151
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Thompson JB, Hernández-Hernández T, Keeling G, Vásquez-Cruz M, Priest NK. Identifying the multiple drivers of cactus diversification. Nat Commun 2024; 15:7282. [PMID: 39179557 PMCID: PMC11343764 DOI: 10.1038/s41467-024-51666-2] [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: 06/13/2023] [Accepted: 08/14/2024] [Indexed: 08/26/2024] Open
Abstract
Our understanding of the complexity of forces at play in the rise of major angiosperm lineages remains incomplete. The diversity and heterogeneous distribution of most angiosperm lineages is so extraordinary that it confounds our ability to identify simple drivers of diversification. Using machine learning in combination with phylogenetic modelling, we show that five separate abiotic and biotic variables significantly contribute to the diversification of Cactaceae. We reconstruct a comprehensive phylogeny, build a dataset of 39 abiotic and biotic variables, and predict the variables of central importance, while accounting for potential interactions between those variables. We use state-dependent diversification models to confirm that five abiotic and biotic variables shape diversification in the cactus family. Of highest importance are diurnal air temperature range, soil sand content and plant size, with lesser importance identified in isothermality and geographic range size. Interestingly, each of the estimated optimal conditions for abiotic variables were intermediate, indicating that cactus diversification is promoted by moderate, not extreme, climates. Our results reveal the potential primary drivers of cactus diversification, and the need to account for the complexity underlying the evolution of angiosperm lineages.
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Affiliation(s)
- Jamie B Thompson
- School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, UK.
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom.
| | | | - Georgia Keeling
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Marilyn Vásquez-Cruz
- Instituto Tecnológico Superior de Irapuato, Tecnológico Nacional de México, Irapuato, Guanajuato, México
| | - Nicholas K Priest
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
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152
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Selci M, Correggia M, Cordone A, Guida M, Quero GM, Piredda R, Vetriani C, Ramirez C, Lloyd KG, de Moor JM, Barry PH, Schrenk MO, Giovannelli D. Recreational hot springs as environmental reservoir of potential multidrug-resistant pathogens. ENVIRONMENTAL RESEARCH 2024:119841. [PMID: 39182755 DOI: 10.1016/j.envres.2024.119841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Affiliation(s)
- Matteo Selci
- Department of Biology, University of Naples Federico II, Naples, Italy; Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, USA
| | - Monica Correggia
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Angelina Cordone
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Marco Guida
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Grazia Marina Quero
- Institute for Marine Biological and Biotechnological Resources, National Research Council of Italy (CNR-IRBIM), Ancona, Italy
| | - Roberta Piredda
- Department of Veterinary Medicine - University of Bari Aldo Moro, Bari, Italy
| | - Costantino Vetriani
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, USA; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, USA
| | | | - Karen G Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN, USA
| | - J Maarten de Moor
- Observatorio Volcanológico y Sismológico de Costa Rica (OVSICORI), Universidad Nacional, Heredia, Costa Rica
| | - Peter H Barry
- Marine Chemistry & Geochemistry Department - Woods Hole Oceanographic Institution, MA, USA
| | - Matthew O Schrenk
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, USA
| | - Donato Giovannelli
- Department of Biology, University of Naples Federico II, Naples, Italy; Institute for Marine Biological and Biotechnological Resources, National Research Council of Italy (CNR-IRBIM), Ancona, Italy; Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, USA; Marine Chemistry & Geochemistry Department - Woods Hole Oceanographic Institution, MA, USA; Earth-Life Science Institute, Tokyo Institute for Technology, Tokyo, Japan.
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153
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Inoue S, Masaki Y, Nakagawa S, Yokoi S. An evolutionarily distinct Hmgn2 variant influences shape recognition in Medaka Fish. Commun Biol 2024; 7:973. [PMID: 39179658 PMCID: PMC11344144 DOI: 10.1038/s42003-024-06667-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 08/01/2024] [Indexed: 08/26/2024] Open
Abstract
Protein sequence diversification significantly impacts physiological traits. In this study, using medaka fish (Oryzias latipes), we identify a novel protein variant affecting shape preference behavior. Re-analysis of sequencing data reveals that LOC101156433 encodes a unique Hmgn2 variant with unusual subnuclear localization, clustered separately from the Hmgn2 clades of other species. Medaka mutants with this variant showed reduce telencephalic regions and altered shape preference, suggesting a link between protein sequence variation and behavioral changes. Additionally, this Hmgn2 variant is common in Acanthopterygii fishes, which are adapted to a variety of environments, indicating its potential evolutionary significance. Our findings highlight the relationship between amino acid sequence variation and the development of new molecular and behavioral adaptations, providing insights into the visual shape perception system in fish.
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Affiliation(s)
- Shuntaro Inoue
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Yume Masaki
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Saori Yokoi
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan.
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154
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Molina M, Oliveira G, Oliveira RRM, Nunes GL, Pires ES, Prous X, Ribeiro M, Vasconcelos S. Complete mitochondrial genomes of three vulnerable cave bat species and their phylogenetic relationships within the order Chiroptera. PLoS One 2024; 19:e0308741. [PMID: 39172941 PMCID: PMC11340975 DOI: 10.1371/journal.pone.0308741] [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: 02/06/2024] [Accepted: 07/30/2024] [Indexed: 08/24/2024] Open
Abstract
The IUCN Red List of Threatened Species contains 175 Brazilian bat species that are threatened by extinction in some degree. From this perspective, it is essential to expand the knowledge about the genetic diversity of vulnerable bats. Genomic sequencing can be useful to generate robust and informative genetic references, increasing resolution when analyzing relationships among populations, species, or higher taxonomic levels. In this study, we sequenced and characterized in detail the first complete mitochondrial genomes of Furipterus horrens, Lonchorhina aurita, and Natalus macrourus, and investigated their phylogenetic position based on amino acid sequences of protein-coding genes (PCGs). The mitogenomes of these species are 16,516, 16,697, and 16,668 bp in length, respectively, and each comprises 13 PCGs, 22 tRNA genes, two rRNA genes, and a putative control region (CR). In the three species, genes were arranged similarly to all other previously described bat mitogenomes, and nucleotide composition was also consistent with the reported range. The length and arrangement of rrnS and rrnL were also consistent with those of other bat species, showing a positive AT-skew and a negative GC-skew. Except for trnS1, for which we did not observe the DHU arm, all other tRNAs showed the cloverleaf secondary structure in the three species. In addition, the mitogenomes showed minor differences in start and stop codons, and in all PCGs, codons ending in adenine were more common compared to those ending in guanine. We found that PCGs of the three species use multiple codons to encode each amino acid, following the previously documented pattern. Furthermore, all PCGs are under purifying selection, with atp8 experiencing the most relaxed purifying selection. Considering the phylogenetic reconstruction, F. horrens was recovered as sister to Noctilio leporinus, L. aurita and Tonatia bidens shared a node within Phyllostomidae, and N. macrourus appeared as sister to Molossidae and Vespertilionidae.
