnidaria microparasite Myxobolus rousseauxii n. sp. infecting the gill arches of Brachyplatystoma rousseauxii (Siluriformes). Parasitol Int 2024; 103:102943. [PMID: 39098654 DOI: 10.1016/j.parint.2024.102943] [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: 03/27/2024] [Revised: 07/13/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024]
Abstract
From genus Myxobolus, cnidarians of Myxozoa class, is well known for infecting economically important fish species and, as result, relevant losses in aquaculture production can be observed. They are present in a big range of fish in its natural habitat, including the migratory Brachyplatystoma rousseauxii catfish. This study aimed is to develop an integrative characterization of a new species of Myxobolus, located in B. rousseauxii's gills. To accomplish this, 30 specimens of B. rousseauxii catfish were collected from Mosqueiro Island in Pará, Brazil; necropsied and analyzed for morphology, histology and molecular characteristics. Cysts with conjunctival capsule development made up of fibroblasts were observed at the gill arches; such proliferation caused bone tissue loss and cartilage compression. The cysts contained Myxobolus myxospores measuring 9.9 μm of length and 9.6 μm of width, whereas polar capsules were 5.4 μm long and 3.4 μm wide, with 8 to 9 coils of polar tubules. Phylogenetic analyses revealed that new species were included in a subclade alongside species from the same geographic location and infection site that infect Siluriformes fish. Morphological and molecular differences revealed that Myxobolus spp. parasite-host associations through histopathology supporting the designation of a new M. rousseauxii n. sp. species in B. rousseauxii, a commercially important fish.
Collapse
Affiliation(s)
- Michele Velasco
- Morpho-Molecular Integration Laboratory and Technologies, Federal Rural University of the Amazon (UFRA), Belém, Pará, Brazil.
| | - Jhonata Eduard
- Morpho-Molecular Integration Laboratory and Technologies, Federal Rural University of the Amazon (UFRA), Belém, Pará, Brazil; Postgraduate Program in the Biology of Infectious and Parasitic Agents (BAIP), Federal University of Pará (UFPA), Belem, Brazil
| | - Isabely Beatriz Araujo Lago
- Morpho-Molecular Integration Laboratory and Technologies, Federal Rural University of the Amazon (UFRA), Belém, Pará, Brazil
| | - Walter Barros Gomes Netto
- Morpho-Molecular Integration Laboratory and Technologies, Federal Rural University of the Amazon (UFRA), Belém, Pará, Brazil
| | | | - José Ledamir Sindeaux-Neto
- Morpho-Molecular Integration Laboratory and Technologies, Federal Rural University of the Amazon (UFRA), Belém, Pará, Brazil
| |
Collapse
|
3
|
Bakker JW, Esser HJ, Sprong H, Godeke GJ, Hoornweg TE, de Boer WF, Pijlman GP, Koenraadt CJM. Differential susceptibility of geographically distinct Ixodes ricinus populations to tick-borne encephalitis virus and louping ill virus. Emerg Microbes Infect 2024; 13:2321992. [PMID: 38484290 PMCID: PMC10946273 DOI: 10.1080/22221751.2024.2321992] [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: 03/19/2024]
Abstract
Tick-borne encephalitis virus (TBEV) is an emerging pathogen in the Netherlands. Multiple divergent viral strains are circulating and the focal distribution of TBEV remains poorly understood. This may, however, be explained by differences in the susceptibility of tick populations for specific viruses and viral strains, and by viral strains having higher infection success in their local tick population. We investigated this hypothesis by exposing Dutch Ixodes ricinus ticks to two different TBEV strains: TBEV-NL from the Netherlands and TBEV-Neudoerfl from Austria. In addition, we exposed ticks to louping Ill virus (LIV), which is endemic to large parts of the United Kingdom and Ireland, but has not been reported in the Netherlands. Ticks were collected from two locations in the Netherlands: one location without evidence of TBEV circulation and one location endemic for the TBEV-NL strain. Ticks were infected in a biosafety level 3 laboratory using an artificial membrane feeding system. Ticks collected from the region without evidence of TBEV circulation had lower infection rates for TBEV-NL as compared to TBEV-Neudoerfl. Vice versa, ticks collected from the TBEV-NL endemic region had higher infection rates for TBEV-NL compared to TBEV-Neudoerfl. In addition, LIV infection rates were much lower in Dutch ticks compared to TBEV, which may explain why LIV is not present in the Netherlands. Our findings show that ticks from two distinct geographical populations differ in their susceptibility to TBEV strains, which could be the result of differences in the genetic background of the tick populations.
Collapse
Affiliation(s)
- Julian W. Bakker
- Laboratory of Entomology, Wageningen University & Research, Wageningen, Netherlands
| | - Helen J. Esser
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, Netherlands
| | - Hein Sprong
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Gert-Jan Godeke
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Tabitha E. Hoornweg
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Willem F. de Boer
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, Netherlands
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University & Research, Wageningen, Netherlands
| | | |
Collapse
|
4
|
Liu Q, Wingfield MJ, Duong TA, Wingfield BD, Chen S. Diversity of Calonectria species from leaves and soils in diseased southern China Eucalyptus plantation. Fungal Biol 2024; 128:2007-2021. [PMID: 39174236 DOI: 10.1016/j.funbio.2024.07.007] [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: 08/16/2023] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 08/24/2024]
Abstract
Calonectria leaf blight (CLB) is one of the best-known diseases of Eucalyptus spp., particularly in Asia and South America. Recently, typical symptoms of leaf and shoot blight caused by Calonectria spp. Were observed in a Eucalyptus plantation in the YunNan Province of southwestern China. Isolations were made from diseased leaves and top soil collected below the diseased trees to determine the causal agent of the disease and to consider the distribution characteristics of the Calonectria species. This resulted in 417 isolates, of which 228 were from leaves and 189 were from soil. Based on comparisons of DNA sequences for the act (actin), cmdA (calmodulin), his3 (histone H3), rpb2 (the second largest subunit of RNA polymerase), tef1 (translation elongation factor 1-alpha) and tub2 (β-tubulin) gene regions, as well as morphological characteristics, 11 Calonectria species were identified. These included Calonectria aciculata (0.7 %), Ca. colhounii (1.2 %), Ca. eucalypti (10.6 %) and Ca. honghensis (43.2 %) in the Ca. colhounii species complex, and Ca. aconidialis (15.3 %), Ca. asiatica (9.8 %), Ca. hongkongensis (1.0 %), Ca. ilicicola (6.0 %), Ca. kyotensis (0.5 %), and Ca. yunnanensis (11.3 %) in the Ca. kyotensis species complex. In addition, a novel species, accounting for 0.5 % of the isolates, was discovered and is described here as Ca. dianii sp. nov. in the Ca colhounii species complex. Most (99.1 %) of the isolates collected from the leaves resided in the Ca. colhounii species complex and a majority (95.8 %) of those from the soils were in Ca. kyotensis species complex. These results suggest that Calonectria spp. in the Ca. colhounii species complex infecting leaves might be adapted to that niche and that those in the Ca. kyotensis species complex are better adapted to a soil habitat.
Collapse
Affiliation(s)
- QianLi Liu
- Research Institute of Fast-growing Trees (RIFT), Chinese Academy of Forestry (CAF), ZhanJiang, 524022, GuangDong Province, China; Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa
| | - ShuaiFei Chen
- Research Institute of Fast-growing Trees (RIFT), Chinese Academy of Forestry (CAF), ZhanJiang, 524022, GuangDong Province, China; Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0028, South Africa.
| |
Collapse
|
5
|
Fang J, Lin A, Yan H, Feng L, Lin S, Mason P, Zhou L, Xu X, Zhao K, Huang Y, Henry RJ. Cytoplasmic genomes of Jasminum sambac reveal divergent sub-mitogenomic conformations and a large nuclear chloroplast-derived insertion. BMC PLANT BIOLOGY 2024; 24:861. [PMID: 39272034 DOI: 10.1186/s12870-024-05557-9] [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: 08/30/2024] [Indexed: 09/15/2024]
Abstract
BACKGROUND Jasminum sambac, a widely recognized ornamental plant prized for its aromatic blossoms, exhibits three flora phenotypes: single-petal ("SP"), double-petal ("DP"), and multi-petal ("MP"). The lack of detailed characterization and comparison of J. sambac mitochondrial genomes (mitogenomes) hinders the exploration of the genetic and structural diversity underlying the varying floral phenotypes in jasmine accessions. RESULTS Here, we de novo assembled three mitogenomes of typical phenotypes of J. sambac, "SP", "DP", and "MP-hutou" ("HT"), with PacBio reads and the "HT" chloroplast (cp) genome with Illumina reads, and verified them with read mapping and fluorescence in situ hybridization (FISH). The three mitogenomes present divergent sub-genomic conformations, with two, two, and four autonomous circular chromosomes ranging in size from 35.7 kb to 405.3 kb. Each mitogenome contained 58 unique genes. Ribosome binding sites with conserved AAGAAx/AxAAAG motifs were detected upstream of uncanonical start codons TTG, CTG and GTG. The three mitogenomes were similar in genomic content but divergent in structure. The structural variations were mainly attributed to recombination mediated by a large (~ 5 kb) forward repeat pair and several short repeats. The three jasmine cp. genomes showed a well-conserved structure, apart from a 19.9 kb inversion in "HT". We identified a 14.3 kb "HT"-specific insertion on Chr7 of the "HT" nuclear genome, consisting of two 7 kb chloroplast-derived fragments with two intact ndhH and rps15 genes, further validated by polymerase chain reaction (PCR). The well-resolved phylogeny suggests faster mitogenome evolution in J. sambac compared to other Oleaceae species and outlines the mitogenome evolutionary trajectories within Lamiales. All evidence supports that "DP" and "HT" evolved from "SP", with "HT" being the most recent derivative of "DP". CONCLUSION The comprehensive characterization of jasmine organelle genomes has added to our knowledge of the structural diversity and evolutionary trajectories behind varying jasmine traits, paving the way for in-depth exploration of mechanisms and targeted genetic research.
Collapse
Affiliation(s)
- Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, China.
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
| | - Aiting Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hansong Yan
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liqing Feng
- College of Life Science, Fujian Normal University, Fuzhou, China
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Shaoqing Lin
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Patrick Mason
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Linwei Zhou
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Xiuming Xu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Zhao
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Yongji Huang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China.
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
| |
Collapse
|
6
|
Pancaldi F, Gulisano A, Severing EI, van Kaauwen M, Finkers R, Kodde L, Trindade LM. The genome of Lupinus mutabilis: Evolution and genetics of an emerging bio-based crop. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39264984 DOI: 10.1111/tpj.17021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/02/2024] [Accepted: 08/23/2024] [Indexed: 09/14/2024]
Abstract
Lupinus mutabilis is an under-domesticated legume species from the Andean region of South America. It belongs to the New World lupins clade, which groups several lupin species displaying large genetic variation and adaptability to highly different environments. L. mutabilis is attracting interest as a potential multipurpose crop to diversify the European supply of plant proteins, increase agricultural biodiversity, and fulfill bio-based applications. This study reports the first high-quality L. mutabilis genome assembly, which is also the first sequenced assembly of a New World lupin species. Through comparative genomics and phylogenetics, the evolution of L. mutabilis within legumes and lupins is described, highlighting both genomic similarities and patterns specific to L. mutabilis, potentially linked to environmental adaptations. Furthermore, the assembly was used to study the genetics underlying important traits for the establishment of L. mutabilis as a novel crop, including protein and quinolizidine alkaloids contents in seeds, genomic patterns of classic resistance genes, and genomic properties of L. mutabilis mycorrhiza-related genes. These analyses pointed out copy number variation, differential genomic gene contexts, and gene family expansion through tandem duplications as likely important drivers of the genomic diversity observed for these traits between L. mutabilis and other lupins and legumes. Overall, the L. mutabilis genome assembly will be a valuable resource to conduct genetic research and enable genomic-based breeding approaches to turn L. mutabilis into a multipurpose legume crop.
Collapse
Affiliation(s)
- Francesco Pancaldi
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Agata Gulisano
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Edouard I Severing
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Martijn van Kaauwen
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
- Gennovation B.V, Agro Business Park 10, 6708PW, Wageningen, The Netherlands
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
- Gennovation B.V, Agro Business Park 10, 6708PW, Wageningen, The Netherlands
| | - Linda Kodde
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Luisa M Trindade
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| |
Collapse
|
7
|
Zhang L, Xu W, Zhao Y, Sui L, Song M, Liu Q. Identification and characterization of Jingmen tick virus from Rhipicephalus microplus in Hunan, China. Acta Trop 2024; 260:107378. [PMID: 39245157 DOI: 10.1016/j.actatropica.2024.107378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/10/2024]
Abstract
Jingmen tick virus (JMTV) is a tick-borne pathogen known to affect human beings, characterized by a segmented genome structure that defies the conventional understanding of the Flaviviridae family. In the present study, we employed metagenomic analysis to screen for tick-borne viruses in Hunan Province, China, and identified five JMTV variants with complete genomes from Rhipicephalus microplus ticks sampled from cattle. These viral strains exhibited the highest sequence similarity to JMTV isolates previously reported in Hubei Province, China. However, evidence of genomic reassortment was detected, particularly with the S2 segment showing greater similarity to the strains from Japan. Phylogenetic analysis demonstrated that JMTV strains cluster predominantly based on their geographic origin. In agreement with the homology data, the S1, S3, and S4 segments of the strains identified in this study grouped with those from Hubei Province, while the S2 segment displayed a distinct topological structure. Moreover, JMTV displayed limited replication in mammal-derived cells, but thrived in tick-derived cell lines. In addition to the commonly used R. microplus-derived BME/CTVM23 cells, we found that JMTV also proliferated robustly in both Ixodes scapularis-derived ISE6 and Ixodes ricinus-derived IRE/CTVM19 cells, offering new avenues for in vitro production of the virus. In summary, this study expands the known geographic distribution and genetic diversity of JMTV, providing valuable insights into its epidemiology and potential for in vitro cultivation.
Collapse
Affiliation(s)
- Li Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Wenbo Xu
- Department of Infectious Diseases and Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Yinghua Zhao
- Department of Infectious Diseases and Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Liyan Sui
- Department of Infectious Diseases and Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Mingxin Song
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.
| | - Quan Liu
- Department of Infectious Diseases and Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, The First Hospital of Jilin University, Changchun, China; Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China.
| |
Collapse
|
8
|
Lan T, Yang S, Li H, Zhang Y, Li R, Sahu SK, Deng W, Liu B, Shi M, Wang S, Du H, Huang X, Lu H, Liu S, Deng T, Chen J, Wang Q, Han L, Zhou Y, Li Q, Li D, Kristiansen K, Wan QH, Liu H, Fang SG. Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives. Proc Natl Acad Sci U S A 2024; 121:e2406343121. [PMID: 39186654 PMCID: PMC11388402 DOI: 10.1073/pnas.2406343121] [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: 03/28/2024] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
The extinction risk of the giant panda has been demoted from "endangered" to "vulnerable" on the International Union for Conservation of Nature Red List, but its habitat is more fragmented than ever before, resulting in 33 isolated giant panda populations according to the fourth national survey released by the Chinese government. Further comprehensive investigations of the genetic background and in-depth assessments of the conservation status of wild populations are still necessary and urgently needed. Here, we sequenced the genomes of 612 giant pandas with an average depth of ~26× and generated a high-resolution map of genomic variation with more than 20 million variants covering wild individuals from six mountain ranges and captive representatives in China. We identified distinct genetic clusters within the Minshan population by performing a fine-grained genetic structure. The estimation of inbreeding and genetic load associated with historical population dynamics suggested that future conservation efforts should pay special attention to the Qinling and Liangshan populations. Releasing captive individuals with a genetic background similar to the recipient population appears to be an advantageous genetic rescue strategy for recovering the wild giant panda populations, as this approach introduces fewer deleterious mutations into the wild population than mating with differentiated lineages. These findings emphasize the superiority of large-scale population genomics to provide precise guidelines for future conservation of the giant panda.
Collapse
Affiliation(s)
- Tianming Lan
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Shangchen Yang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haimeng Li
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin 150040, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
| | - Yi Zhang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- BGI Research, Beijing Genomics Institute, Wuhan 430074, China
| | - Wenwen Deng
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Boyang Liu
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Shiqing Wang
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Hanyu Du
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyu Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Haorong Lu
- China National GeneBank, BGI Research, Beijing Genomics Institute, Shenzhen 518120, China
| | - Shanlin Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Deng
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Jin Chen
- China National GeneBank, BGI Research, Beijing Genomics Institute, Shenzhen 518120, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Lei Han
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yajie Zhou
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Qiye Li
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- BGI Research, Beijing Genomics Institute, Wuhan 430074, China
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Karsten Kristiansen
- Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao 266555, China
| | - Qiu-Hong Wan
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin 150040, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Sheng-Guo Fang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
9
|
Sanabria-Velazquez AD, Enciso-Maldonado GA, Thiessen LD, Shew HD. The Origin of the Problem: Characterization of Paraguayan Septoria steviae, Causal Agent of Septoria Leaf Spot of Stevia, Based on Multilocus Sequence Analysis. PLANT DISEASE 2024:PDIS11232362RE. [PMID: 38764335 DOI: 10.1094/pdis-11-23-2362-re] [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
Septoria leaf spot is a significant disease affecting cultivated stevia, potentially reducing yields by > 50%. The disease is caused by Septoria steviae, first identified in 1978 in Japan as a new pathogen of stevia. Understanding the origin of S. steviae could clarify how it spread to new production areas. To investigate this, 12 isolates of Septoria sp. were obtained from stevia's native range in the Amambay forests and field plantings in Paraguay from 2018 to 2020. These isolates underwent colony morphology and molecular characterization of Actin, β-Tubulin, Calmodulin, ITS, LSU, RPB2, and TEF1α loci. GenBank sequences from S. steviae isolates collected in France, Japan, and the United States were included. Multilocus sequence phylogenetic analysis generated a maximum likelihood (ML) tree. The morphological characteristics of Paraguayan isolates were similar to those of previously reported S. steviae type cultures from Japan. The ML analysis showed that Paraguayan isolates formed a monophyletic group with S. steviae isolates from France, Japan, and the United States. During blotter tests, pycnidia and cirri of S. steviae were observed on multiple stevia seed surfaces from different sources. Further characterization confirmed viable pathogenic conidia of S. steviae. This observation suggests that S. steviae could be associated with stevia seed, possibly spreading from the center of origin to other countries. This research is the first to genetically characterize S. steviae from Paraguay and propose its potential spread mechanism from the center of origin to the rest of the world.
Collapse
Affiliation(s)
| | | | - Lindsey D Thiessen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Raleigh, NC 27603, U.S.A
| | - H David Shew
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, U.S.A
| |
Collapse
|
10
|
Myburgh AM, Barnes A, Henriques R, Daniels SR. Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki). Mol Phylogenet Evol 2024; 198:108132. [PMID: 38909874 DOI: 10.1016/j.ympev.2024.108132] [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: 03/22/2024] [Revised: 05/24/2024] [Accepted: 06/15/2024] [Indexed: 06/25/2024]
Abstract
In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.
Collapse
Affiliation(s)
- Angus Macgregor Myburgh
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Aaron Barnes
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa
| | - Romina Henriques
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, South Africa
| | - Savel R Daniels
- Department of Botany and Zoology, Private Bag X1, Stellenbosch University, 7602, South Africa.
| |
Collapse
|
11
|
Grecco S, Condon E, Bucafusco D, Bratanich AC, Panzera Y, Pérez R. Comparative genomics of canine parvovirus in South America: Diversification patterns in local populations. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105633. [PMID: 38969193 DOI: 10.1016/j.meegid.2024.105633] [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: 04/06/2024] [Revised: 06/05/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
Canine parvovirus (CPV) is a significant pathogen in domestic dogs worldwide, causing a severe and often fatal disease. CPV comprises three antigenic variants (2a, 2b, and 2c) distributed unevenly among several phylogenetic groups. The present study compared genetic variability and evolutionary patterns in South American CPV populations. We collected samples from puppies suspected of CPV infection in the neighboring Argentina and Uruguay. Antigenic variants were preliminarily characterized using PCR-RFLP and partial vp2 sequencing. Samples collected in Argentina during 2008-2018 were mainly of the 2c variant. In the Uruguayan strains (2012-2019), the 2a variant wholly replaced the 2c from 2014. Full-length coding genome and vp2 sequences were compared with global strains. The 2c and 2a strains fell by phylogenetic analysis into two phylogroups (Europe I and Asia I). The 2c strains from Argentina and Uruguay clustered in the Europe I group, with strains from America, Europe, Asia, and Oceania. Europe I is widely distributed in South America in the dog population and is also being detected in the wildlife population. The 2a strains from Uruguay formed the distinct Asia I group with strains from Asia, Africa, America, and Oceania. This Asia I group is increasing its distribution in South America and worldwide. Our research reveals high genetic variability in adjacent synchronic samples and different evolutionary patterns in South American CPV. We also highlight the importance of ancestral migrations and local diversification in the evolution of global CPV strains.
Collapse
Affiliation(s)
- Sofía Grecco
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Emma Condon
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Danilo Bucafusco
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Virología. Av. Chorroarín 280, C1427CWO, Ciudad Autónoma de Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), Buenos Aires, Argentina
| | - Ana Cristina Bratanich
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Virología. Av. Chorroarín 280, C1427CWO, Ciudad Autónoma de Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), Buenos Aires, Argentina
| | - Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| |
Collapse
|
12
|
Cabrera-Soregui M, Torres-Lozano K, Garcia-Candela E, Mesias-Valle F, Martinez-Rojas R, Cruz-Neyra L, Mondragón-Martínez A, Ebert MB, da Silva RJ, Cala-Delgado DL. Molecular identification of Mymarothecium viatorum and Anacanthorus penilabiatus in extensive native fish farming systems of the Peruvian Amazon. Vet Parasitol Reg Stud Reports 2024; 54:101085. [PMID: 39237229 DOI: 10.1016/j.vprsr.2024.101085] [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: 05/06/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 09/07/2024]
Abstract
Piaractus brachypomus (Pacú) is the main native fish species cultivated in Peru and holds great potential for growth in aquaculture from the Peruvian Amazon. Between October 2021 and January 2022 in two fish producing farms in the Amazon region of San Martín in Peru, P. brachypomus individuals were examined for parasite evaluation. A total of 6366 monogeneans were isolated from the gills of 30 fish, revealing a prevalence of 100%, with an abundance and mean intensity of 212 parasites per fish. Monogeneans were morphologically identified as Mymarothecium viatorum and Anacanthorus penilabiatus. The genetic divergence in the 28S rDNA gene found among A. penilabiatus sequences was 0.1% and among Anacanthorus spp. it ranged from 0.9% to 7.5%. The genetic divergence found among the M. viatorum sequences was 0.3%. These finding represents the first molecular data of M. viatorum and A. penilabiatus in Peru using the 28S rDNA gene of these monogeneans. The new sequences obtained will contribute to future studies on the phylogenetic relationships among dactylogyrids. However, further research with a broader range of host-parasite samples and additional genetic markers is needed to clarify these relationships and provide stronger support for the phylogenetic positions.
Collapse
Affiliation(s)
| | - Karel Torres-Lozano
- Escuela Profesional de Medicina Veterinaria, Universidad Nacional de San Martín, Tarapoto, Peru
| | - Enrique Garcia-Candela
- CITEacuícola pesquero Ahuashiyacu, Instituto Tecnológico de la Producción, San Martín, Peru; Escuela Profesional de Medicina Veterinaria, Universidad Nacional de San Martín, Tarapoto, Peru
| | - Fernando Mesias-Valle
- CITEacuícola pesquero Ahuashiyacu, Instituto Tecnológico de la Producción, San Martín, Peru
| | - Rosa Martinez-Rojas
- Laboratory of Parasitology in Wildlife and Zoonoses, Faculty of Biological Sciences, National University of San Marcos, Lima, Peru; Laboratory of Biology and Molecular Genetics, Faculty of Biological Sciences, Universidad Ricardo Palma, Santiago de Surco, Lima, Peru
| | - Lidia Cruz-Neyra
- Laboratory of Biology and Molecular Genetics, Faculty of Biological Sciences, Universidad Ricardo Palma, Santiago de Surco, Lima, Peru
| | - Aarón Mondragón-Martínez
- Laboratory of Parasitology in Wildlife and Zoonoses, Faculty of Biological Sciences, National University of San Marcos, Lima, Peru; Laboratory of Biology and Molecular Genetics, Faculty of Biological Sciences, Universidad Ricardo Palma, Santiago de Surco, Lima, Peru
| | - Mariana Bertholdi Ebert
- Departamento de Biodiversidade e Bioestatística, Setor de Parasitologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Paulo, Brazil
| | - Reinaldo José da Silva
- Departamento de Biodiversidade e Bioestatística, Setor de Parasitologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Paulo, Brazil
| | - Daniel Leonardo Cala-Delgado
- Grupo de Investigación en Ciencias Animales-GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, Bucaramanga 680002, Colombia.
| |
Collapse
|
13
|
Ebert MB, Hernández-Mena DI, de León GPP, da Silva RJ. A New Species of Creptotrematina (Trematoda: Allocreadiidae) from the Red Minor Tetra, Hyphessobrycon eques (Steindachner, 1882) (Characidae) from Brazil, with Comments on the Genetic Divergence of C. Aguirrepequenoi Jiménez-Guzmán, 1973 across a Wide Geographical Range in Middle America. Acta Parasitol 2024:10.1007/s11686-024-00877-0. [PMID: 39190278 DOI: 10.1007/s11686-024-00877-0] [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: 04/09/2024] [Accepted: 07/30/2024] [Indexed: 08/28/2024]
Abstract
BACKGROUND Allocreadiids are relatively small digeneans that appear to be restricted to freshwater systems distributed across the world. Allocreadiids are highly diverse in the Americas, particularly in the Neotropical biogeographical region. Their taxonomic history has been rather controversial, with several taxonomic reassessments and the description of new genera and species. METHODS We sampled Creptotrematina specimens from a characid collected in the Pardo River, Paranapanema River basin in Brazil, and specimens of C. aguirrepequenoi, from Astyanax spp. in several localities between northern Mexico and Costa Rica. The specimens were studied through integrative approaches using morphological and molecular analyses of the 28S rDNA gene and two different regions of the COI mtDNA gene. RESULTS We describe a new species of Creptotrematina which is differentiated from other congeners by the overall body size, but in particular by the size and position of the cirrus-sac, distribution of the vitelline follicles, and extension of uterine loops in the posterior end of body. Phylogenetic analyses of the 28S rDNA and COI mtDNA genes placed the new species in a monophyletic clade together with all other sequenced species of Creptotrematina, and as a sister species of C. batalhensis. Genetic divergences between the new species and other Creptotrematina spp. varied from 1.1 to 1.2% for the 28S rDNA and 12.4-14.3% for the COI mtDNA. Phylogenetic analysis based on COI mtDNA showed the isolates of C. aguirrepequenoi grouped in four monophyletic clades representing populations geographically separated along a wide geographical range spanning between northern Mexico and Costa Rica, with an estimated genetic divergence between 3.9% and 8.9%. CONCLUSIONS Our findings based on integrative analyses recognize Creptotrematina saltograndensis n. sp. from a characid collected in the Pardo River, Paranapanema River basin in Brazil and provide validation of the wide geographical distribution of C. aguirrepequenoi across Middle-America parasitizing Astyanax spp.; the genetic divergence of the species through the analysis of two regions of COI mtDNA points towards considering it represent a species complex, although we refrain at the moment on describing a new species, awaiting for further verification using other molecular markers, and obtaining fresh material for a more detailed taxonomic analyses. This study increases the known diversity of allocreadiids and contributes to the understanding of evolutionary relationships, host-parasite relationships, and biogeographic history of the group.
Collapse
Affiliation(s)
- Mariana Bertholdi Ebert
- Institute of Biosciences, Section of Parasitology, São Paulo State University (UNESP), Botucatu, São Paulo state, Brazil.
| | | | - Gerardo Pérez-Ponce de León
- Escuela Nacional de Estudios Superiores, Unidad Mérida, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Reinaldo José da Silva
- Institute of Biosciences, Section of Parasitology, São Paulo State University (UNESP), Botucatu, São Paulo state, Brazil
| |
Collapse
|
14
|
Zhang XJ, Huang XH, Landis JB, Fu QS, Chen JT, Luo PR, Li LJ, Lu HY, Sun H, Deng T. Shifts in reproductive strategies in the evolutionary trajectory of plant lineages. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2597-9. [PMID: 39190128 DOI: 10.1007/s11427-024-2597-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 04/16/2024] [Indexed: 08/28/2024]
Abstract
Understanding the maintenance and shift in reproductive strategies is a fundamental question in evolutionary research. Although many efforts have been made to compare different reproductive strategies, the association between reproductive strategies and lineage divergence is largely unknown. To explore the impact of different reproductive strategies on lineage divergence, we investigated the evolution of clonality in Saxifraga sect. Irregulares+Heterisia. By integrating several lines of evidence, we found that the loss of clonality in Irregulares+Heterisia was associated with a progressive increase in diversification rate and intraspecific morphological diversity but with a reduction in species distribution range. Our findings provide insights into the ecological and evolutionary effects of different reproductive strategies, suggesting the necessity of integrating clonality into ecological and evolutional research.