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Affiliation(s)
- Michele Molina
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Guilherme Oliveira
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém, Pará, Brazil
| | | | | | | | - Xavier Prous
- Gerência de Espeleologia, Vale, Nova Lima, Minas Gerais, Brazil
| | - Mariane Ribeiro
- Gerência de Espeleologia, Vale, Nova Lima, Minas Gerais, Brazil
| | - Santelmo Vasconcelos
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa de Pós-Graduação em Biodiversidade e Evolução, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
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155
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Liu L, Chen A, Li Y, Mulder J, Heyn H, Xu X. Spatiotemporal omics for biology and medicine. Cell 2024; 187:4488-4519. [PMID: 39178830 DOI: 10.1016/j.cell.2024.07.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/05/2024] [Accepted: 07/23/2024] [Indexed: 08/26/2024]
Abstract
The completion of the Human Genome Project has provided a foundational blueprint for understanding human life. Nonetheless, understanding the intricate mechanisms through which our genetic blueprint is involved in disease or orchestrates development across temporal and spatial dimensions remains a profound scientific challenge. Recent breakthroughs in cellular omics technologies have paved new pathways for understanding the regulation of genomic elements and the relationship between gene expression, cellular functions, and cell fate determination. The advent of spatial omics technologies, encompassing both imaging and sequencing-based methodologies, has enabled a comprehensive understanding of biological processes from a cellular ecosystem perspective. This review offers an updated overview of how spatial omics has advanced our understanding of the translation of genetic information into cellular heterogeneity and tissue structural organization and their dynamic changes over time. It emphasizes the discovery of various biological phenomena, related to organ functionality, embryogenesis, species evolution, and the pathogenesis of diseases.
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Affiliation(s)
| | - Ao Chen
- BGI Research, Shenzhen 518083, China
| | | | - Jan Mulder
- Department of Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Xun Xu
- BGI Research, Hangzhou 310030, China; BGI Research, Shenzhen 518083, China.
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156
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Low GW, Pavlova A, Gan HM, Ko MC, Sadanandan KR, Lee YP, Amos JN, Austin L, Falk S, Dowling DK, Sunnucks P. Accelerated differentiation of neo-W nuclear-encoded mitochondrial genes between two climate-associated bird lineages signals potential co-evolution with mitogenomes. Heredity (Edinb) 2024:10.1038/s41437-024-00718-w. [PMID: 39174672 DOI: 10.1038/s41437-024-00718-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 08/11/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
There is considerable evidence for mitochondrial-nuclear co-adaptation as a key evolutionary driver. Hypotheses regarding the roles of sex-linkage have emphasized Z-linked nuclear genes with mitochondrial function (N-mt genes), whereas it remains contentious whether the perfect co-inheritance of W genes with mitogenomes could hinder or facilitate co-adaptation. Young (neo-) sex chromosomes that possess relatively many N-mt genes compared to older chromosomes provide unprecedented hypothesis-testing opportunities. Eastern Yellow Robin (EYR) lineages in coastal and inland habitats with different climates are diverged in mitogenomes, and in a ~ 15.4 Mb nuclear region enriched with N-mt genes, in contrast with otherwise-similar nuclear genomes. This nuclear region maps to passerine chromosome 1A, previously found to be neo-sex in the inland EYR genome. To compare sex-linked Chr1A-derived genes between lineages, we assembled and annotated the coastal EYR genome. We found that: (i) the coastal lineage shares a similar neo-sex system with the inland lineage, (ii) neo-W and neo-Z N-mt genes are not more diverged between lineages than are comparable non-N-mt genes, and showed little evidence for broad positive selection, (iii) however, W-linked N-mt genes are more diverged between lineages than are their Z-linked gametologs. The latter effect was ~7 times stronger for N-mt than non-N-mt genes, suggesting that W-linked N-mt genes might have diverged between lineages under environmental selection through co-evolution with mitogenomes. Finally, we identify a candidate gene driver for divergent selection, NDUFA12. Our data represent a rare example suggesting a possible role for W-associated mitochondrial-nuclear interactions in climate-associated adaptation and lineage differentiation.
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Affiliation(s)
- Gabriel Weijie Low
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany.
- National Parks Board, 1 Cluny Road, Singapore Botanical Gardens, Singapore, 259569, Singapore.
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia
- Patriot Biotech Sdn Bhd, 47500, Subang Jaya, Selangor, Malaysia
| | - Meng-Ching Ko
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany
| | - Keren R Sadanandan
- Evolution of Sensory and Physiological Systems, Max Planck Institute for Biological Intelligence, 82319, Seewiesen, Germany
| | - Yin Peng Lee
- Deakin Genomics Centre, Deakin University, Geelong, VIC 3220, Australia
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3220, Australia
| | - J Nevil Amos
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Arthur Rylah Institute for Environmental Research, Heidelberg, VIC 3084, Australia
| | - Lana Austin
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Stephanie Falk
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
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157
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Bierenbroodspot MJ, Pröschold T, Fürst-Jansen JMR, de Vries S, Irisarri I, Darienko T, de Vries J. Phylogeny and evolution of streptophyte algae. ANNALS OF BOTANY 2024; 134:385-400. [PMID: 38832756 PMCID: PMC11341676 DOI: 10.1093/aob/mcae091] [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: 03/02/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
The Streptophyta emerged about a billion years ago. Nowadays, this branch of the green lineage is most famous for one of its clades, the land plants (Embryophyta). Although Embryophyta make up the major share of species numbers in Streptophyta, there is a diversity of probably >5000 species of streptophyte algae that form a paraphyletic grade next to land plants. Here, we focus on the deep divergences that gave rise to the diversity of streptophytes, hence particularly on the streptophyte algae. Phylogenomic efforts have not only clarified the position of streptophyte algae relative to land plants, but recent efforts have also begun to unravel the relationships and major radiations within streptophyte algal diversity. We illustrate how new phylogenomic perspectives have changed our view on the evolutionary emergence of key traits, such as intricate signalling networks that are intertwined with multicellular growth and the chemodiverse hotbed from which they emerged. These traits are key for the biology of land plants but were bequeathed from their algal progenitors.
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Affiliation(s)
- Maaike J Bierenbroodspot
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Thomas Pröschold
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Research Department for Limnology, University of Innsbruck, Mondseestr. 9, 5310 Mondsee, Austria
| | - Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
| | - Iker Irisarri
- Section of Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Martin-Luther-King Platz 3, 20146 Hamburg, Germany
| | - Tatyana Darienko
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Department of Experimental Phycology and Culture Collection of Algae, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Nikolausberger Weg 18, 37073 Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goldschmidstraße 1, 37077 Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goldschmidtstraße 1, 37077 Goettingen, Germany
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158
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Fitzgibbons E, Lastovich J, Scott S, Groth N, Grusz AL, Busta L. Herbarium specimens as tools for exploring the evolution of fatty acid-derived natural products in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39171845 DOI: 10.1111/tpj.16989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/20/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
Plants synthesize natural products via lineage-specific offshoots of their core metabolic pathways, including fatty acid synthesis. Recent studies have shed light on new fatty acid-derived natural products and their biosynthetic pathways in disparate plant species. Inspired by this progress, we set out to develop tools for exploring the evolution of fatty-acid derived products. We sampled multiple species from all major clades of euphyllophytes, including ferns, gymnosperms, and angiosperms (monocots and eudicots), and we show that the compositional profiles (though not necessarily the total amounts) of fatty-acid derived surface waxes from preserved plant specimens are consistent with those obtained from freshly collected tissue in a semi-quantitative and sometimes quantitative manner. We then sampled herbarium specimens representing 57 monocot species to assess the phylogenetic distribution and evolution, of two fatty acid-derived natural products found in that clade: beta-diketones and alkylresorcinols. These chemical data, combined with analyses of 26 monocot genomes, revealed a co-occurrence (though not necessarily a causal relationship) between whole genome duplication and the evolution of diketone synthases from an ancestral alkylresorcinol synthase-like polyketide synthase. Limitations of using herbarium specimen wax profiles as proxies for those of fresh tissue seem likely to include effects from loss of epicuticular wax crystals, effects from preservation techniques, and variation in wax chemical profiles due to genotype or environment. Nevertheless, this work reinforces the widespread utility of herbarium specimens for studying leaf surface waxes (and possibly other chemical classes) and reveals some of the evolutionary history of fatty acid-derived natural products within monocots.