Collapse
Affiliation(s)
- Xin-Jian Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-Han Huang
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium, Cornell University, New York, 14850, USA
- BTI Computational Biology Center, Boyce Thompson Institute, New York, 14853, USA
| | - Quan-Sheng Fu
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-Tong Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Peng-Rui Luo
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Juan Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Heng-Yi Lu
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Hang Sun
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Tao Deng
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| |
Collapse
|
15
|
Mhlanga TA, Chitanga S, Matthee S, Malatji MP, Mukaratirwa S. Prevalence and genetic diversity of Bartonella spp. in wild small mammals from South Africa. Appl Environ Microbiol 2024; 90:e0084224. [PMID: 39058027 PMCID: PMC11338311 DOI: 10.1128/aem.00842-24] [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: 04/30/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Bartonella spp. are intracellular bacteria associated with several re-emerging human diseases. Small mammals play a significant role in the maintenance and spread of Bartonella spp. Despite the high small mammal biodiversity in South Africa, there is limited epidemiological information regarding Bartonella spp. in these mammals. The main aim of this study was to determine the prevalence and genetic diversity of Bartonella spp. from wild small mammals from 15 localities in 8 provinces of South Africa. Small mammals (n = 183) were trapped in the Eastern Cape, Free State, Gauteng, Limpopo, Mpumalanga, Northern Cape, North West, and Western Cape provinces of South Africa between 2010 and 2018. Heart, kidney, liver, lung, and spleen were harvested for Bartonella DNA screening, and prevalence was determined based on the PCR amplification of partial fragments of the 16S-23S rRNA intergenic spacer (ITS) region, gltA, and rpoB genes. Bartonella DNA was detected in Aethomys chrysophilus, Aethomys ineptus, Gerbillurus spp., Lemniscomys rosalia, Mastomys coucha, Micaelamys namaquensis, Rhabdomys pumilio, and Thallomys paedulcus. An overall prevalence of 16.9% (31/183, 95% CI: 12.2%-23%) was observed. Bartonella elizabethae, Bartonella grahamii, and Bartonella tribocorum were the zoonotic species identified, while the remaining sequences were aligned to uncultured Bartonella spp. with unknown zoonotic potential. Phylogenetic analyses confirmed five distinct Bartonella lineages (I-V), with lineage IV displaying strong M. coucha host specificity. Our results confirm that South African wild small mammals are natural reservoirs of a diverse assemblage of Bartonella spp., including some zoonotic species with high genetic diversity, although prevalence was relatively low.IMPORTANCESmall mammals play a significant role in the maintenance and spread of zoonotic pathogens such as Bartonella spp. Despite the high small mammal biodiversity in southern Africa including South Africa, there is limited epidemiological information regarding Bartonella spp. in these mammals across the country. Results from our study showed the liver and spleen had the highest positive cases for Bartonella spp. DNA among the tested organs. Bartonella elizabethae, B. grahamii, and B. tribocorum were the three zoonotic species identified and five distinct Bartonella lineages (I-V) were confirmed through phylogenetic analyses. To the best of our knowledge, this study presents the first extensive nuclear diversity investigation of Bartonella spp. in South African small mammals in South Africa.
Collapse
Affiliation(s)
- Tapiwanashe Annamary Mhlanga
- School of Life
Sciences, College of Agriculture, Engineering and Sciences, University
of KwaZulu-Natal, Westville Campus,
Durban, South Africa
| | - Simbarashe Chitanga
- Department of
Preclinical Studies, School of Veterinary Medicine, University of
Namibia, Windhoek,
Namibia
- Department of
Biomedical Sciences, School of Health Sciences, University of
Zambia, Lusaka,
Zambia
| | - Sonja Matthee
- Department of
Conservation Ecology and Entomology, Stellenbosch
University, Stellenbosch,
South Africa
| | - Mokgadi Pulane Malatji
- School of Life
Sciences, College of Agriculture, Engineering and Sciences, University
of KwaZulu-Natal, Westville Campus,
Durban, South Africa
| | - Samson Mukaratirwa
- School of Life
Sciences, College of Agriculture, Engineering and Sciences, University
of KwaZulu-Natal, Westville Campus,
Durban, South Africa
- One Health Centre for
Zoonoses and Tropical Veterinary Medicine, Ross University School of
Veterinary Medicine,
Basseterre, West Indies, Saint Kitts
and Nevis
| |
Collapse
|
16
|
Zhao Y, Kipkoech A, Li ZP, Xu L, Yang JB. Deciphering the Plastome and Molecular Identities of Six Medicinal "Doukou" Species. Int J Mol Sci 2024; 25:9005. [PMID: 39201691 PMCID: PMC11354342 DOI: 10.3390/ijms25169005] [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: 06/04/2024] [Revised: 08/01/2024] [Accepted: 08/16/2024] [Indexed: 09/03/2024] Open
Abstract
The genus Amomum includes over 111 species, 6 of which are widely utilized as medicinal plants and have already undergone taxonomic revision. Due to their morphological similarities, the presence of counterfeit and substandard products remains a challenge. Accurate plant identification is, therefore, essential to address these issues. This study utilized 11 newly sequenced samples and extensive NCBI data to perform molecular identification of the six medicinal "Doukou" species. The plastomes of these species exhibited a typical quadripartite structure with a conserved gene content. However, independent variation shifts of the SC/IR boundaries existed between and within species. The comprehensive set of genetic sequences, including ITS, ITS1, ITS2, complete plastomes, matK, rbcL, psbA-trnH, and ycf1, showed varying discrimination of the six "Doukou" species based on both distance and phylogenetic tree methods. Among these, the ITS, ITS1, and complete plastome sequences demonstrated the highest identification success rate (3/6), followed by ycf1 (2/6), and then ITS2, matK, and psbA-trnH (1/6). In contrast, rbcL failed to identify any species. This research established a basis for a reliable molecular identification method for medicinal "Doukou" plants to protect wild plant resources, promote the sustainable use of medicinal plants, and restrict the exploitation of these resources.
Collapse
Affiliation(s)
- Ying Zhao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (A.K.); (Z.-P.L.)
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Research Center of Perennial Rice Engineering and Technology, School of Agriculture, Yunnan University, Kunming 650201, China;
| | - Amos Kipkoech
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (A.K.); (Z.-P.L.)
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhi-Peng Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (A.K.); (Z.-P.L.)
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650091, China
| | - Ling Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources, Research Center of Perennial Rice Engineering and Technology, School of Agriculture, Yunnan University, Kunming 650201, China;
| | - Jun-Bo Yang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
| |
Collapse
|
17
|
Qi Z, Shi J, Yu Y, Yin G, Zhou X, Yu Y. Paternal Mitochondrial DNA Leakage in Natural Populations of Large-Scale Loach, Paramisgurnus dabryanus. BIOLOGY 2024; 13:604. [PMID: 39194542 DOI: 10.3390/biology13080604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/02/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024]
Abstract
Animal mitochondrial DNA is usually considered to comply with strict maternal inheritance, and only one mitochondrial DNA haplotype exists in an individual. However, mitochondrial heteroplasmy, the occurrence of more than one mitochondrial haplotype, has recently been reported in some animals, such as mice, mussels, and birds. This study conducted extensive field surveys to obtain representative samples to investigate the existence of paternal inheritance of mitochondrial DNA (mtDNA) in natural fish populations. Evidence of paternal mitochondrial DNA leakage of P. dabryanus was discovered using high-throughput sequencing and bioinformatics methods. Two distinct mitochondrial haplotypes (16,569 bp for haplotype I and 16,646 bp for haplotype II) were observed, differing by 18.83% in nucleotide sequence. Phylogenetic analysis suggests divergence between these haplotypes and potential interspecific hybridization with M. anguillicaudatus, leading to paternal leakage. In natural populations of P. dabryanus along the Yangtze River, both haplotypes are present, with Type I being dominant (75% copy number). Expression analysis shows that Type I has higher expression levels of ND3 and ND6 genes compared to Type II, suggesting Type I's primary role. This discovery of a species with two mitochondrial types provides a model for studying paternal leakage heterogeneity and insights into mitochondrial genome evolution and inheritance.
Collapse
Affiliation(s)
- Zixin Qi
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaoxu Shi
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Agronomy and Life Science Department, Zhaotong University, Zhaotong 657000, China
| | - Yue Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangmei Yin
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyun Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongyao Yu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| |
Collapse
|
18
|
Barido-Sottani J, Schwery O, Warnock RCM, Zhang C, Wright AM. Practical guidelines for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC). OPEN RESEARCH EUROPE 2024; 3:204. [PMID: 38481771 PMCID: PMC10933576 DOI: 10.12688/openreseurope.16679.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 07/30/2024] [Indexed: 06/06/2024]
Abstract
Phylogenetic estimation is, and has always been, a complex endeavor. Estimating a phylogenetic tree involves evaluating many possible solutions and possible evolutionary histories that could explain a set of observed data, typically by using a model of evolution. Values for all model parameters need to be evaluated as well. Modern statistical methods involve not just the estimation of a tree, but also solutions to more complex models involving fossil record information and other data sources. Markov chain Monte Carlo (MCMC) is a leading method for approximating the posterior distribution of parameters in a mathematical model. It is deployed in all Bayesian phylogenetic tree estimation software. While many researchers use MCMC in phylogenetic analyses, interpreting results and diagnosing problems with MCMC remain vexing issues to many biologists. In this manuscript, we will offer an overview of how MCMC is used in Bayesian phylogenetic inference, with a particular emphasis on complex hierarchical models, such as the fossilized birth-death (FBD) model. We will discuss strategies to diagnose common MCMC problems and troubleshoot difficult analyses, in particular convergence issues. We will show how the study design, the choice of models and priors, but also technical features of the inference tools themselves can all be adjusted to obtain the best results. Finally, we will also discuss the unique challenges created by the incorporation of fossil information in phylogenetic inference, and present tips to address them.
Collapse
Affiliation(s)
- Joëlle Barido-Sottani
- Institut de Biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, Île-de-France, 75005, France
| | - Orlando Schwery
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana, 70402, USA
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, 24061, USA
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA
| | - Rachel C. M. Warnock
- GeoZentrum Nordbayern, Department of Geography and Geosciences, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Bavaria, 91054, Germany
| | - Chi Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - April Marie Wright
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, Louisiana, 70402, USA
| |
Collapse
|
19
|
Lian L, Peng HW, Erst AS, Ortiz RDC, Jabbour F, Chen ZD, Wang W. Bayesian tip-dated phylogeny and biogeography of Cissampelideae (Menispermaceae): Mitigating the effects of homoplastic morphological characters. Cladistics 2024; 40:391-410. [PMID: 38469932 DOI: 10.1111/cla.12573] [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: 11/16/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
The integration of morphological and molecular data is essential to understand the affinities of fossil taxa and spatio-temporal evolutionary processes of organisms. However, homoplastic morphological characters can mislead the placement of fossil taxa and impact downstream analyses. Here, we provide an example of how to mitigate effectively the effect of morphological homoplasy on the placement of fossil taxa and biogeographic inferences of Cissampelideae. We assembled three data types, morphological data only, morphological data with a molecular scaffold and combined morphological and molecular data. By removing high-level homoplastic morphological data or reweighting the morphological characters, we conducted 15 parsimony, 12 undated Bayesian and four dated Bayesian analyses. Our results show that the 14 selected Cissampelideae fossil taxa are placed poorly when based only on morphological data, but the addition of molecular scaffold and combination of morphological and molecular data greatly improve the resolution of fossil nodes. We raise the monotypic Stephania subg. Botryodiscia to generic status and discover that three fossils previously assigned to Stephania should be members of Diploclisia. The Bayesian tip-dated tree recovered by removing homoplastic morphological characters with a Rescaled Consistency Index <0.25 has the highest stratigraphic fit and consequently generates more reasonable biogeographic reconstruction for Cissampelideae. Cissampelideae began to diversify in Asia in the latest Cretaceous and subsequently dispersed to South America around the Cretaceous-Palaeogene boundary. Two dispersal events from Asia to Africa occurred in the Early Eocene and the Late Eocene-Late Oligocene, respectively. These findings provide guidelines and practical methods for mitigating the effects of homoplastic morphological characters on fossil placements and Bayesian tip-dating, as well as insights into the past tropical floristic exchanges among different continents.
Collapse
Affiliation(s)
- Lian Lian
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Huan-Wen Peng
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Andrey S Erst
- Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Zolotodolinskaya str. 101, Novosibirsk, 630090, Russia
| | - Rosa Del C Ortiz
- Missouri Botanical Garden, 4344 Shaw Blvd, St Louis, Missouri, 63110, USA
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, Université des Antilles, EPHE, 57 rue Cuvier, CP39, Paris, 75005, France
| | - Zhi-Duan Chen
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Wang
- State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
20
|
Zhou SB, Zhao ZY, Guan P, Qu B. New geographical records and molecular investigation of the ciliate Spirostomum. Protist 2024; 175:126047. [PMID: 38964211 DOI: 10.1016/j.protis.2024.126047] [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: 01/14/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 07/06/2024]
Abstract
Spirostomum is a genus of large ciliates, and its species are distributed worldwide. However, there has been limited research conducted on their geographical distribution and genomics. We obtained nine samples of ciliates from eight regions in Liaoning Province, China, and conducted a study on their geographical distribution and characteristics. Morphological and second-generation high-throughput sequencing methods were applied to identify the species, and a phylogenetic tree was established to gain a deeper understanding of the geographical distribution and evolutionary relationships of Spirostomum in Northeast China. The results identified Spirostomum yagiui and Spirostomum subtilis as a newly recorded species in Northeast China region. There are now five species of Spirostomum that have been recorded in China, and new details on the genomic characteristics of Spirostomum yagiui were provided. In addition, this study also identified the main branches of Spirostomum teres and Spirostomum minus in northern China, and provided a theoretical basis for the existence of hidden species. Spirostomum yagiui is the first species in the family Spirostomidae to have undergone mitochondrial genome sequencing.
Collapse
Affiliation(s)
- Sheng-Bo Zhou
- Key Laboratory of Global Changes and Biological Invasions, Bioscience and Technology College, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhi-Yu Zhao
- Key Laboratory of Global Changes and Biological Invasions, Bioscience and Technology College, Shenyang Agricultural University, Shenyang 110866, China
| | - Ping Guan
- Key Laboratory of Global Changes and Biological Invasions, Bioscience and Technology College, Shenyang Agricultural University, Shenyang 110866, China.
| | - Bo Qu
- Key Laboratory of Global Changes and Biological Invasions, Bioscience and Technology College, Shenyang Agricultural University, Shenyang 110866, China.
| |
Collapse
|
21
|
Olguin-Perglione C, Politzki R, Alvarez I, Ruiz V. First report of Equine Parvovirus-Hepatitis (EqPV-H) in Argentina. Vet J 2024; 306:106204. [PMID: 39047972 DOI: 10.1016/j.tvjl.2024.106204] [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: 04/26/2024] [Revised: 07/04/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
The novel Equine Parvovirus-Hepatitis (EqPV-H) was first identified in the serum and liver of a horse that died of equine serum hepatitis, also known as Theiler's disease. Several reports in recent years strongly suggest that EqPV-H is the etiologic agent of Theiler's disease. Brazil is the only South American country where infection with this virus has been reported. This study investigated the presence of EqPV-H DNA in horse serum pools (n=51), commercial horse serum batches (n=5) and individual serum samples from donor horses (n=175) from Argentina. All serum samples were analyzed by quantitative polymerase chain reaction (qPCR) and samples with positive or indeterminate results were further analyzed by NS1 nested-PCR for phylogenetic studies. None of the serum pools was positive by qPCR but 9/51 pools were indeterminate (one or both test sample's Ct values were higher than the limit of detection). The NS1 nested-PCR detected the EqPV-H DNA in 8 of these indeterminate samples (15.7 % of serum pools). Three of the commercial horse serum batches (60 %) contained EqPV-H DNA, detected either by qPCR and/or nested-PCR. From the 175 individual horse serum samples, three (1.71 %) were positive for EqPV-H by both techniques. The genetic analysis of the 12 partial NS1 sequences obtained showed that the local isolates were similar to EqPV-H sequences from Germany and China. This study provides the first evidence of the presence of EqPV-H in horses and in horse sera commercially available in Argentina and emphasizes the importance of controlling the biosecurity of commercial equine sera as well as any other blood-derived biological products of equine origin. DATA AVAILABILITY: Viral sequences generated in this study were uploaded to the NCBI nucleotide database and are available with the accession numbers PP408676-PP408687.
Collapse
Affiliation(s)
- C Olguin-Perglione
- Laboratorio de Virus Adventicios, Instituto de Virología e Innovaciones Tecnológicas (IVIT), INTA-CONICET, Nicolás Repetto y De los Reseros (s/n), Hurlingham, Buenos Aires CP1686, Argentina
| | - R Politzki
- Laboratorio de Virus Adventicios, Instituto de Virología e Innovaciones Tecnológicas (IVIT), INTA-CONICET, Nicolás Repetto y De los Reseros (s/n), Hurlingham, Buenos Aires CP1686, Argentina
| | - I Alvarez
- Laboratorio de Virus Adventicios, Instituto de Virología e Innovaciones Tecnológicas (IVIT), INTA-CONICET, Nicolás Repetto y De los Reseros (s/n), Hurlingham, Buenos Aires CP1686, Argentina
| | - V Ruiz
- Laboratorio de Virus Adventicios, Instituto de Virología e Innovaciones Tecnológicas (IVIT), INTA-CONICET, Nicolás Repetto y De los Reseros (s/n), Hurlingham, Buenos Aires CP1686, Argentina.
| |
Collapse
|
22
|
Catanese G, Vázquez‐Luis M, Giacobbe S, García‐March JR, Zotou M, Patricia P, Papadakis O, Tena‐Medialdea J, Katsanevakis S, Grau A. Internal transcribed spacer as effective molecular marker for the detection of natural hybridization between the bivalves Pinna nobilis and Pinna rudis. Ecol Evol 2024; 14:e70227. [PMID: 39193167 PMCID: PMC11347391 DOI: 10.1002/ece3.70227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/01/2024] [Accepted: 08/12/2024] [Indexed: 08/29/2024] Open
Abstract
The Pinna nobilis, a Mediterranean mollusc, has suffered population declines due to a massive mortality event associated with various factors including the parasite Haplosporidium pinnae. Some populations show resilience, possibly due to local environmental conditions. In this study, a molecular multiplex PCR method was developed using species-specific primers targeting Internal Transcribed Spacer (ITS) regions of P. nobilis and P. rudis, allowing accurate species identification and hybrid detection. Samples from Mediterranean areas were analysed, including putative hybrids and individuals from five other bivalve species. DNA was isolated, ITS regions were amplified and sequenced, and phylogenetic analyses confirmed species differentiation and primer specificity. The multiplex-PCR successfully identified P. nobilis, P. rudis, and their hybrids based on distinct amplicon patterns. This study highlights the value of molecular tools in species conservation, especially for monitoring and managing hybridization, supporting effective biodiversity conservation strategies.
Collapse
Affiliation(s)
- Gaetano Catanese
- IRFAP LIMIA (Laboratorio de Investigaciones Marinas y Acuicultura) – Govern de les Illes BalearsPort d'AndratxBalearic IslandsSpain
| | - Maite Vázquez‐Luis
- IEO‐CSIC, Centro Oceanográfico de Baleares Instituto Español de OceanografíaPalma de MallorcaSpain
| | - Salvatore Giacobbe
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, ChiBioFarAmUniversità Degli Studi di MessinaMessinaItaly
| | - José Rafael García‐March
- Instituto de Investigación en Medio Ambiente y Ciencia Marina (IMEDMAR‐UCV)Universidad Católica de ValenciaCalpeSpain
| | - Maria Zotou
- Department of Marine SciencesUniversity of the AegeanMytileneGreece
| | - Prado Patricia
- Instituto de Investigación en Medio Ambiente y Ciencia Marina (IMEDMAR‐UCV)Universidad Católica de ValenciaCalpeSpain
- Institut d'Estudis Professionals Aqüícoles i Ambientals de Catalunya (IEPAAC)TarragonaSpain
- IRTA‐La RàpitaTarragonaSpain
| | | | - José Tena‐Medialdea
- Instituto de Investigación en Medio Ambiente y Ciencia Marina (IMEDMAR‐UCV)Universidad Católica de ValenciaCalpeSpain
| | | | - Amalia Grau
- IRFAP LIMIA (Laboratorio de Investigaciones Marinas y Acuicultura) – Govern de les Illes BalearsPort d'AndratxBalearic IslandsSpain
| |
Collapse
|
23
|
Cantillo-Barraza O, Jaimes-Dueñez J, Marcet PL, Triana-Chavez O, Gómez-Palacio A. Multilocus genetic analysis of Trypanosoma cruzi supports non-domestic intrusion into domestic transmission in an endemic region of Colombia. Parasite Epidemiol Control 2024; 26:e00364. [PMID: 39021811 PMCID: PMC11253143 DOI: 10.1016/j.parepi.2024.e00364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/27/2024] [Accepted: 06/17/2024] [Indexed: 07/20/2024] Open
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, is primarily transmitted to humans by hematophagous bugs of the Triatominae subfamily. In the Colombian Caribbean region, particularly on Margarita Island, T. cruzi transmission is highly endemic and associated with vectors such as Triatoma maculata and Rhodnius pallescens. Additionally, T. cruzi-infected Didelphis marsupialis are commonly found in close proximity to human dwellings. Given the complex transmission dynamics involving various domestic and non-domestic hosts, this study aimed to analyze 145 T. cruzi clones from twelve strains isolated from T. maculata, R. pallescens, and D. marsupialis using spliced leader intergenic region (SL-IR) sequences and nine polymorphic microsatellite loci. The results indicate the presence of a single polymorphic T. cruzi population, suggesting sustained local transmission dynamics between triatomines adapted to A. butyracea forests and peridomestic areas inhabited by synanthropic mammal reservoir such as D. marsupialis. Notably, this population appears to lack substructure, highlighting the importance of adopting an alternative eco-health approach to complement traditional chemical vector control methods for more effective and sustainable interruption of transmission.
Collapse
Affiliation(s)
- Omar Cantillo-Barraza
- Grupo Biología y Control de Enfermedades Infecciosas (BCEI), Universidad de Antioquia, Medellín, Colombia
| | - Jeiczon Jaimes-Dueñez
- Grupo de Investigación en Ciencias Animales (GRICA), Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia (UCC), Bucaramanga, Colombia
| | - Paula L. Marcet
- Centers for Disease Control and Prevention (CDC), Division of Parasitic Diseases and Malaria, Entomology Branch, Atlanta, GA, USA
| | - Omar Triana-Chavez
- Grupo Biología y Control de Enfermedades Infecciosas (BCEI), Universidad de Antioquia, Medellín, Colombia
| | - Andrés Gómez-Palacio
- Laboratorio de Investigación en Genética Evolutiva (LIGE), Universidad Pedagógica y Tecnológica de Colombia, Tunja, Boyacá, Colombia
| |
Collapse
|
24
|
Umbrello LS, Newton H, Baker AM, Travouillon KJ, Westerman M. Vicariant speciation resulting from biogeographic barriers in the Australian tropics: The case of the red-cheeked dunnart ( Sminthopsis virginiae). Ecol Evol 2024; 14:e70215. [PMID: 39206453 PMCID: PMC11349609 DOI: 10.1002/ece3.70215] [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: 06/16/2024] [Revised: 08/02/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
Global biodiversity loss continues unabated, and in Australia, the rate of recent mammal extinctions is among the worst in the world. Meanwhile, the diversity among and within many endemic mammal species remains undescribed. This information is crucial to delineate species boundaries and thus inform decision-making for conservation. Sminthopsis virginiae (the red-cheeked dunnart) is a small, dasyurid marsupial found in four disjunct populations around the northern coast of Australia and New Guinea. There are three currently recognized subspecies, each occupying a distinct geographic location. Sminthopsis v. virginiae occurs in Queensland, S. v. rufigenis is distributed across New Guinea and the Aru Islands, and S. v. nitela has populations in the Top End of the Northern Territory and the Kimberley region of Western Australia. Previous molecular work has suggested the current subspecies definitions are not aligned with DNA sequence data, though the sampling was limited. We undertook a comprehensive genetic and morphological review of S. virginiae to clarify relationships within the species. This included mitochondrial (CR, 12S, and cytb) and nuclear (omega-globin, IRBP, and bfib7) loci, and morphometric analysis of skulls and whole wet-preserved specimens held in museums. Maximum Likelihood and Bayesian phylogenetic analyses resolved samples into two distinct clades, demarcated by the Gulf of Carpentaria in Australia's north. Sminthopsis. v. nitela was consistently separated from S. v. virginiae and S. v. rufigenis, based on the overall body and skull size and craniodental features, while S. v. virginiae and S. v. rufigenis were more difficult to distinguish from each other. Thus, we redescribed S. virginiae, recognizing two species, S. nitela (raised from subspecies) and S. virginiae (now comprising the subspecies S. v. virginiae and S. v. rufigenis). This study highlights the importance of recognizing cryptic mammal fauna to help address the gap in our knowledge about diagnosing diversity during a time of conservation crisis.
Collapse
Affiliation(s)
- Linette S. Umbrello
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQueenslandAustralia
- Collections and ResearchWestern Australian MuseumWelshpoolWestern AustraliaAustralia
| | - Hayley Newton
- Collections and ResearchWestern Australian MuseumWelshpoolWestern AustraliaAustralia
- School of Environmental and Conservation SciencesMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Andrew M. Baker
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQueenslandAustralia
- Biodiversity and Geosciences ProgramQueensland MuseumSouth BrisbaneQueenslandAustralia
| | - Kenny J. Travouillon
- Collections and ResearchWestern Australian MuseumWelshpoolWestern AustraliaAustralia
| | - Michael Westerman
- Department of Ecology and GeneticsLa Trobe UniversityBundooraVictoriaAustralia
| |
Collapse
|
25
|
Qu J, Lu X, Teng X, Xing Z, Wang S, Feng C, Wang X, Wang L. Mitochondrial Genomes of Streptopelia decaocto: Insights into Columbidae Phylogeny. Animals (Basel) 2024; 14:2220. [PMID: 39123752 PMCID: PMC11310995 DOI: 10.3390/ani14152220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/18/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
In this research, the mitochondrial genome of the Streptopelia decaocto was sequenced and examined for the first time to enhance the comprehension of the phylogenetic relationships within the Columbidae. The complete mitochondrial genome of Streptopelia decaocto (17,160 bp) was structurally similar to the recognized members of the Columbidae family, but with minor differences in gene size and arrangement. The structural AT content was 54.12%. Additionally, 150 mitochondrial datasets, representing valid species, were amassed in this investigation. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees and evolutionary time relationships of species were reconstructed based on cytb gene sequences. The findings from the phylogenetic evaluations suggest that the S. decaocto was classified under the Columbinae subfamily, diverging from the Miocene approximately 8.1 million years ago, indicating intricate evolutionary connections with its close relatives, implying a history of species divergence and geographic isolation. The diversification of the Columbidae commenced during the Late Oligocene and extended into the Miocene. This exploration offers crucial molecular data for the S. decaocto, facilitating the systematic taxonomic examination of the Columbidae and Columbiformes, and establishing a scientific foundation for species preservation and genetic resource management.
Collapse
Affiliation(s)
- Jiangyong Qu
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Xiaofei Lu
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Xindong Teng
- Qingdao International Travel Healthcare Center, Qingdao 266071, China;
| | - Zhikai Xing
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Shuang Wang
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Chunyu Feng
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Xumin Wang
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| | - Lijun Wang
- College of Life Science, Yantai University, Yantai 264005, China; (J.Q.); (X.L.); (Z.X.); (S.W.); (C.F.)
| |
Collapse
|
26
|
Musser G, Clarke JA. A new Paleogene fossil and a new dataset for waterfowl (Aves: Anseriformes) clarify phylogeny, ecological evolution, and avian evolution at the K-Pg Boundary. PLoS One 2024; 19:e0278737. [PMID: 39078833 PMCID: PMC11288464 DOI: 10.1371/journal.pone.0278737] [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: 11/21/2022] [Accepted: 05/05/2024] [Indexed: 08/02/2024] Open
Abstract
Despite making up one of the most ecologically diverse groups of living birds, comprising soaring, diving and giant flightless taxa, the evolutionary relationships and ecological evolution of Anseriformes (waterfowl) remain unresolved. Although Anseriformes have a comparatively rich, global Cretaceous and Paleogene fossil record, morphological datasets for this group that include extinct taxa report conflicting relationships for all known extinct taxa. Correct placement of extinct taxa is necessary to understand whether ancestral anseriform feeding ecology was more terrestrial or one of a set of diverse aquatic ecologies and to better understand avian evolution around the K-T boundary. Here, we present a new morphological dataset for Anseriformes that includes more extant and extinct taxa than any previous anseriform-focused dataset and describe a new anseriform species from the early Eocene Green River Formation of North America. The new taxon has a mediolaterally narrow bill which is rarely found in previously described anseriform fossils. The matrix created to assess the placement of this taxon comprises 41 taxa and 719 discrete morphological characters describing skeletal morphology, musculature, syringeal morphology, ecology, and behavior. We additionally combine the morphological dataset with published sequences using Bayesian methods and perform ancestral state reconstruction for select morphological, ecological and behavioral characters. We recover the new Eocene taxon as the sister taxon to (Anseranatidae+Anatidae) across all analyses, and find that the new taxon represents a novel ecology within known Anseriformes and the Green River taxa. Results provide insight into avian evolution during and following the K-Pg mass extinction and indicate that Anseriformes were likely ancestrally aquatic herbivores with rhamphothecal lamellae..