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Affiliation(s)
- Emma Fitzgibbons
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Jacob Lastovich
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Samuel Scott
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Nicole Groth
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| | - Amanda L Grusz
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Lucas Busta
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota, USA
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159
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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.
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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.
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160
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Eleiwa A, Nadal J, Vilaprinyo E, Marin-Sanguino A, Sorribas A, Basallo O, Lucido A, Richart C, Pena RN, Ros-Freixedes R, Usie A, Alves R. Hybrid assembly and comparative genomics unveil insights into the evolution and biology of the red-legged partridge. Sci Rep 2024; 14:19531. [PMID: 39174643 PMCID: PMC11341709 DOI: 10.1038/s41598-024-70018-0] [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: 06/13/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
The red-legged partridge Alectoris rufa plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation and management. Here we sequence, assemble, and annotate a highly contiguous and nearly complete version of its genome. This assembly encompasses 96.9% of the avian genes flagged as essential in the BUSCO aves_odb10 dataset. Moreover, we pinpointed RNA and protein-coding genes, 95% of which had functional annotations. Notably, we observed significant chromosome rearrangements in comparison to quail (Coturnix japonica) and chicken (Gallus gallus). In addition, a comparative phylogenetic analysis of these genomes suggests that A. rufa and C. japonica diverged roughly 20 million years ago and that their common ancestor diverged from G. gallus 35 million years ago. Our assembly represents a significant advancement towards a complete reference genome for A. rufa, facilitating comparative avian genomics, and providing a valuable resource for future research and conservation efforts for the red-legged partridge.
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Affiliation(s)
| | | | - Ester Vilaprinyo
- Institut de Recerca Biomédica (IRBLleida), Lleida, Spain
- Universitat de Lleida (UdL), Lleida, Spain
| | - Alberto Marin-Sanguino
- Institut de Recerca Biomédica (IRBLleida), Lleida, Spain
- Universitat de Lleida (UdL), Lleida, Spain
| | - Albert Sorribas
- Institut de Recerca Biomédica (IRBLleida), Lleida, Spain
- Universitat de Lleida (UdL), Lleida, Spain
| | - Oriol Basallo
- Institut de Recerca Biomédica (IRBLleida), Lleida, Spain
- Universitat de Lleida (UdL), Lleida, Spain
| | - Abel Lucido
- Institut de Recerca Biomédica (IRBLleida), Lleida, Spain
- Universitat de Lleida (UdL), Lleida, Spain
| | | | - Ramona N Pena
- Universitat de Lleida (UdL), Lleida, Spain
- AGROTECNIO CERCA Center, Lleida, Spain
| | - Roger Ros-Freixedes
- Universitat de Lleida (UdL), Lleida, Spain
- AGROTECNIO CERCA Center, Lleida, Spain
| | - Anabel Usie
- Universitat de Lleida (UdL), Lleida, Spain
- Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Beja, Portugal
- MED-Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento & CHANGE-Global Change and Sustainability Institute, Évora, Portugal
| | - Rui Alves
- Institut de Recerca Biomédica (IRBLleida), Lleida, Spain.
- Universitat de Lleida (UdL), Lleida, Spain.
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161
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Sanchez-Godoy FD, Martinez-Guzmán JRE, Hernandez-Castro R, Martinez-Hernandez F, Urquiza-Bravo O, Rivas N, Alejandre-Aguilar R, Palma-Irizarry M, Hernandez-Velasco X. Acanthocephaliasis by Plagiorhynchus sp. (Acanthocephala:Plagiorhynchidae) associated with necrotic enteritis in quetzals (Pharomachrus mocinno) maintained in captivity. Parasitol Int 2024; 103:102954. [PMID: 39181313 DOI: 10.1016/j.parint.2024.102954] [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: 05/27/2024] [Revised: 08/12/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
The present report describes a case of acanthocephaliasis associated with necrotic enteritis in quetzals (Pharomachrus mocinno). Three juvenile quetzals exhibited depression, anorexia, ruffled feathers, and sudden death. They were submitted to the laboratory for examination. The birds had hatched and lived in captivity in an aviary in Mexico. Gross lesions observed were hemorrhagic, fibrinoid necrotic enteritis, with acanthocephalans adhered to the intestinal mucosa. The specimens were identified by parasitology, electronic microscopy, and molecular biology as Plagiorhynchus (Prosthorhynchus) sp. Lesions compatible with necrotic enteritis were also confirmed by isolation and genotyping of Clostridium perfringens type E. This is the first report of Plagiorhynchus (Prosthorhynchus) sp. in quetzals in captivity in Mexico. The findings in this manuscript suggest that this parasite could be a predisposing factor for necrotic enteritis as well as a risk component in the breeding programs and survival of this avian species in captivity.
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Affiliation(s)
- F D Sanchez-Godoy
- Department of Avian Medicine and Zootechnics, College of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico (UNAM), Av. Universidad 3000, UNAM, C.U, 04510 Mexico City, Mexico
| | | | - R Hernandez-Castro
- Department of Pathogenic Agent Ecology, General Hospital "Dr. Manuel Gea González", 14080 Mexico City, Mexico
| | - F Martinez-Hernandez
- Department of Pathogenic Agent Ecology, General Hospital "Dr. Manuel Gea González", 14080 Mexico City, Mexico
| | - O Urquiza-Bravo
- Department of Avian Medicine and Zootechnics, College of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico (UNAM), Av. Universidad 3000, UNAM, C.U, 04510 Mexico City, Mexico
| | - N Rivas
- Medical Entomology Laboratory, Department of Parasitology, National College of Biological Sciences, National Polytechnic Institute (IPN), Prol. Carpio y Plan de Ayala S/N Col. Casco de Santo Tomas, 11340 Mexico City, Mexico
| | - R Alejandre-Aguilar
- Medical Entomology Laboratory, Department of Parasitology, National College of Biological Sciences, National Polytechnic Institute (IPN), Prol. Carpio y Plan de Ayala S/N Col. Casco de Santo Tomas, 11340 Mexico City, Mexico
| | - M Palma-Irizarry
- Aquarium and Zoological Park Association of Mexico C. S. (AZCARM), Goethe 16 piso 3 Col. Anzures, 11590 Mexico City, Mexico
| | - X Hernandez-Velasco
- Department of Avian Medicine and Zootechnics, College of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico (UNAM), Av. Universidad 3000, UNAM, C.U, 04510 Mexico City, Mexico.