Collapse
Affiliation(s)
- Grace Musser
- Department of Vertebrate Zoology, Division of Birds, The Smithsonian National Museum of Natural History, Washington, District of Columbia, United States of America
- Department of Earth and Planetary Sciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Julia A. Clarke
- Department of Earth and Planetary Sciences, The University of Texas at Austin, Austin, Texas, United States of America
| |
Collapse
|
27
|
Liu S, Li K, Zheng Y, Xue J, Wang S, Li S, Cao P, Liu F, Dai Q, Feng X, Yang R, Ping W, Wu D, Fan P, Fu Q, Chen Z. Mitogenomes of museum specimens provide new insight into species classification and recently reduced diversity of highly endangered Nomascus gibbons. Integr Zool 2024. [PMID: 39075927 DOI: 10.1111/1749-4877.12878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Our findings reveal that the western black crested gibbon (Nomascus concolor) did not divide into different subspecies, and the relatively low level of genetic diversity emphasizes the importance of monitoring this indicator for vulnerable wildlife. Meanwhile, phylogeographic analysis of the Nomascus genus shows a north-to-south trend of ancestral geographic distribution.
Collapse
Affiliation(s)
- Siqiong Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kexin Li
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuxin Zheng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Jiayang Xue
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Song Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center, and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Pengfei Fan
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zehui Chen
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
28
|
Lisnerova M, Bartosova-Sojkova P, Lovy A, Blabolil P, Fiala I. Evidence of striking morphological similarity and tissue tropism of phylogenetically distant myxozoan genera: Myxidium and Paramyxidium in the kidney of the European eel. Folia Parasitol (Praha) 2024; 71:2024.013. [PMID: 39101756 DOI: 10.14411/fp.2024.013] [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: 01/10/2024] [Accepted: 07/01/2024] [Indexed: 08/06/2024]
Abstract
European eel, Anguilla anguilla (Linnaeus) (Elopomorpha: Anguilliformes), is a critically endangered fish of ecological and economic importance, hosting numerous parasites, including myxozoans (Cnidaria). Since its initial discovery in the kidney of European eel, Myxidium giardi Cépède, 1906 has been reported with numerous spore sizes and shapes from various tissues of multiple anguillid species. Morphological variability, wide host and tissue spectrum, and lack of sequence data raised doubts about the conspecificity of reported isolates. Subsequent studies provided 18S rDNA sequences of several isolates from anguillids and other elopiform fish, and demonstrated a split of parasite data into two distinct phylogenetic lineages, one comprising the M. giardi sequence, and the other all species infecting elopiform fishes classified under the recently established genus Paramyxidium Freeman et Kristmundsson, 2018. Myxidium giardi was, however, transferred to this genus as Paramyxidium giardi n. comb. and designated as the type species of the genus. In line with this change, the sequence originally identified as M. giardi was considered to have been incorrectly associated with this species. To shed light on the status of M. giardi originally described by Cépède (1906), we conducted microscopic and molecular examinations of various organs of 24 individuals of European eel, originating from diverse Czech habitats. Through morphometric and molecular analyses, we demonstrated that spore and polar capsule morphology, morphometry and tissue tropism of our European eel kidney parasite isolates matched the features of the original M. giardi description. Our isolates clustered in the lineage encompassing the first published M. giardi sequence. Thus, the originally described M. giardi indeed represents an existing species within the genus Myxidium Bütschli, 1882, which we formally resurrect and redescribe. Due to the morphological and molecular differences between M. giardi and P. giardi of Freeman et Kristmundsson (2018), we additionally rename the latter species as Paramyxidium freemani nom. nov.
Collapse
Affiliation(s)
- Martina Lisnerova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Pavla Bartosova-Sojkova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Alena Lovy
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Petr Blabolil
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Institute of Hydrobiology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Ivan Fiala
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| |
Collapse
|
29
|
Sarkar S, Kang M, Angurana SK, Prasad S, Bora I, Singh P, Sharma V, Rana M, Singh B, Jayashree M, Ratho RK. Clinical Course and Molecular Characterization of Human Bocavirus Associated with Acute Lower Respiratory Tract Infections in a Tertiary Care Hospital in Northern India. Jpn J Infect Dis 2024; 77:227-235. [PMID: 38417867 DOI: 10.7883/yoken.jjid.2023.251] [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: 03/01/2024]
Abstract
Respiratory samples from 139 hospitalized children were screened for the human bocavirus (HBoV) genome. Positive samples were sequenced for the partial VP1/VP2 gene followed by molecular and phylogenetic analyses. HBoV positivity was noted in 7.2% (10/139) of patients. All HBoV-positive children presented with fever, cough, and respiratory distress (90%, 9/10). Three children developed multisystemic viral illness, with one fatality. Eight children required intensive care management and five required mechanical ventilation. The nucleotide percent identity of the partial VP1/VP2 gene in the HBoV study strains ranged from 97.52% to 99.67%. Non-synonymous mutations in the VP1 protein were T591S (n = 8) and Y517S (n = 1) in the HBoV St1 strain and N475S (n = 8) and S591T (n = 2) in the HBoV St2 strain. One strain showed A556P, H556P, I561S, and M562R non-synonymous mutations. All the study strains belonged to the HBoV1 type. Seven HBoV strains belonged to the same lineage, and three belonged to another lineage. For evolutionary dynamics, GTR+I substitution model with uncorrelated relaxed lognormal clock and Bayesian Skyline tree prior showed 9.0 × 10-4 (95% highest probability density interval: 3.1 × 10-6, 2.1 × 10-3) nucleotide substitutions per site per year. Clinical suspicion and virological screening are necessary to identify HBoV infections in children.
Collapse
Affiliation(s)
- Subhabrata Sarkar
- Department of Virology, Post Graduate Institute of Medical Education and Research, India
| | - Mannat Kang
- Department of Virology, Post Graduate Institute of Medical Education and Research, India
| | - Suresh Kumar Angurana
- Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, India
| | - Shankar Prasad
- Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, India
| | - Ishani Bora
- Department of Virology, Post Graduate Institute of Medical Education and Research, India
| | - Pankaj Singh
- National Institute of Virology, Indian Council of Medical Research, India
| | - Vikrant Sharma
- Department of Virology, Post Graduate Institute of Medical Education and Research, India
| | - Meenakshi Rana
- Department of Virology, Post Graduate Institute of Medical Education and Research, India
| | - Bhartendu Singh
- Department of Virology, Post Graduate Institute of Medical Education and Research, India
| | - Muralidharan Jayashree
- Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, India
| | - Radha Kanta Ratho
- Department of Virology, Post Graduate Institute of Medical Education and Research, India
| |
Collapse
|
30
|
Yao XY, Shi BW, Li HP, Han YQ, Zhong K, Shao JW, Wang YY. Epidemiology and genotypic diversity of feline bocavirus identified from cats in Harbin, China. Virology 2024; 598:110188. [PMID: 39059190 DOI: 10.1016/j.virol.2024.110188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/14/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024]
Abstract
Feline bocavirus (FBoV) is a globally distributed linear, single-stranded DNA virus infect cats, currently classified into three distinct genotypes. Although FBoV can lead to systemic infections, its complete pathogenic potential remains unclear. In this study, 289 blood samples were collected from healthy cats in Harbin, revealing an overall FBoV prevalence of 12.1%. Notably, genotypes 1 and 3 of FBoV were found co-circulating among the cat population in Harbin. Additionally, recombination events were detected, particularly in the newly discovered NG/104 and DL/102 strains. Furthermore, negative selection sites were predominantly observed across the protein coding genes of FBoV. These findings suggest a co-circulation of genetically diverse FBoV strains among cats in Harbin, indicate that purifying selection is the primary driving force shaping the genomic evolution of FBoV, and also underscore the importance of comprehensive surveillance efforts to enhance our understanding of the epidemiology and evolutionary characteristics of FBoV.
Collapse
Affiliation(s)
- Xin-Yan Yao
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, China; School of Life Science and Engineering, Foshan University, Foshan, 528225, Guangdong province, China
| | - Bo-Wen Shi
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan province, China; School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, Chongqing, China
| | - He-Ping Li
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan province, China
| | - Ying-Qian Han
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan province, China
| | - Kai Zhong
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan province, China
| | - Jian-Wei Shao
- School of Life Science and Engineering, Foshan University, Foshan, 528225, Guangdong province, China.
| | - Yue-Ying Wang
- Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan province, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, China.
| |
Collapse
|
31
|
Askari F, Paksa A, Shahabi S, Saeedi S, Sofizadeh A, Vahedi M, Soltani A. Population genetic structure and phylogenetic analysis of Anopheles hyrcanus (Diptera: Culicidae) inferred from DNA sequences of nuclear ITS2 and the mitochondrial COI gene in the northern part of Iran. BMC Infect Dis 2024; 24:724. [PMID: 39044181 PMCID: PMC11264359 DOI: 10.1186/s12879-024-09626-0] [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: 05/13/2024] [Accepted: 07/16/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND The Anopheles hyrcanus group is distributed throughout the Oriental and Palaearctic regions and can transmit diseases such as malaria, Japanese encephalitis virus, and filariasis. This investigation marks the inaugural comprehensive study to undertake a phylogenetic analysis of the constituents of this malaria vector group in the northeastern region of Iran, juxtaposed with documented occurrences from different areas within Iran and worldwide. METHODS Mosquitoes were collected using various methods from nine different locations in Golestan province from April to December 2023. The collected mosquitoes were identified morphologically using valid taxonomic keys. DNA was isolated using the Sambio™ Kit. COI and ITS2 primers were designed using Oligo7 and GeneRunner. PCR and purification were performed with the Qiagen kit. Subsequently, sequencing was carried out at the Mehr Mam GENE Center using an Applied Biosystems 3730XL sequencer. The nucleotide sequences were then analyzed and aligned with GenBank data using BioEdit. Kimura 2-parameter was Utilized for base substitutions. DNA models were selected based on AIC and BIC criteria. Bayesian and Maximum Likelihood trees were constructed, along with a haplotype network. Molecular diversity statistics computed using DnaSP software. RESULTS In this study, a total of 819 adult mosquitoes were collected. An. hyrcanus was the second most abundant species, predominantly found in Kalaleh and Turkman counties. The sequenced and edited COI and ITS2 sequences were deposited in GenBank under specific accession numbers. Phylogenetic analyses using ML, BI, and NJ methods confirmed a monophyletic lineage for An. hyrcanus with strong support. Molecular analysis of Iranian An. hyrcanus found 11 diverse haplotypes, with the COI gene displaying low diversity. The ITS2 gene revealed two clades - one associating with Iran, Europe, and Asia; the other originating from southwestern Iran. The haplotype network showed two main groups - one from southwest Iran and the other from north Iran. Iran exhibited six distinct haplotypes, while Turkey showcased the highest diversity. CONCLUSIONS An. hyrcanus in southwestern Iran exhibits a distinct haplogroup, suggesting possible subspecies differentiation. Additional studies are required to validate this phenomenon.
Collapse
Affiliation(s)
- Fatemeh Askari
- Student Research Committee, Department of Biology and Control of Disease Vectors, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Azim Paksa
- Department of Biology and Control of Disease Vectors, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Shahabi
- Department of Biology and Control of Disease Vectors, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shahin Saeedi
- Student Research Committee, Department of Biology and Control of Disease Vectors, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Aioub Sofizadeh
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mozaffar Vahedi
- Student Research Committee, Department of Biology and Control of Disease Vectors, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aboozar Soltani
- Research Center for Health Sciences, Institute of Health, Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
32
|
Morelli S, Traversa D, Di Cesare A, Colombo M, Grillini M, Paoletti B, Mondazzi A, Frangipane di Regalbono A, Iorio R, Astuti C, Tsokana CN, Diakou A. Geographical isolation and hyperendemicity of Hepatozoon felis: Epidemiological scenario in Skopelos, Greece, and phylogenetic analysis. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2024; 6:100202. [PMID: 39139660 PMCID: PMC11320469 DOI: 10.1016/j.crpvbd.2024.100202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/09/2024] [Accepted: 07/18/2024] [Indexed: 08/15/2024]
Abstract
Feline hepatozoonosis is a vector-borne disease caused by different species of the genus Hepatozoon, i.e. Hepatozoon felis, Hepatozoon silvestris and Hepatozoon canis. Knowledge on the biology, epidemiology and taxonomy of Hepatozoon spp. is still limited, despite the fact that the number of documented Hepatozoon spp. infections in domestic cats increased in recent years in different countries. This study was carried out to evaluate the prevalence and the genetic profile of Hepatozoon spp. in cats living on the island of Skopelos, Greece. Individual blood samples were collected from 54 owned cats and were subjected to Giemsa-stained blood smear examination to investigate the presence of Hepatozoon spp. gamonts and to a specific PCR protocol targeting the 18S rRNA gene of Hepatozoon. A total of 45 cats (83.3%) were found infected by Hepatozoon spp. by at least one of the methods applied. In particular, 43 (79.6%) of the cats were PCR-positive, and in 6 (11.1%) cats gamonts of Hepatozoon spp. were found in the blood smears. A total of 26 H. felis sequences were obtained and the presence of three undescribed single nucleotide polymorphisms were detected. The present results indicate that H. felis species complex may be hyperendemic in isolated/confined areas. In such contexts, geographical isolation may favor the origin of new genotypes or haplotypes or even new species.
Collapse
Affiliation(s)
- Simone Morelli
- Department of Veterinary Medicine, University of Teramo, Località Piano d’Accio snc, 64100, Teramo, Italy
| | - Donato Traversa
- Department of Veterinary Medicine, University of Teramo, Località Piano d’Accio snc, 64100, Teramo, Italy
| | - Angela Di Cesare
- Department of Veterinary Medicine, University of Teramo, Località Piano d’Accio snc, 64100, Teramo, Italy
| | - Mariasole Colombo
- Department of Veterinary Medicine, University of Teramo, Località Piano d’Accio snc, 64100, Teramo, Italy
| | - Marika Grillini
- Department of Animal Medicine, Production and Health, University of Padova, 35020, Legnaro, Padova, Italy
| | - Barbara Paoletti
- Department of Veterinary Medicine, University of Teramo, Località Piano d’Accio snc, 64100, Teramo, Italy
| | - Aurora Mondazzi
- Department of Veterinary Medicine, University of Teramo, Località Piano d’Accio snc, 64100, Teramo, Italy
| | | | - Raffaella Iorio
- Department of Veterinary Medicine, University of Teramo, Località Piano d’Accio snc, 64100, Teramo, Italy
| | - Chiara Astuti
- Department of Veterinary Medicine, University of Teramo, Località Piano d’Accio snc, 64100, Teramo, Italy
| | - Constantina N. Tsokana
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Anastasia Diakou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| |
Collapse
|
33
|
Alawfi MS, Alzahrani DA, Albokhari EJ. Complete plastome genomes of three medicinal heliotropiaceae species: comparative analyses and phylogenetic relationships. BMC PLANT BIOLOGY 2024; 24:654. [PMID: 38987665 PMCID: PMC11234707 DOI: 10.1186/s12870-024-05388-8] [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: 07/29/2023] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND Heliotropiaceae is a family of the order Boraginales and has over 450 species. The members of the family Heliotropiaceae have been widely reported to be used in traditional medicine Over time, the classification of Heliotropiaceae has remained uncertain and has moved from family to subfamily, or conversely. RESULTS In the present study, we sequenced, analyzed, and compared the complete plastomes of Euploca strigosa, Heliotropium arbainense, and Heliotropium longiflorum with the genomes of related taxa. The lengths of the plastomes of E. strigosa, H. arbainense, and H. longiflorum were 155,174 bp, 154,709 bp, and 154,496 bp, respectively. Each plastome consisted of 114 genes: 80 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. The long repeats analysis indicated that reverse, palindromic, complement and forward repeats were all found in the three plastomes. The simple repeats analysis showed that the plastomes of E. strigosa, H. arbainense, and H. longiflorum contained 158, 165, and 151 microsatellites, respectively. The phylogenetic analysis confirmed two major clades in the Boraginales: clade I comprised Boraginaceae, while clade II included Heliotropiaceae, Ehretiaceae, Lennoaceae, and Cordiaceae. Inside the family Heliotropiaceae, E. strigosa is nested within the Heliotropium genus. CONCLUSIONS This study expands our knowledge of the evolutionary relationships within Heliotropiaceae and offers useful genetic resources.
Collapse
Affiliation(s)
- Mohammad S Alawfi
- Department of Biology, College of Sciences, King Khalid University, Abha, Saudi Arabia.
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Dhafer A Alzahrani
- Department of Biological Sciences, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Enas J Albokhari
- Department of Biological Sciences, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| |
Collapse
|
34
|
Yu ZB, Kasyoka Kilunda F, Wang K, Cao YY, Wu CL, Duan ZP, Zuo CS, Zhang DC, Wu YH, Che J. The first discovery of Polypedatesteraiensis (Dubois, 1987) (Rhacophoridae, Anura) in China. Biodivers Data J 2024; 12:e127029. [PMID: 39015795 PMCID: PMC11249848 DOI: 10.3897/bdj.12.e127029] [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: 05/07/2024] [Accepted: 06/19/2024] [Indexed: 07/18/2024] Open
Abstract
Background The genus of Polypedates Tschudi, 1838 currently comprises 25 recognised species with four of these species reported in Yunnan, China. Dubois (1987) speculated the distribution of P.teraiensis in China; however, there was no study carried out to confirm its distribution in the region. New information We herein describe P.teraiensis as a new national record, based on a specimen collected from Yunnan border region. Phylogenetically, our sequence clustered with the sequences of recognised P.teraiensis specimens from Bangladesh, Myanmar and India. The uncorrected pairwise distances between the specimens from China and other P.teraiensis localities was small, ranging from 0.0-0.7%, based on 16S rRNA gene. Therefore, we report P.teraiensis as a new species record for China.
Collapse
Affiliation(s)
- Zhong-Bin Yu
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, ChinaKey Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223Kunming, YunnanChina
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, 05282, Yezin, Nay Pyi Taw, MyanmarSoutheast Asia Biodiversity Research Institute, Chinese Academy of Sciences, 05282Yezin, Nay Pyi TawMyanmar
| | - Felista Kasyoka Kilunda
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, ChinaKey Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223Kunming, YunnanChina
- Kunming College of Life Science, University of the Chinese Academy of Sciences, 650204, Kunming, Yunnan, ChinaKunming College of Life Science, University of the Chinese Academy of Sciences, 650204Kunming, YunnanChina
| | - Kai Wang
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, ChinaKey Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223Kunming, YunnanChina
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, 05282, Yezin, Nay Pyi Taw, MyanmarSoutheast Asia Biodiversity Research Institute, Chinese Academy of Sciences, 05282Yezin, Nay Pyi TawMyanmar
| | - Yu-Yang Cao
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, ChinaKey Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223Kunming, YunnanChina
- Key Laboratory of Southwest China Wildlife Resources Conservation, China West Normal University, Ministry of Education, 637009, Nanchong, Sichuan, ChinaKey Laboratory of Southwest China Wildlife Resources Conservation, China West Normal University, Ministry of Education, 637009Nanchong, SichuanChina
| | - Chun-Lian Wu
- Key Laboratory of Southwest China Wildlife Resources Conservation, China West Normal University, Ministry of Education, 637009, Nanchong, Sichuan, ChinaKey Laboratory of Southwest China Wildlife Resources Conservation, China West Normal University, Ministry of Education, 637009Nanchong, SichuanChina
| | - Zheng-Pan Duan
- Administrative Bureau of Tongbiguan Provincial Nature Reserve, 679300, Dehong, Yunnan, ChinaAdministrative Bureau of Tongbiguan Provincial Nature Reserve, 679300Dehong, YunnanChina
| | - Chang-Sheng Zuo
- Administrative Bureau of Tongbiguan Provincial Nature Reserve, 679300, Dehong, Yunnan, ChinaAdministrative Bureau of Tongbiguan Provincial Nature Reserve, 679300Dehong, YunnanChina
| | - Ding-Can Zhang
- Administrative Bureau of Tongbiguan Provincial Nature Reserve, 679300, Dehong, Yunnan, ChinaAdministrative Bureau of Tongbiguan Provincial Nature Reserve, 679300Dehong, YunnanChina
| | - Yun-He Wu
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, ChinaKey Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223Kunming, YunnanChina
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, 05282, Yezin, Nay Pyi Taw, MyanmarSoutheast Asia Biodiversity Research Institute, Chinese Academy of Sciences, 05282Yezin, Nay Pyi TawMyanmar
| | - Jing Che
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, Yunnan, ChinaKey Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223Kunming, YunnanChina
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, 05282, Yezin, Nay Pyi Taw, MyanmarSoutheast Asia Biodiversity Research Institute, Chinese Academy of Sciences, 05282Yezin, Nay Pyi TawMyanmar
| |
Collapse
|
35
|
Kaewmong P, Kittiwattanawong K, Nganvongpanit K, Piboon P. Unusual Patterns of Lateral Scutes in Two Olive Ridley Turtles and Their Genetic Assignment to the Thai Andaman Sea Populations of Lepidochelys olivacea Eschscholtz, 1829. BIOLOGY 2024; 13:500. [PMID: 39056694 PMCID: PMC11273376 DOI: 10.3390/biology13070500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024]
Abstract
Two stranded Lepidochelys-like sea turtles were rescued from the Thai Andaman Sea coastline by veterinarians of the Phuket Marine Biological Center (PMBC), one in May of 2019 and another in July of 2021. They were first identified as olive ridley turtles (Lepidochelys olivacea), as the external appearance of both turtles was closer to that species than the other four species found in the Thai Andaman Sea. In fact, when carefully examined, an unusual pattern of the lateral scutes on each turtle was observed, specifically symmetric 5/5 and asymmetric 5/6, both of which are considered rare for L. olivacea and had never been reported in the Thai Andaman Sea. In contrast, this characteristic was more common for the closely related species, Kemp's ridley (L. kempii), although this species is not distributed in the Indo-Pacific Ocean. Thus, we further investigated their genetic information to confirm species identification using two molecular markers, namely the mtDNA control region and nDNA RAG2. The results from the mtDNA control region sequences using the Basic Local Alignment Search Tool (BLAST) indicated that both individuals exhibited a higher percent identity with L. olivacea (99.81-100.00%) rather than L. kempii (94.29-95.41%) or any other species. A phylogenetic tree confirmed that these two turtles belonged to the L. olivacea clade. Moreover, the results of RAG2 also supported the mtDNA result, as both individuals shared the same RAG2 haplotype with L. olivacea. Thus, we have concluded that the two turtles with unusual lateral scute patterns exhibited genetic consistency with their original species, L. olivacea, which has brought attention to the importance of exploring rare phenotypes in sea turtle populations residing in Thai Seas.
Collapse
Affiliation(s)
| | | | - Korakot Nganvongpanit
- The School of Veterinary Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand;
| | - Promporn Piboon
- The School of Veterinary Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand;
| |
Collapse
|
36
|
Baiko D, Lisnerová M, Bartošová-Sojková P, Holzer AS, Blabolil P, Schabuss M, Fiala I. Solving the Myxidium rhodei (Myxozoa) puzzle: insights into its phylogeny and host specificity in Cypriniformes. Parasite 2024; 31:35. [PMID: 38949637 PMCID: PMC11216160 DOI: 10.1051/parasite/2024030] [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: 02/21/2023] [Accepted: 05/16/2024] [Indexed: 07/02/2024] Open
Abstract
Myxidium rhodei Léger, 1905 (Cnidaria: Myxozoa) is a kidney-infecting myxosporean that was originally described from the European bitterling Rhodeus amarus. Subsequently, it has been documented based on spore morphology in more than 40 other cypriniform species, with the roach Rutilus rutilus being the most commonly reported host. This study introduces the first comprehensive data assessment of M. rhodei, conducted through morphological, ecological and molecular methods. The morphological and phylogenetic analyses of SSU rDNA sequences of Myxidium isolates obtained from European bitterling and roach did not support parasite conspecificity from these fish. In fact, the roach-infecting isolates represent three distinct parasite species. The first two, M. rutili n. sp. and M. rutilusi n. sp., are closely related cryptic species clustering with other myxosporeans in the freshwater urinary clade, sharing the same tissue tropism. The third one, M. batuevae n. sp., previously assigned to M. cf. rhodei, clustered in the hepatic biliary clade sister to bitterling-infecting M. rhodei. Our examination of diverse cypriniform fishes, coupled with molecular and morphological analyses, allowed us to untangle the cryptic species nature of M. rhodei and discover the existence of novel species. This underscores the largely undiscovered range of myxozoan diversity and highlights the need to incorporate sequence data in diagnosing novel species.
Collapse
Affiliation(s)
- Dariya Baiko
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences České Budějovice 37005 Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice České Budějovice 37005 Czech Republic
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg Oldenburg 26129 Germany
| | - Martina Lisnerová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences České Budějovice 37005 Czech Republic
| | - Pavla Bartošová-Sojková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences České Budějovice 37005 Czech Republic
| | - Astrid S. Holzer
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences České Budějovice 37005 Czech Republic
- Fish Health Division, University of Veterinary Medicine Vienna 1210 Austria
| | - Petr Blabolil
- Faculty of Science, University of South Bohemia in České Budějovice České Budějovice 37005 Czech Republic
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences České Budějovice 37005 Czech Republic
| | | | - Ivan Fiala
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences České Budějovice 37005 Czech Republic
- Faculty of Science, University of South Bohemia in České Budějovice České Budějovice 37005 Czech Republic
| |
Collapse
|
37
|
Özkan M, Gürün K, Yüncü E, Vural KB, Atağ G, Akbaba A, Fidan FR, Sağlıcan E, Altınışık EN, Koptekin D, Pawłowska K, Hodder I, Adcock SE, Arbuckle BS, Steadman SR, McMahon G, Erdal YS, Bilgin CC, Togan İ, Geigl EM, Götherström A, Grange T, Özer F, Somel M. The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus). Mol Ecol 2024; 33:e17440. [PMID: 38946459 DOI: 10.1111/mec.17440] [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: 07/11/2023] [Revised: 05/17/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024]
Abstract
We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6-6.4×. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass, secular name 'hydruntine'. Further, the Anatolian wild ass whole genome profiles fell outside the genomic diversity of other extant and past Asiatic wild ass (E. hemionus) lineages. These observations suggest that the three Anatolian wild asses represent hydruntines, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Our mitogenomic and genomic analyses indicate that E. h. hydruntinus was a clade belonging to ancient and present-day E. hemionus lineages that radiated possibly between 0.6 and 0.8 Mya. We also find evidence consistent with recent gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity suggest that the Anatolian wild ass population may have lost genetic diversity by the mid-first millennium BCE, a possible sign of its eventual demise.
Collapse
Affiliation(s)
- Mustafa Özkan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ali Akbaba
- Department of Anthropology, Ankara University, Ankara, Turkey
- Alparslan University, Muş, Turkey
| | - Fatma Rabia Fidan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Ekin Sağlıcan
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Ezgi N Altınışık
- Department of Anthropology, Human_G Laboratory, Hacettepe University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Kamilla Pawłowska
- Department of Palaeoenvironmental Research, Adam Mickiewicz University, Poznań, Poland
| | - Ian Hodder
- Department of Anthropology, Stanford University, Stanford, California, USA
| | - Sarah E Adcock
- Institute for the Study of the Ancient World, New York University, New York, New York, USA
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon R Steadman
- Department of Sociology/Anthropology, SUNY Cortland, Cortland, New York, USA
| | - Gregory McMahon
- Classics, Humanities and Italian Studies Department, University of New Hampshire, Durham, New Hampshire, USA
| | - Yılmaz Selim Erdal
- Department of Anthropology, Human_G Laboratory, Hacettepe University, Ankara, Turkey
| | - C Can Bilgin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, Université de Paris, Paris, France
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Thierry Grange
- Institut Jacques Monod, CNRS, Université de Paris, Paris, France
| | - Füsun Özer
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| |
Collapse
|
38
|
Nguyen HD, Do HDK, Vu MT. Comparative genomics revealed new insights into the plastome evolution of Ludwigia (Onagraceae, Myrtales). Sci Prog 2024; 107:368504241272741. [PMID: 39150375 PMCID: PMC11329976 DOI: 10.1177/00368504241272741] [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: 08/17/2024]
Abstract
The primrose-willow (Ludwigia L.), a well-defined genus of the Onagraceae family, comprises 87 species widely distributed worldwide. In this study, we sequenced and characterized the complete chloroplast (cp) genomes of three species in the genus, including Ludwigia adscendens, Ludwigia hyssopifolia, and Ludwigia prostrata. Three Ludwigia cp genomes ranged from 158,354 to 159,592 bp in size, and each contained 113 genes, including 79 unique protein-coding genes (PCGs), four rRNA genes, and 30 tRNA genes. A comparison of the Ludwigia cp genomes revealed that they were highly conserved in gene composition, gene orientation, and GC content. Moreover, we compared the structure of cp genomes and reconstructed phylogenetic relationships with related species in the Onagraceae family. Regarding contraction/expansion of inverted repeat (IR) region, two kinds of expansion IR region structures were found in Oenothera, Chamaenerion, and Epilobium genera, with primitive IR structures in Ludwigia and Circeae genera. The regions clpP, ycf2, and ycf1 genes possessed highly divergent nucleotides among all available cp genomes of the Onagraceae family. The phylogenetic reconstruction using 79 PCGs from 39 Onagraceae cp genomes inferred that Ludwigia (including L. adscendens, L. hyssopifolia, L. prostrata, and Ludwigia octovalvis) clade was monophyletic and well-supported by the bootstrap and posterior probability values. This study provides the reference cp genomes of three Ludwigia species, which can be used for species identification and phylogenetic reconstruction of Ludwigia and Onagraceae taxa.