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162
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Ikeda S, Inoue Y, Imada Y. Unveiled species diversity of moss-feeding mites (Stigmaeidae: Eustigmaeus): a research on their distribution, habitat, and host plant use in Japan. EXPERIMENTAL & APPLIED ACAROLOGY 2024:10.1007/s10493-024-00954-z. [PMID: 39172294 DOI: 10.1007/s10493-024-00954-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024]
Abstract
The genus Eustigmaeus Berlese, 1910 represents the unique phytophagous group within the superfamily Raphignathoidea. Four species within this genus have been known to inhabit mosses and feed on them as larvae, nymphs, and adults. However, the interactions with mosses have remained poorly understood. In order to reveal the diversity and host-plant use of the moss-feeding species, we conducted an extensive field study in Japan. This study revealed an array of moss-feeding species inhabiting various moss species, with 10 morphologically distinctive species newly documented in Japan. Through DNA barcoding based on cytochrome c oxidase subunit I (COI) sequences, these morphospecies were recovered as distinct entities. Notably, the host-plant use of four species was elucidated. Among these, Eustigmaeus sp. 9 exhibited polyphagy, while three species (Eustigmaeus spp. 1-3) demonstrated varying degrees of host specificity, each using moss species from the Hypnales, Philonotis, and Dicranidae, respectively. While a few moss-feeding species were frequently found in the same geographic area, more than one species rarely co-occurred within the same moss colonies. Eustigmaeus offers a unique study system, with its diverse moss-feeding species and indications of specific host plant use. Consequently, the moss-feeding Eustigmaeus serves as a valuable model for exploring the macroevolutionary patterns underlying diversification in moss-feeding arthropods.
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Affiliation(s)
- Satsuki Ikeda
- Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan.
- Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-Cho, Sakyo, Kyoto, 606-8502, Japan.
| | - Yuya Inoue
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
| | - Yume Imada
- Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime, 790-8577, Japan
- Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-Cho, Sakyo, Kyoto, 606-8502, Japan
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163
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Pereira AC, Pérez de Val B, Cunha MV. Phylogenetic analysis of Mycobacterium caprae highlights past and present epidemiological links at the Iberian Peninsula scale. Microbes Infect 2024:105405. [PMID: 39173900 DOI: 10.1016/j.micinf.2024.105405] [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: 05/17/2024] [Revised: 07/23/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024]
Abstract
Mycobacterium caprae is linked to regular outbreaks of tuberculosis (TB) in geographically distinct caprine populations across Europe, namely Iberia where this ecovar may represent up to 8% of total animal TB cases, circulating in multi-host communities encompassing domestic ruminants and wildlife, representing severe financial losses. It also causes zoonotic human disease. In this work, we undertake the first phylodynamic and phylogeographic analyses of M. caprae to reconstruct past demography and transmission chains. First, we examined the worldwide diversity of M. caprae based on 229 unpublished and publicly available whole genome sequences, depicting Asian, Central-East European, and Iberian clades. Phylodynamic analyses of the SB0157 Iberian clade (n = 81) positioned the most recent common ancestor in goats, around 100 years ago. Host transition events were common between goats, wild boars, and humans, possibly resulting from mixed farming, extensive management, and close human proximity, facilitating interspecific transmission. We show the spread of M. caprae on multiple scales due to local and transnational animal trade, supporting historical and sustained cross-species transmission in Iberia. We highlight the value of intersecting genomic epidemiology with molecular ecology to resolve epidemiological links and show that an EU-official eradication program in goats is utterly needed to control TB in a multi-host scenario.
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Affiliation(s)
- André C Pereira
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Bernat Pérez de Val
- Unitat Mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Catalonia, Spain; IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la UAB, Bellaterra, Catalonia, Spain; WOAH collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Catalonia, Spain
| | - Mónica V Cunha
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; National Institute for Agrarian and Veterinary Research (INIAV IP), Av. da República, Quinta do Marquês, Edifício Principal, 2780-157 Oeiras, Portugal.
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164
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Thiiru JW, Langat S, Mulwa F, Cinkovich S, Koka H, Yalwala S, Khamadi S, Onguso J, Odemba N, Ngere F, Johnson J, Egbo T, Garges E, Ojwang E, Eyase F. Characterization of West Nile virus Koutango lineage from phlebotomine sandflies in Kenya. PLoS One 2024; 19:e0301956. [PMID: 39173002 PMCID: PMC11341046 DOI: 10.1371/journal.pone.0301956] [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: 03/25/2024] [Accepted: 07/16/2024] [Indexed: 08/24/2024] Open
Abstract
The West Nile virus (WNV), primarily transmitted by mosquitoes, is one of the most widespread flaviviruses globally, with past outbreaks occurring in the USA and Europe. Recent studies in parts of Africa, including Kenya, have identified the West Nile virus Koutango lineage (WN-KOUTV) among phlebotomine sandfly populations, however, our understanding of this virus remains limited. This study aimed to characterize WN-KOUTV from phlebotomine sandflies. Sandflies were sampled between 12th -16th March 2021 and 16th -20th March 2023 from six villages each in Baringo and Isiolo Counties, using CDC light traps. Female sandflies were taxonomically identified and pooled based on genus and site of collection. Virus isolation was performed in Vero cells. Viral genomes were determined using next-generation sequencing. Phylogenetic and molecular clock analyses were done to decipher the virus's evolutionary relationships. Comparative analyses of amino acid sequences were performed to determine variations. Protein modeling in Pymol was conducted to elucidate variations in key protein regions. Evolutionary pressure analysis investigated the selection pressures on the virus. In vitro experiments were done to investigate the virus growth kinetics in mammalian Vero E6 and mosquito C6/36 cells. We report the isolation of WN-KOUTV from Salabani in Baringo and Aremet in Isiolo, Kenya. The isolated WN-KOUTVs clustered with previously identified WN-KOUTV strains. Comparative analysis revealed a unique amino acid at NS5 653. The WN-KOUTV lineage as a whole is under purifying selective pressure, with diversifying pressure acting at site NS3 267. The current WN-KOUTV replicated in Vero E6 and C6/36 cells comparable to West Nile virus Lineage 1a, isolated from mosquitoes. Subsequent isolations of WN-KOUTV in phlebotomine sandflies suggest potential vectors, however, vector competence studies would confirm this. Replication in mammalian and insect cell lines suggests there may exist a vector/host relationship. We speculate the close genetic relationship of WN-KOUTV strains from East and West Africa may potentially be enabled by bird migratory routes between the two regions. If proven, this could point to a potential future pandemic pathway for this virus.
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Affiliation(s)
- Jane Wambui Thiiru
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Solomon Langat
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Francis Mulwa
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Stephanie Cinkovich
- Global Emerging Infections Surveillance Branch, United States Armed Forces Health Surveillance Division, Silver Spring, Maryland, United States of America
| | - Hellen Koka
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Santos Yalwala
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Samoel Khamadi
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Justus Onguso
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Nicholas Odemba
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Francis Ngere
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Jaree Johnson
- United States Armed Forces Pest Management Board, Silver Spring, Maryland, United States of America
| | - Timothy Egbo
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Eric Garges
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Elly Ojwang
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Fredrick Eyase
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate-Africa, Nairobi, Kenya
- Centre for Virus Research, Kenya Medical Research Institute, Nairobi, Kenya
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165
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Wang S, Wu L, Zhu Q, Wu J, Tang S, Zhao Y, Cheng Y, Zhang D, Qiao G, Zhang R, Lei F. Trait Variation and Spatiotemporal Dynamics across Avian Secondary Contact Zones. BIOLOGY 2024; 13:643. [PMID: 39194581 DOI: 10.3390/biology13080643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024]
Abstract
A secondary contact zone (SCZ) is an area where incipient species or divergent populations may meet, mate, and hybridize. Due to the diverse patterns of interspecific hybridization, SCZs function as field labs for illuminating the on-going evolutionary processes of speciation and the establishment of reproductive isolation. Interspecific hybridization is widely present in avian populations, making them an ideal system for SCZ studies. This review exhaustively summarizes the variations in unique traits within avian SCZs (vocalization, plumage, beak, and migratory traits) and the various movement patterns of SCZs observed in previous publications. It also highlights several potential future research directions in the genomic era, such as the relationship between phenotypic and genomic differentiation in SCZs, the genomic basis of trait differentiation, SCZs shared by multiple species, and accurate predictive models for forecasting future movements under climate change and human disturbances. This review aims to provide a more comprehensive understanding of speciation processes and offers a theoretical foundation for species conservation.