Collapse
Affiliation(s)
- Hoang Danh Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Minh Thiet Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| |
Collapse
|
39
|
Xu H, Guo Y, Xia M, Yu J, Chi X, Han Y, Li X, Zhang F. An updated phylogeny and adaptive evolution within Amaranthaceae s.l. inferred from multiple phylogenomic datasets. Ecol Evol 2024; 14:e70013. [PMID: 39011133 PMCID: PMC11246835 DOI: 10.1002/ece3.70013] [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: 09/03/2023] [Revised: 06/17/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024] Open
Abstract
Amaranthaceae s.l. is a widely distributed family consisting of over 170 genera and 2000 species. Previous molecular phylogenetic studies have shown that Amaranthaceae s.s. and traditional Chenopodiaceae form a monophyletic group (Amaranthaceae s.l.), however, the relationships within this evolutionary branch have yet to be fully resolved. In this study, we assembled the complete plastomes and full-length ITS of 21 Amaranthaceae s.l. individuals and compared them with 38 species of Amaranthaceae s.l. Through plastome structure and sequence alignment analysis, we identified a reverse complementary region approximately 5200 bp long in the genera Atriplex and Chenopodium. Adaptive evolution analysis revealed significant positive selection in eight genes, which likely played a driving role in the evolution of Amaranthaceae s.l., as demonstrated by partitioned evolutionary analysis. Furthermore, we found that about two-thirds of the examined species lack the ycf15 gene, potentially associated with natural selection pressures from their adapted habitats. The phylogenetic tree indicated that some genera (Chenopodium, Halogeton, and Subtr. Salsolinae) are paraphyletic lineages. Our results strongly support the clustering of Amaranthaceae s.l. with monophyletic traditional Chenopodiaceae (Clades I and II) and Amaranthaceae s.s. After a comprehensive analysis, we determined that cytonuclear conflict, gene selection by adapted habitats, and incomplete lineage sorting (ILS) events were the primary reasons for the inconsistent phylogeny of Amaranthaceae s.l. During the last glacial period, certain species within Amaranthaceae s.l. underwent adaptations to different environments and began to differentiate rapidly. Since then, these species may have experienced morphological and genetic changes distinct from those of other genera due to intense selection pressure.
Collapse
Affiliation(s)
- Hao Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yuqin Guo
- Qinghai National Park Research Monitoring and Evaluation CenterXiningChina
| | - Mingze Xia
- School of PharmacyWeifang Medical UniversityWeifangChina
| | - Jingya Yu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaofeng Chi
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
| | - Yun Han
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoping Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- University of Chinese Academy of SciencesBeijingChina
| | - Faqi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology and Institute of Sanjiangyuan National ParkChinese Academy of SciencesXiningChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningChina
| |
Collapse
|
40
|
Jeong JS, Kim HK, Park JS, Hwang HS, Kim I. Complete mitochondrial genome of the European common barnacle Perforatus perforatus Bruguière, 1789 (balanomorpha: balanidae). Mitochondrial DNA B Resour 2024; 9:823-827. [PMID: 38911522 PMCID: PMC11191835 DOI: 10.1080/23802359.2024.2368727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/11/2024] [Indexed: 06/25/2024] Open
Abstract
This study is the first to sequence the complete mitochondrial genome (mitogenome) of Perforatus perforatus Bruguière, 1789 (Balanomorpha: Balanidae). The 15,536-bp long P. perforatus mitogenome contained a typical set of animal mitochondrial genes, along with one control region. The P. perforatus mitogenome had an inverted gene block (trnP-ND4L-ND4-trnH-ND5-trnF) between trnS(gct) and trnT. This inverted gene block had been detected six species in three subfamilies of the Balanidae family (Balaninae, Acastinae and Megabalaninae), but our results show that it is also present in Concavinae, in which P. perforatus is included. The phylogenetic tree based on the concatenated sequences of the 13 protein-coding genes and two rRNA genes showed that P. perforatus is closely associated with Acasta sulcate and Balanus trigonus within Balanidae.
Collapse
Affiliation(s)
- Jun Seong Jeong
- Division of Genetic Resources, Honam National Institute of Biological Resources, Mokpo, Republic of Korea
| | - Hyun Kyong Kim
- Division of Zoology, Honam National Institute of Biological Resources, Mokpo, Republic of Korea
| | - Jeong Sun Park
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Hee-Seung Hwang
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Iksoo Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| |
Collapse
|
41
|
Dei Giudici S, Mura L, Bonelli P, Ferretti L, Hawko S, Franzoni G, Angioi PP, Ladu A, Puggioni G, Antuofermo E, Sanna ML, Burrai GP, Oggiano A. First Molecular Characterisation of Porcine Parvovirus 7 (PPV7) in Italy. Viruses 2024; 16:932. [PMID: 38932224 PMCID: PMC11209580 DOI: 10.3390/v16060932] [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] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Porcine parvoviruses (PPVs) are among the most important agents of reproductive failure in swine worldwide. PPVs comprise eight genetically different species ascribed to four genera: Protoparvovirus (PPV1, PPV8), Tetraparvovirus (PPV2-3), Copiparvovirus (PPV4-6), and Chaphamaparvovirus (PPV7). In 2016, PPV7 was firstly detected in the USA and afterwards in Europe, Asia, and South America. Recently, it was also identified in Italy in pig farms with reproductive failure. This study aimed to evaluate the circulation of PPV7 in domestic and wild pigs in Sardinia, Italy. In addition, its coinfection with Porcine Circovirus 2 (PCV2) and 3 (PCV3) was analysed, and PPV7 Italian strains were molecularly characterised. PPV7 was detected in domestic pigs and, for the first time, wild pigs in Italy. The PPV7 viral genome was detected in 20.59% of domestic and wild pig samples. PPV7 detection was significantly lower in domestic pigs, with higher PCV2/PCV3 co-infection rates observed in PPV7-positive than in PPV7-negative domestic pigs. Molecular characterisation of the NS1 gene showed a very high frequency of recombination that could presumably promote virus spreading.
Collapse
Affiliation(s)
- Silvia Dei Giudici
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Lorena Mura
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Piero Bonelli
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Luca Ferretti
- Nuffield Department of Medicine, Big Data Institute and Pandemic Sciences Institute, University of Oxford, Oxford OX1 4BH, UK
| | - Salwa Hawko
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Giulia Franzoni
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Pier Paolo Angioi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Anna Ladu
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Graziella Puggioni
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | | | - Maria Luisa Sanna
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | | | - Annalisa Oggiano
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| |
Collapse
|
42
|
Sahu K, Gopi GV, Gupta SK. Unveiling the genetic structure of pig population in a Himalayan state Uttarakhand through microsatellite and mitochondrial DNA analyses. Trop Anim Health Prod 2024; 56:183. [PMID: 38831031 DOI: 10.1007/s11250-024-04035-6] [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: 09/30/2023] [Accepted: 05/16/2024] [Indexed: 06/05/2024]
Abstract
This study traced the maternal lineage of the domestic swine populations using mitochondrial DNA control region markers and genetic diversity using microsatellite markers in Uttarakhand, an Indian state situated at the foothills of the world's youngest (geo-dynamically sensitive) mountain system, "the Himalayas". Analysis of 68 maternally unrelated individuals revealed 20 haplotypes. The maternal signature of the Pacific, Southeast Asian, European, and ubiquitously distributed Chinese haplotypes was present in Uttarakhand's domestic pig population. The D3 haplotype reported in wild pigs from North India was also identified in 47 domestic samples. A unique gene pool, UKD (Uttarakhand Domestic), as another lineage specific to this region has been proposed. Genotypes were analyzed, using 13 sets of microsatellite markers. The observed (Ho) and expected (He) heterozygosities were 0.83 ± 0.02 and 0.84 ± 0.01, respectively. The average polymorphic information content value of 0.83 ± 0.01 indicated the high informativeness of the marker. The overall mean FIS value for all the microsatellite markers was low (F = 0.04, P < 0.01). Seven loci deviated from Hardy-Weinberg equilibrium (HWE) at a significant level (p < 0.05). Two clusters were identified, indicating overlapping populations. These results suggested that though belonging to different maternal lineages, the traditional management practices in Uttarakhand have allowed for genetic mixing and the sharing of genetic material among pig populations. It could contribute to increased genetic diversity but might also result in the loss of distinct genetic characteristics or breed purity of the local breeds if not carefully managed.
Collapse
Affiliation(s)
- Khusbu Sahu
- Wildlife Institute of India, Chandrabani, Dehradun, 248001, India
| | | | | |
Collapse
|
43
|
Kuručki M, Sukara R, Ćirković V, Ćirović D, Tomanović S. Molecular Detection and Genetic Variability of Hepatozoon canis in Golden Jackals ( Canis aureus L. 1758) in Serbia. BIOLOGY 2024; 13:411. [PMID: 38927291 PMCID: PMC11201132 DOI: 10.3390/biology13060411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/27/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
Hepatozoon canis is a protozoan tick-borne parasite infecting domestic and wild canids, including foxes, wolves, and jackals. It is mainly found in dogs but has also been detected in several wild carnivores, including foxes, wolves, and jackals. Host transmission primarily occurs through the ingestion of infected ticks, typically Rhipicephalus sanguineus, with documented instances of transplacental transmission from infected females to cubs. In Serbia, the golden jackal is common throughout the country, and its population has increased in recent years. Previous research has documented the presence of several vector-borne pathogens in the jackal population in Serbia, so we conducted this study to determine the presence, prevalence, and genetic variability of H. canis. Over eleven years (2010-2020), 114 animal samples were collected from 23 localities in Serbia. A total of 90/114 (78.95%) jackals were positive for H. canis, and they came from 22 localities. Among 15 juveniles, almost half (6/15 (40%)) tested positive for H. canis. In addition to the high prevalence, high genetic variability of the pathogen was also found. According to the mutated positions, four sequence types (S4-S7) of H. canis were determined. Based on our earlier research on the grey wolf and on this study, it can be observed that various sequence types of H. canis circulate within wild canid populations in Serbia. The prevalence of H. canis infection in wild carnivores raises significant concerns for wildlife conservation and animal health. Infected animals may act as reservoirs for the disease, posing a potential risk to domestic animals by acting as a source of infection.
Collapse
Affiliation(s)
- Milica Kuručki
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia;
| | - Ratko Sukara
- Group for Medical Entomology, Centre of Excellence for Food- and Vector-Borne Zoonoses, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11129 Belgrade, Serbia; (R.S.); (V.Ć.); (S.T.)
| | - Valentina Ćirković
- Group for Medical Entomology, Centre of Excellence for Food- and Vector-Borne Zoonoses, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11129 Belgrade, Serbia; (R.S.); (V.Ć.); (S.T.)
| | - Duško Ćirović
- Faculty of Biology, University of Belgrade, 11000 Belgrade, Serbia;
| | - Snežana Tomanović
- Group for Medical Entomology, Centre of Excellence for Food- and Vector-Borne Zoonoses, Institute for Medical Research, National Institute of Republic of Serbia, University of Belgrade, 11129 Belgrade, Serbia; (R.S.); (V.Ć.); (S.T.)
| |
Collapse
|
44
|
Lopez-Verdejo A, Palomba M, Crocetta F, Santoro M. Integrative taxonomy of metazoan parasites of the bluntnose sixgill shark Hexanchus griseus (Bonnaterre, 1788) in the Mediterranean Sea, with the resurrection of Grillotia acanthoscolex Rees, 1944 (Cestoda: Trypanorhyncha). JOURNAL OF FISH BIOLOGY 2024; 104:1754-1763. [PMID: 38450741 DOI: 10.1111/jfb.15703] [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: 11/13/2023] [Revised: 01/26/2024] [Accepted: 02/13/2024] [Indexed: 03/08/2024]
Abstract
Appropriate diagnoses of parasites of apex marine predators are crucial to understand their biodiversity, host specificity, biogeography, and life cycles. Such diagnoses are also informative of ecological and biological characteristics of both host and environment in which the hosts and their parasites live. We here (i) investigate the parasite fauna of a bluntnose sixgill shark Hexanchus griseus (Bonnaterre, 1788) obtained from the Gulf of Naples (Tyrrhenian Sea), (ii) characterize molecularly all its metazoan parasites, and (iii) resurrect and report the main morphological features and phylogenetic position of Grillotia acanthoscolex, a cestode species previously synonymized with Grillotia adenoplusia. A rich parasite fauna represented by eight different taxa was found, including two monogeneans (Protocotyle grisea and Protocotyle taschenbergi), one digenean (Otodistomum veliporum), four cestodes (Crossobothrium dohrnii, Clistobothrium sp., G. acanthoscolex, and G. adenoplusia), and one copepod (Protodactylina pamelae). Sequencing of these samples accounts for an important molecular baseline to widen the knowledge on the parasitic fauna of bluntnose sixgill sharks worldwide and to reconstruct their correct food chains. The bluntnose sixgill shark was found to be a definitive host for all endoparasites found here, confirming that it occupies an apex trophic level in the Mediterranean Sea. The taxa composition of the trophic parasite fauna confirms that the bluntnose sixgill shark mostly feeds on teleost fish species. However, the occurrence of two phillobothrid cestodes (C. dohrnii and Clistobothrium sp.) suggests that it also feeds on squids. Finally, we emphasize the importance of using integrative taxonomic approaches in the study of parasites from definitive and intermediate hosts to elucidate biology and ecology of taxa generally understudied in the Mediterranean Sea.