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Affiliation(s)
- Shangyu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianghui Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahao Wu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Shiyu Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifang Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalin Cheng
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Runzhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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166
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Döcker J, Linz S, Wicke K. Bounding the Softwired Parsimony Score of a Phylogenetic Network. Bull Math Biol 2024; 86:121. [PMID: 39174812 PMCID: PMC11341636 DOI: 10.1007/s11538-024-01350-9] [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: 05/29/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024]
Abstract
In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction of phylogenetic networks remains challenging and computationally expensive due to their intricate structural properties. For example, the small parsimony problem that is solvable in polynomial time for phylogenetic trees, becomes NP-hard on phylogenetic networks under softwired and parental parsimony, even for a single binary character and structurally constrained networks. To calculate the parsimony score of a phylogenetic network N, these two parsimony notions consider different exponential-size sets of phylogenetic trees that can be extracted from N and infer the minimum parsimony score over all trees in the set. In this paper, we ask: What is the maximum difference between the parsimony score of any phylogenetic tree that is contained in the set of considered trees and a phylogenetic tree whose parsimony score equates to the parsimony score of N? Given a gap-free sequence alignment of multi-state characters and a rooted binary level-k phylogenetic network, we use the novel concept of an informative blob to show that this difference is bounded by k + 1 times the softwired parsimony score of N. In particular, the difference is independent of the alignment length and the number of character states. We show that an analogous bound can be obtained for the softwired parsimony score of semi-directed networks, while under parental parsimony on the other hand, such a bound does not hold.
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Affiliation(s)
- Janosch Döcker
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Simone Linz
- School of Computer Science, University of Auckland, Auckland, New Zealand.
| | - Kristina Wicke
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, USA
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167
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Adamo M, Fochi V, Mucciarelli M. Complete plastome sequence of Narcissus pseudonarcissus L., one of the most iconic European plants. Mitochondrial DNA B Resour 2024; 9:1132-1136. [PMID: 39183765 PMCID: PMC11342812 DOI: 10.1080/23802359.2024.2392758] [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: 05/31/2024] [Accepted: 08/09/2024] [Indexed: 08/27/2024] Open
Abstract
Narcissus pseudonarcissus L. is one of the most iconic plants of the European flora. It is a species of great horticultural interest, but also an endangered and protected plant in the wild as a consequence of loss of natural habitats. Complete plastid genome was assembled from next-generation sequencing data obtaining a circular genome of 160,008 bp long assembly. It comprises a pair of inverted repeat regions, a large single-copy region (108,400 bp), and a small single-copy region (16,434 bp). It encodes 131 genes, including 87 protein coding genes, 37 tRNA genes and seven rRNA genes. Phylogeny showed the strict relationship between N. pseudonarcissus and Narcissus poeticus L. The complete plastome will provide a useful genetic resource for future conservation programmes, phylogenetic studies and horticultural applications.
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Affiliation(s)
- Martino Adamo
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Valeria Fochi
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Marco Mucciarelli
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
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168
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Song J, Li Z, Zhou L, Chen X, Sew WQG, Herranz H, Ye Z, Olsen JV, Li Y, Nygaard M, Christensen K, Tong X, Bohr VA, Rasmussen LJ, Dai F. FOXO-regulated OSER1 reduces oxidative stress and extends lifespan in multiple species. Nat Commun 2024; 15:7144. [PMID: 39164296 PMCID: PMC11336091 DOI: 10.1038/s41467-024-51542-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 08/12/2024] [Indexed: 08/22/2024] Open
Abstract
FOXO transcription factors modulate aging-related pathways and influence longevity in multiple species, but the transcriptional targets that mediate these effects remain largely unknown. Here, we identify an evolutionarily conserved FOXO target gene, Oxidative stress-responsive serine-rich protein 1 (OSER1), whose overexpression extends lifespan in silkworms, nematodes, and flies, while its depletion correspondingly shortens lifespan. In flies, overexpression of OSER1 increases resistance to oxidative stress, starvation, and heat shock, while OSER1-depleted flies are more vulnerable to these stressors. In silkworms, hydrogen peroxide both induces and is scavenged by OSER1 in vitro and in vivo. Knockdown of OSER1 in Caenorhabditis elegans leads to increased ROS production and shorter lifespan, mitochondrial fragmentation, decreased ATP production, and altered transcription of mitochondrial genes. Human proteomic analysis suggests that OSER1 plays roles in oxidative stress response, cellular senescence, and reproduction, which is consistent with the data and suggests that OSER1 could play a role in fertility in silkworms and nematodes. Human studies demonstrate that polymorphic variants in OSER1 are associated with human longevity. In summary, OSER1 is an evolutionarily conserved FOXO-regulated protein that improves resistance to oxidative stress, maintains mitochondrial functional integrity, and increases lifespan in multiple species. Additional studies will clarify the role of OSER1 as a critical effector of healthy aging.
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Affiliation(s)
- Jiangbo Song
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China
| | - Zhiquan Li
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Lei Zhou
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China
| | - Xin Chen
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China
| | - Wei Qi Guinevere Sew
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Héctor Herranz
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Zilu Ye
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200, Copenhagen, Denmark
- Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China
| | - Jesper Velgaard Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Yuan Li
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Marianne Nygaard
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
| | - Xiaoling Tong
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China
| | - Vilhelm A Bohr
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
- Section on DNA repair, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark.
| | - Fangyin Dai
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China.
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169
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Varsani A, Krupovic M. 2024 Smacoviridae family update: 59 new species in seven genera. Arch Virol 2024; 169:184. [PMID: 39167240 DOI: 10.1007/s00705-024-06116-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Family Smacoviridae (order Cremevirales, class Arfiviricetes, phylum Cressdnaviricota) comprises viruses with small circular genomes of ~2300-3000 nt in length that encode at least two proteins, the rolling-circle replication associated protein (Rep) and the capsid protein (CP). Smacovirids have been discovered in fecal samples of various animals and display remarkable sequence diversity. Here, we provide an overview of the genomic properties of classified smacovirids and report on the latest taxonomy update in the family Smacoviridae. The family has been expanded by 59 new species in the genera Porprismacovirus (n = 25), Inpeasmacovirus (n = 1), Felismacovirus (n = 22), Drosmacovirus (n = 4), Dragsmacovirus (n = 2), Bovismacovirus (n = 4), and Bonzesmacovirus (n = 1) and currently includes 12 genera with 143 species officially recognized by the International Committee on Taxonomy of Viruses (ICTV).
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ, 85287-5001, USA.
- Structural Biology Research Unit, Department of Integrative, Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 25 rue du Dr Roux, 75015, Paris, France.
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Ceres K, Zehr JD, Murrell C, Millet JK, Sun Q, McQueary HC, Horton A, Cazer C, Sams K, Reboul G, Andreopoulos WB, Mitchell PK, Anderson R, Franklin-Guild R, Cronk BD, Stanhope BJ, Burbick CR, Wolking R, Peak L, Zhang Y, McDowall R, Krishnamurthy A, Slavic D, Sekhon PK, Tyson GH, Ceric O, Stanhope MJ, Goodman LB. Evolutionary genomic analyses of canine E. coli infections identify a relic capsular locus associated with resistance to multiple classes of antimicrobials. Appl Environ Microbiol 2024; 90:e0035424. [PMID: 39012166 PMCID: PMC11337803 DOI: 10.1128/aem.00354-24] [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: 02/28/2024] [Accepted: 06/08/2024] [Indexed: 07/17/2024] Open
Abstract
Infections caused by antimicrobial-resistant Escherichia coli are the leading cause of death attributed to antimicrobial resistance (AMR) worldwide, and the known AMR mechanisms involve a range of functional proteins. Here, we employed a pan-genome wide association study (GWAS) approach on over 1,000 E. coli isolates from sick dogs collected across the US and Canada and identified a strong statistical association (empirical P < 0.01) of AMR, involving a range of antibiotics to a group 1 capsular (CPS) gene cluster. This cluster included genes under relaxed selection pressure, had several loci missing, and had pseudogenes for other key loci. Furthermore, this cluster is widespread in E. coli and Klebsiella clinical isolates across multiple host species. Earlier studies demonstrated that the octameric CPS polysaccharide export protein Wza can transmit macrolide antibiotics into the E. coli periplasm. We suggest that the CPS in question, and its highly divergent Wza, functions as an antibiotic trap, preventing antimicrobial penetration. We also highlight the high diversity of lineages circulating in dogs across all regions studied, the overlap with human lineages, and regional prevalence of resistance to multiple antimicrobial classes. IMPORTANCE Much of the human genomic epidemiology data available for E. coli mechanism discovery studies has been heavily biased toward shiga-toxin producing strains from humans and livestock. E. coli occupies many niches and produces a wide variety of other significant pathotypes, including some implicated in chronic disease. We hypothesized that since dogs tend to share similar strains with their owners and are treated with similar antibiotics, their pathogenic isolates will harbor unexplored AMR mechanisms of importance to humans as well as animals. By comparing over 1,000 genomes with in vitro antimicrobial susceptibility data from sick dogs across the US and Canada, we identified a strong multidrug resistance association with an operon that appears to have once conferred a type 1 capsule production system.
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Affiliation(s)
| | | | | | - Jean K. Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, Paris, France
| | - Qi Sun
- Cornell University, Ithaca, New York, USA
| | | | | | | | - Kelly Sams
- Cornell University, Ithaca, New York, USA
| | | | | | | | | | | | | | | | - Claire R. Burbick
- Washington Animal Disease Diagnostic Laboratory, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Rebecca Wolking
- Washington Animal Disease Diagnostic Laboratory, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Laura Peak
- Louisiana Animal Disease Diagnostic Laboratory, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Yan Zhang
- Ohio Department of Agriculture Animal Disease Diagnostic Laboratory, Reynoldsburg, Ohio, USA
| | - Rebeccah McDowall
- University of Guelph, Animal Health Laboratory, Guelph, Ontario, Canada
| | | | - Durda Slavic
- University of Guelph, Animal Health Laboratory, Guelph, Ontario, Canada
| | | | - Gregory H. Tyson
- US Food and Drug Administration, Veterinary Laboratory Investigation and Response Network, Laurel, Maryland, USA
| | - Olgica Ceric
- US Food and Drug Administration, Veterinary Laboratory Investigation and Response Network, Laurel, Maryland, USA
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171
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Kim DH, Kim MS, Lee JS, Yoon DS, Lee JS. Genome-wide identification of 769 G protein-coupled receptor (GPCR) genes from the marine medaka Oryzias melastigma. MARINE POLLUTION BULLETIN 2024; 207:116868. [PMID: 39173477 DOI: 10.1016/j.marpolbul.2024.116868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/14/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024]
Abstract
The marine medaka Oryzias melastigma is a useful fish model for marine and estuarine ecotoxicology studies and can be applied to field-based population genomics because of its distribution in Asian estuaries and other coastal areas. We identified 769 full-length G protein-coupled receptor genes in the O. melastigma genome and classified them into five distinct classes. A phylogenetic comparison of GPCR genes in O. melastigma to humans and two other small fish species revealed a high-level orthological relationship. Purinergic and chemokine receptors were highly differentiated in humans whereas significant differentiation of chemosensory receptors was evident in fish species. Our results suggest that the GPCR gene families among the species used in this study exhibit evidence of sporadic evolutionary processes. These results may help improve our understanding of the advanced repertoires of GPCR and expand our knowledge of physiological mechanisms of fish in response to various environmental stimuli.
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Affiliation(s)
- Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jin-Sol Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Deok-Seo Yoon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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172
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Blom P, Smith GJ, van Kessel MAHJ, Koch H, Lücker S. Comprehensive evaluation of primer pairs targeting the ammonia monooxygenase subunit A gene of complete ammonia-oxidizing Nitrospira. Microbiol Spectr 2024:e0051624. [PMID: 39166864 DOI: 10.1128/spectrum.00516-24] [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: 02/26/2024] [Accepted: 07/26/2024] [Indexed: 08/23/2024] Open
Abstract
Since the discovery of complete ammonia oxidizers (comammox) within the genus Nitrospira, their distribution and abundance across habitats have been intensively studied to better understand their ecological significance. Many primers targeting their ammonia monooxygenase subunit A gene (amoA) have been designed to detect and quantify comammox bacteria and to describe their community structure. We identified 38 published primers, but only few had high coverage and specificity for all known comammox Nitrospira or one of the two described subclades. For each target group, we comprehensively evaluated selected primer pairs using in silico analyses, endpoint PCRs, qPCRs, and amplicon sequencing on samples from various environments. Endpoint PCRs and qPCRs showed that the most commonly used primer pairs (comaA-244F/659R, comaB-244F/659R, and Ntsp-amoA162F/359R) produced several bands, which likely inflated quantifications via qPCR. In contrast, the recently published primer combinations CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R resulted mostly in a single band. Furthermore, amplicon sequencing demonstrated that these primer combinations also captured the highest richness of comammox Nitrospira. Taken together, our results indicate that few existing comammox amoA primer combinations have both high specificity and coverage and that the choice of these high-specificity and high-coverage primer pairs substantially impacts the accurate detection, quantification, and community description of comammox bacteria. We, therefore, recommend using the CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R primer pairs.IMPORTANCEBacteria that can fully convert ammonia via nitrite to nitrate, the complete ammonia oxidizers (comammox), were recently discovered and are found in many natural and engineered environments. PCR-based tools to study their abundance and diversity were rapidly developed, resulting in a plethora of primers available, many of which are widely used. The presence of comammox bacteria in an environment can, however, only be correctly determined if the used primers detect all members of this group while not detecting any other guilds. This study assesses the coverage and specificity of existing primers targeting comammox bacteria using both computational and standard molecular techniques, revealing large differences in their performance. The uniform usage of well-performing primers across studies could aid in generating comparable and generalizable data to better understand the importance of comammox bacteria in the environment.