Collapse
Affiliation(s)
- Alejandro Lopez-Verdejo
- Marine Zoology Unit, Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Spain
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Marialetizia Palomba
- Department of Biological and Ecological Sciences, University of Tuscia, Viterbo, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Fabio Crocetta
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Mario Santoro
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| |
Collapse
|
45
|
Li J, Jiang J, Jin Q, Yuan Z, Qiu J. Mitochondrial DNA evidence reflects high genetic divergence of Amynthas aspergillum (Oligochaeta: Megascolecidae) in southern China. Ecol Evol 2024; 14:e11452. [PMID: 38826156 PMCID: PMC11140451 DOI: 10.1002/ece3.11452] [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: 01/05/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 06/04/2024] Open
Abstract
Amynthas aspergillum (Perrier, 1872), a natural resource used in traditional Chinese medicine (Guang-dilong) with high economic value, is widely distributed in forests and farmland habitats in the hilly areas of southern China. To investigate the extent of genetic differentiation and diversity in A. aspergillum, a population genetic structure study was performed on 157 samples from 75 locations in southern China using the mitochondrial genes COI, COII, 12S rRNA, 16S rRNA, and NDI. The results indicated that A. aspergillum had a high level of genetic diversity, and variation within populations was the main source of the total variation. Six deeply divergent mitochondrial clades (I-VI) were detected using both phylogenetic tree and haplotype network analyses. This finding was supported by the high Kimura two-parameter genetic distance and the pairwise fixation index value obtained based on the COI gene. No significant phylogeographic structures were observed. The widespread geographic distribution of clades II, IV, and VI suggested a recent demographic expansion based on multiple analysis results. These results include a high level of Hd and low π, star-shaped haplotype network structures with a high number of less frequent haplotypes, significantly negative neutrality test values, and a unimodal mismatch distribution pattern. The divergence time estimates and reconstruction of the ancestral area revealed that A. aspergillum originated in Guangxi Province and underwent initial intraspecific diversification in the early Pliocene to generate clade I. Then, it gradually dispersed eastward and rapidly differentiated into clades II-V during the Pleistocene. The Yunnan-Guizhou Plateau and Nanling and Wuyi Mountains might act as geographical barriers for the spread of A. aspergillum to the west and north.
Collapse
Affiliation(s)
- Jiali Li
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Jibao Jiang
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Qing Jin
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Zhu Yuan
- School of PharmacyShanghai University of Medicine & Health SciencesShanghaiChina
| | - Jiangping Qiu
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| |
Collapse
|
46
|
Larbi I, Arbi M, Souiai O, Tougorti H, Butcher GD, Nsiri J, Badr C, Behi IE, Lachhab J, Ghram A. Phylogeographic Dynamics of H9N2 Avian Influenza Viruses in Tunisia. Virus Res 2024; 344:199348. [PMID: 38467378 PMCID: PMC10995884 DOI: 10.1016/j.virusres.2024.199348] [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: 01/09/2024] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024]
Abstract
Avian influenza virus subtype H9N2 is endemic in commercial poultry in Tunisia. This subtype affects poultry and wild birds in Tunisia and poses a potential zoonotic risk. Tunisian H9N2 strains carry, in their hemagglutinins, the human-like marker 226 L that is most influential in avian-to-human viral transmission. For a better understanding of how ecological aspects of the H9N2 virus and its circulation in poultry, migratory birds and environment shapes the spread of the dissemination of H9N2 in Tunisia, herein, we investigate the epidemiological, evolutionary and zoonotic potential of seven H9N2 poultry isolates and sequence their whole genome. Phylogeographic and phylodymanic analysis were used to examine viral spread within and among wild birds, poultry and environment at geographical scales. Genetic evolution results showed that the eight gene sequences of Tunisian H9N2 AIV were characterized by molecular markers involved with virulence and mammalian infections. The geographical distribution of avian influenza virus appears as a network interconnecting countries in Europe, Asia, North Africa and West Africa. The spatiotemporal dynamics analysis showed that the H9N2 virus was transmitted from Tunisia to neighboring countries notably Libya and Algeria. Interestingly, this study also revealed, for the first time, that there was a virus transmission between Tunisia and Morocco. Bayesian analysis showed exchanges between H9N2 strains of Tunisia and those of the Middle Eastern countries, analysis of host traits showed that duck, wild birds and environment were ancestry related to chicken. The subtypes phylodynamic showed that PB1 segment was under multiple inter-subtype reassortment events with H10N7, H12N5, H5N2 and H6N1 and that PB2 was also a subject of inter-subtype reassortment with H10N4.
Collapse
Affiliation(s)
- Imen Larbi
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia.
| | - Marwa Arbi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Halima Tougorti
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Gary David Butcher
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Jihene Nsiri
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Chaima Badr
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Imen El Behi
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Jihene Lachhab
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Abdeljelil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| |
Collapse
|
47
|
Fukuda Y, Kondo K, Nakata S, Morita Y, Adachi N, Kogawa K, Ukae S, Kudou Y, Adachi S, Yamamoto M, Fukumura S, Tsugawa T. Whole-genome analysis of human group A rotaviruses in 1980s Japan and evolutionary assessment of global Wa-like strains across half a century. J Gen Virol 2024; 105. [PMID: 38836747 DOI: 10.1099/jgv.0.001998] [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] Open
Abstract
Historically, the Wa-like strains of human group A rotavirus (RVA) have been major causes of gastroenteritis. However, since the 2010s, the circulation of non-Wa-like strains has been increasingly reported, indicating a shift in the molecular epidemiology of RVA. Although understanding RVA evolution requires the analysis of both current and historical strains, comprehensive pre-1980's sequencing data are scarce globally. We determined the whole-genome sequences of representative strains from six RVA gastroenteritis outbreaks observed at an infant home in Sapporo, Japan, between 1981 and 1989. These outbreaks were mainly caused by G1 or G3 Wa-like strains, resembling strains from the United States in the 1970s-1980s and from Malawi in the 1990s. Phylogenetic analysis of these infant home strains, together with Wa-like strains collected worldwide from the 1970s to 2020, revealed a notable trend: pre-2010 strains diverged into multiple lineages in many genomic segments, whereas post-2010 strains tended to converge into a single lineage. However, Bayesian skyline plot indicated near-constant effective population sizes from the 1970s to 2020, and selection pressure analysis identified positive selection only at amino acid 75 of NSP2. These results suggest that evidence supporting the influence of rotavirus vaccines, introduced globally since 2006, on Wa-like RVA molecular evolution is lacking at present, and phylogenetic analysis may simply reflect natural fluctuations in RVA molecular evolution. Evaluating the long-term impact of RV vaccines on the molecular evolution of RVA requires sustained surveillance.
Collapse
Affiliation(s)
- Yuya Fukuda
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Kenji Kondo
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shuji Nakata
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yasuyuki Morita
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noriaki Adachi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Keiko Kogawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Susumu Ukae
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yoshimasa Kudou
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shuhei Adachi
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Masaki Yamamoto
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shinobu Fukumura
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Japan
| |
Collapse
|
48
|
Spetik M, Pecenka J, Stuskova K, Stepanova B, Eichmeier A, Kiss T. Fungal Trunk Diseases Causing Decline of Apricot and Plum Trees in the Czech Republic. PLANT DISEASE 2024; 108:1425-1436. [PMID: 38085239 DOI: 10.1094/pdis-06-23-1080-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Fungal trunk diseases (FTDs) have been a significant threat to the global stone fruit industry. FTDs are caused by a consortium of wood-decaying fungi. These fungi colonize woody tissues, causing cankers, dieback, and other decline-related symptoms in host plants. In this study, a detailed screening of the fungal microbiota associated with the decline of stone fruit trees in the Czech Republic was performed. The wood fragments of plum and apricot trees showing symptoms of FTDs were subjected to fungal isolation. The partial internal transcribed spacer region, partial beta-tubulin, and translation elongation factor 1-α genes were amplified from genomic DNA extracted from fungal cultures. All isolates were classified, and the taxonomic placement of pathogenic strains was illustrated in phylogenetic trees. The most abundant pathogenic genus was Dactylonectria (31%), followed by Biscogniauxia (13%), Thelonectria (10%), Eutypa (9%), Dothiorella (7%), Diplodia (6%), and Diaporthe (6%). The most frequent endophytic genus was Aposphaeria (17%). The pathogenicity of six fungal species (Cadophora daguensis, Collophorina africana, Cytospora sorbicola, Dothiorella sarmentorum, Eutypa lata, and E. petrakii var. petrakii) to four Prunus spp. was evaluated, and Koch's postulates were fulfilled. All tested isolates caused lesions on at least one Prunus sp. The most aggressive species was E. lata, which caused the largest lesions on all four tested Prunus spp., followed by E. petrakii var. petrakii and D. sarmentorum. Japanese plum (Prunus salicina) and almond (P. amygdalus) were the most susceptible hosts, while apricot (P. armeniaca) was the least susceptible host in the pathogenicity trial.
Collapse
Affiliation(s)
- Milan Spetik
- Mendeleum-Institute of Genetics, Mendel University in Brno 691 44, Lednice na Morave, Czech Republic
| | - Jakub Pecenka
- Mendeleum-Institute of Genetics, Mendel University in Brno 691 44, Lednice na Morave, Czech Republic
| | - Katerina Stuskova
- Mendeleum-Institute of Genetics, Mendel University in Brno 691 44, Lednice na Morave, Czech Republic
| | - Bara Stepanova
- Department of Fruit Science, Mendel University in Brno 691 44, Lednice na Morave, Czech Republic
| | - Ales Eichmeier
- Mendeleum-Institute of Genetics, Mendel University in Brno 691 44, Lednice na Morave, Czech Republic
| | - Tomas Kiss
- Department of Fruit Science, Mendel University in Brno 691 44, Lednice na Morave, Czech Republic
| |
Collapse
|
49
|
Merchioratto I, Mucellini CI, Lopes TRR, de Oliveira PSB, Silva Júnior JVJ, Brum MCS, Weiblen R, Flores EF. Phylogenetic analysis of papillomaviruses in dogs from southern Brazil: molecular epidemiology and investigation of mixed infections and spillover events. Braz J Microbiol 2024; 55:2025-2033. [PMID: 38710991 PMCID: PMC11153379 DOI: 10.1007/s42770-024-01349-3] [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: 10/05/2023] [Accepted: 04/18/2024] [Indexed: 05/08/2024] Open
Abstract
Papillomaviruses (PVs) have been identified in several animal species, including dogs (canine papillomaviruses, CPVs) and cattle (bovine papillomaviruses, BPVs). Although some BPVs may occasionally infect species other than cattle, to the best of our knowledge, BPVs have not been reported in dogs to date. Herein, we carried out a retrospective phylogenetic study of PVs circulating in dogs from southern Brazil between 2017 and 2022, also investigating possible mixed infections and spillover events. For this, we screened 32 canine papilloma samples by PCR using the degenerate primers FAP59/64 and/or MY09/11, which amplify different regions of the L1 gene; the genomic target often used for PV classification/typing. Out these, 23 PV DNA samples were successfully amplified and sequenced. All PVs amplified by FAP59/64 (n = 22) were classified as CPV-1. On the other hand, PVs amplified by MY09/11 (n = 4) were classified as putative BPV-1. Among these, three samples showed mixed infection by CPV-1 and putative BPV-1. One of the putative BPV-1 detected in co-infected samples had the L1 gene full-sequenced, confirming the gene identity. Furthermore, the phylogenetic classifications from the FAP59/64 and/or MY09/11 amplicons were supported by a careful in silico analysis, which demonstrated that the analysis based on them matches to the classification from the complete L1 gene. Overall, we described CPV-1 circulation in southern Brazil over the years and the potencial BPV infection in dogs (potential spillover event), as well as possible CPV/1/BPV-1 co-infections. Finally, we suggest the analysis of the complete genome of the putative BPVs detected in dogs in order to deepen the knowledge about the PV-host interactions.
Collapse
Affiliation(s)
- Ingryd Merchioratto
- Programa de Pós-Graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA
| | - Carolina Isabela Mucellini
- Programa de Pós-Graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
- Departamento de Ciências Veterinárias, Universidade Federal do Paraná, Paraná, Brazil
| | - Thaísa Regina Rocha Lopes
- Programa de Pós-Graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Pablo Sebastian Britto de Oliveira
- Programa de Pós-Graduação em Medicina Veterinária, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - José Valter Joaquim Silva Júnior
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil.
- Setor de Virologia, Instituto Keizo Asami, Universidade Federal de Pernambuco, Pernambuco, Brazil.
- Laboratório NB3 de Neuroimunologia, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil.
- Departamento de Microbiologia e Parasitologia, Universidade Federal de Santa Maria, Av. Roraima, 1000, Prédio 20, Rio Grande do Sul, Brazil.
| | | | - Rudi Weiblen
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil
| | - Eduardo Furtado Flores
- Setor de Virologia, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil.
| |
Collapse
|
50
|
Kochanova E, Mayor T, Väinölä R. Cryptic diversity and speciation in an endemic copepod crustacean Harpacticella inopinata within Lake Baikal. Ecol Evol 2024; 14:e11471. [PMID: 38826165 PMCID: PMC11140236 DOI: 10.1002/ece3.11471] [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: 12/14/2023] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 06/04/2024] Open
Abstract
Ancient lakes are hotspots of species diversity, posing challenges and opportunities for exploration of the dynamics of endemic diversification. Lake Baikal in Siberia, the oldest lake in the world, hosts a particularly rich crustacean fauna, including the largest known species flock of harpacticoid copepods with some 70 species. Here, we focused on exploring the diversity and evolution within a single nominal species, Harpacticella inopinata Sars, 1908, using molecular markers (mitochondrial COI, nuclear ITS1 and 28S rRNA) and a set of qualitative and quantitative morphological traits. Five major mitochondrial lineages were recognized, with model-corrected COI distances of 0.20-0.37. A concordant pattern was seen in the nuclear data set, and qualitative morphological traits also distinguish a part of the lineages. All this suggests the presence of several hitherto unrecognized cryptic taxa within the baikalian H. inopinata, with long independent histories. The abundances, distributions and inferred demographic histories were different among taxa. Two taxa, H. inopinata CE and H. inopinata CW, were widespread on the eastern and western coasts, respectively, and were largely allopatric. Patterns in mitochondrial variation, that is, shallow star-like haplotype networks, suggest these taxa have spread through the lake relatively recently. Three other taxa, H. inopinata RE, RW and RW2, instead were rare and had more localized distributions on either coast, but showed deeper intraspecies genealogies, suggesting older regional presence. The rare taxa were often found in sympatry with the others and occasionally introgressed by mtDNA from the common ones. The mitochondrial divergence between and within the H. inopinata lineages is still unexpectedly deep, suggesting an unusually high molecular rate. The recognition of true systematic diversity in the evaluation and management of ecosystems is important in hotspots, as it is everywhere else, while the translation of the diversity into a formal taxonomy remains a challenge.
Collapse
Affiliation(s)
- Elena Kochanova
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| | - Tatyana Mayor
- Laboratory of IchthyologyLimnological Institute SB RASIrkutskRussia
| | - Risto Väinölä
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| |
Collapse
|