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Affiliation(s)
- Pieter Blom
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Garrett J Smith
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Maartje A H J van Kessel
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Hanna Koch
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln an der Donau, Austria
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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173
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Li J, Zhan Z, Li Y, Sun Y, Zhou T, Xu K. Chromosome-level genome assembly of a deep-sea Venus flytrap sea anemone sheds light upon adaptations to an extremely oligotrophic environment. Mol Ecol 2024:e17504. [PMID: 39166453 DOI: 10.1111/mec.17504] [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: 01/12/2024] [Revised: 06/29/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024]
Abstract
The Venus flytrap sea anemone Actinoscyphia liui inhabits the nutrient-limited deep ocean in the tropical western Pacific. Compared with most other sea anemones, it has undergone a distinct modification of body shape similar to that of the botanic flytrap. However, the molecular mechanism by which such a peculiar sea anemone adapts to a deep-sea oligotrophic environment is unknown. Here, we report the chromosomal-level genome of A. liui constructed from PacBio and Hi-C data. The assembled genome is 522 Mb in size and exhibits a continuous scaffold N50 of 58.4 Mb. Different from most other sea anemones, which typically possess 14-18 chromosomes per haplotype, A. liui has only 11. The reduced number of chromosomes is associated with chromosome fusion, which likely represents an adaptive strategy to economize energy in oligotrophic deep-sea environments. Comparative analysis with other deep-sea sea anemones revealed adaptive evolution in genes related to cellular autophagy (TMBIM6, SESN1, SCOCB and RPTOR) and mitochondrial energy metabolism (MDH1B and KAD2), which may aid in A. liui coping with severe food scarcity. Meanwhile, the genome has undergone at least two rounds of expansion in gene families associated with fast synaptic transmission, facilitating rapid responses to water currents and prey. Positive selection was detected on putative phosphorylation sites of muscle contraction-related proteins, possibly further improving feeding efficiency. Overall, the present study provides insights into the molecular adaptation to deep-sea oligotrophic environments and sheds light upon potential effects of a novel morphology on the evolution of Cnidaria.
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Affiliation(s)
- Junyuan Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- College of Agriculture and Bioengineering, Taizhou Vocational College of Science and Technology, Taizhou, China
| | - Zifeng Zhan
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yang Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Yanan Sun
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Tong Zhou
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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174
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Liu JX, Guo C, Ma PF, Zhou MY, Luo YH, Zhu GF, Xu ZC, Milne RI, Vorontsova MS, Li DZ. The origin and morphological character evolution of the paleotropical woody bamboos. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 39166548 DOI: 10.1111/jipb.13751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 08/23/2024]
Abstract
The woody bamboos (Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos (PWB), making it ideal to investigate the factors underlying morphological evolution in woody bamboos. However, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters. We generated a robust and time-calibrated phylogeny of PWB using single nucleotide polymorphisms retrieved from optimized double digest restriction site associated DNA sequencing, and explored the evolutionary trends of habit, inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography. We inferred that the PWB started to diversify across the Oligocene-Miocene boundary and formed four major clades, that is, Melocanninae, Racemobambosinae s.l. (comprising Dinochloinae, Greslanlinae, Racemobambosinae s.str. and Temburongiinae), Hickeliinae and Bambusinae s.l. (comprising Bambusinae s.str. plus Holttumochloinae). The ancestor of PWB was reconstructed as having erect habit, indeterminate inflorescence and basic caryopsis. The characters including climbing/scrambling habit, determinate inflorescence, and nucoid/bacoid caryopsis have since undergone multiple changes and reversals during the diversification of PWB. The evolution of all three traits was correlated with, and hence likely influenced by, aspects of climate, topography, and soil, with climate factors most strongly correlated with morphological traits, and soil factors least so. However, topography had more influence than climate or soil on the evolution of erect habit, whereas both factors had greater effect on the evolution of bacoid caryopsis than did soil. Our results provide novel insights into morphological diversity and adaptive evolution in bamboos for future ecological and evolutionary research.
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Affiliation(s)
- Jing-Xia Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Cen Guo
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ya-Huang Luo
- State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Guang-Fu Zhu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zu-Chang Xu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| | | | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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175
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Walt HK, Bronzato-Badial A, Maedo SE, Hinton JA, King JG, Pietri JE, Hoffmann FG. Under the radar: Differential responses of bed bugs to an entomopathogen, environmental bacteria, and a human pathogen. J Invertebr Pathol 2024:108182. [PMID: 39178984 DOI: 10.1016/j.jip.2024.108182] [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: 05/08/2024] [Revised: 08/14/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
Bed bugs (Hemiptera: Cimicidae) are a widely distributed, obligately blood-feeding insect, but they have never been linked to pathogen transmission in humans. Most other hematophagous insects that frequently bite humans transmit pathogens, and it is unclear why bed bugs do not. One hypothesis is that bed bugs have evolved a highly robust immune system because their mating system, traumatic insemination, exposes females to consistent wounding and bacterial infections. Although this has been proposed, very little is known about the bed bug immune system and how bed bugs respond to microbial challenges introduced by wounding. Similarly, there is little known about how the bed bug immune system responds to human pathogens. Understanding the bed bug immune system could give insight to why bed bugs appear not to transmit disease and under what circumstances they could, while also facilitating biological control efforts involving microbes. To investigate the transcriptomic response of bed bugs to immune challenges, we exposed female bed bugs to three bacterial challenges. 1.) Pseudomonas fluorescens, an entomopathogen known to have harmful effects to bed bugs, 2.) bacteria cultured from a bed bug enclosure (99.9 % Bacillus spp.), likely encountered during traumatic insemination, and 3.) Borrelia duttoni, a human vector-borne pathogen that causes relapsing fever. We compared the transcriptomes of infected bed bugs with uninfected matched controls in a pairwise fashion, focusing on immune-related genes. We found many known antimicrobial effector genes upregulated in response to P. fluorescens and traumatic insemination-associated bacteria, but interestingly, not in response to B. duttoni. In the differentially expressed genes that were shared between experiments, we found significant overlap in the P. fluorescens treatment and the traumatic insemination bacteria treatment, and between the P. fluorescens and B. duttoni treatments, but not between the traumatic insemination bacteria treatment and the B. duttoni treatment. Additionally, we show that the bed bug prolixicin antimicrobial peptide gene underwent lineage-specific gene duplication. Finally, we identify previously overlooked candidates for future studies of immune function in bed bugs, including a peroxidase-like gene, many putative cuticle-associated genes, a laccase-like gene, and a mucin-like gene. By taking a comprehensive transcriptomic approach, our study is an important step in understanding how bed bugs respond to diverse immune challenges.
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Affiliation(s)
- Hunter K Walt
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, USA
| | - Aline Bronzato-Badial
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, USA
| | - Sophie E Maedo
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, USA
| | - Joseph A Hinton
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, USA
| | - Jonas G King
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, USA
| | - Jose E Pietri
- Sanford School of Medicine, Division of Basic Biomedical Sciences, University of South Dakota, Vermillion, SD, USA.
| | - Federico G Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS, USA.
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176
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Bai Y, Xiao J, Moming A, Fu J, Wang J, Zhou M, Chen C, Shi J, Zhang J, Fan Z, Tang S, Wang B, Deng F, Shen S. Identification and characterization of new Siberian subtype of tick-borne encephalitis virus isolates revealed genetic variations of the Chinese strains. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024:105660. [PMID: 39179014 DOI: 10.1016/j.meegid.2024.105660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
Tick-borne encephalitis virus (TBEV) is a pathogen that causes febrile infectious diseases and neurological damage to humans. TBEVs are prevalent from Europe to Far Eastern Asia, including Northeastern China. The understanding of TBEV phylogeny in China has been limited owing to insufficient genomic data on Chinese TBEV strains. Here, six TBEV strains were isolated from ticks collected in Inner Mongolia. The transmission electron microscopy revealed spherical particles with an enveloped structure of 50-60 nm in diameter. Phylogenetic analysis showed that, two strains were classified as the Siberian subtype, while the remaining four were identified as the Far Eastern subtype. Migration analyses based on TBEV ORF and envelope (E) protein sequences revealed that Chinese TBEV strains were migrated from Russia and/or Kazakhstan into China. Hulun Buir and Mudanjiang, the northeastern region of China, are considered hotspots with multiple import and export routes of Chinese TBEV strains. These results promote the understanding of TBEV genetic variations and phylogeny in China and suggest the importance of improving investigation of TBEV prevalence, which would instrumental for vaccine design strategies and better preparation for controlling TBEV infection in humans.
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Affiliation(s)
- Yuan Bai
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China.
| | - Jian Xiao
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Abulimiti Moming
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Jie Fu
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Jun Wang
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Min Zhou
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Chuizhe Chen
- Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), No.19 Xiuhua Road, Xiuying District, Haikou 570311, Hainan Province, China
| | - Junming Shi
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Jingyuan Zhang
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Zhaojun Fan
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Shuang Tang
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Bo Wang
- Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), No.19 Xiuhua Road, Xiuying District, Haikou 570311, Hainan Province, China.
| | - Fei Deng
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China.
| | - Shu Shen
- State Key Laboratory of Virology and National Virus Resource Centre, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China; Hubei Jiangxia Laboratory, 430200 Wuhan, China.
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177
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Largest genomic tree of life of flowering plants to date includes almost 8,000 genera. Nature 2024:10.1038/d41586-024-02631-y. [PMID: 39169130 DOI: 10.1038/d41586-024-02631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
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178
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Newman SA. Form, function, mind: What doesn't compute (and what might). Biochem Biophys Res Commun 2024; 721:150141. [PMID: 38781663 DOI: 10.1016/j.bbrc.2024.150141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/07/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing animal (metazoan) tissues, a non-computational modality, but cell differentiation, which utilizes chromatin-based revisable memory banks and program-like function-calling, via the developmental gene co-expression system unique to the metazoans, has a quasi-computational basis. Multi-attractor dynamical models are argued to be misapplied to global properties of development, and it is suggested that along with computationalism, classic forms of dynamicism are similarly unsuitable to accounting for cognitive phenomena. Proposals are made for treating brains and other nervous tissues as novel forms of excitable matter with inherent properties which enable the intensification of cell-based basal cognition capabilities present throughout the tree of life. Finally, some connections are drawn between the viewpoint described here and active inference models of cognition, such as the Free Energy Principle.
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179
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Glover AN, Sousa VC, Ridenbaugh RD, Sim SB, Geib SM, Linnen CR. Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow. Mol Ecol 2024:e17509. [PMID: 39165007 DOI: 10.1111/mec.17509] [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: 05/03/2024] [Revised: 07/16/2024] [Accepted: 08/02/2024] [Indexed: 08/22/2024]
Abstract
Understanding the genetics of adaptation and speciation is critical for a complete picture of how biodiversity is generated and maintained. Heterogeneous genomic differentiation between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection and reduced recombination rates. Disentangling the roles of each of these non-exclusive processes in shaping genome-wide patterns of divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we combine whole-genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of differentiation for a sister-species pair of haplodiploid pine sawflies, Neodiprion lecontei and Neodiprion pinetum. We find genome-wide correlations between genome features and summary statistics are consistent with pervasive linked selection, with patterns of diversity and divergence more consistently predicted by exon density and recombination rate than the neutral mutation rate (approximated by dS). We also find that both global and local patterns of FST, dXY and π provide strong support for recurrent selection as the primary selective process shaping variation across pine sawfly genomes, with some contribution from balancing selection and lineage-specific linked selection. Because inheritance patterns for haplodiploid genomes are analogous to those of sex chromosomes, we hypothesize that haplodiploids may be especially prone to recurrent selection, even if gene flow occurred throughout divergence. Overall, our study helps fill an important taxonomic gap in the genomic landscape literature and contributes to our understanding of the processes that shape genome-wide patterns of genetic variation.
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Affiliation(s)
- Ashleigh N Glover
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Vitor C Sousa
- Department of Animal Biology, CE3C - Center for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Lisbon, Lisboa, Portugal
| | - Ryan D Ridenbaugh
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Sheina B Sim
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, Hawaii, USA
| | - Scott M Geib
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, Hawaii, USA
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Franco-Mena D, De la Riva I, Vega-Yánez MA, Székely P, Amador L, Batallas D, Reyes-Puig JP, Cisneros-Heredia DF, Venegas-Valencia K, Galeano SP, Culebras J, Guayasamin JM. Simplifying the Centrolene buckleyi complex (Amphibia: Anura: Centrolenidae): a taxonomic review and description of two new species. PeerJ 2024; 12:e17712. [PMID: 39193520 PMCID: PMC11348905 DOI: 10.7717/peerj.17712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 06/18/2024] [Indexed: 08/29/2024] Open
Abstract
Centrolenidae is a Neotropical family widely distributed in Central and South America, with its species richness concentrated in the tropical Andes. Several taxonomic problems have been identified within this family, mostly related to species with broad geographic distributions. In this study, we assessed and redefined the species boundaries of the Centrolene buckleyi species complex, and formally described two new species from the Andes of Ecuador. These new taxa are recognized by a combination of morphometric, osteological, acoustic, and genetic data. Following IUCN criteria, we propose that the two new species should to be considered as Endangered (EN), mainly because of their small distributions and habitat loss. The C. buckleyi complex provides insights into the biogeography of closely related Andean species. As in other glassfrogs, speciation in Centrolene seems to be mediated by the linearity of the Andes, where gene flow can be restricted by topography and, also, local extinctions.
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Affiliation(s)
- Daniela Franco-Mena
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Ignacio De la Riva
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain
| | - Mateo A. Vega-Yánez
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
- Unidad de Investigación, Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador
| | - Paul Székely
- Museo de Zoología, Universidad Técnica Particular de Loja, Loja, Ecuador
- Laboratorio de Ecología Tropical y Servicios Ecosistémicos (EcoSs-Lab), Facultad de Ciencias Exactas y Naturales, Departamento de Ciencias Biológicas y Agropecuarias, Universidad Técnica Particular de Loja, Loja, Ecuador
- Research Center of the Department of Natural Sciences, Faculty of Natural and Agricultural Sciences, Ovidius University Constanţa, Constanța, Romania
| | - Luis Amador
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM, USA
- Instituto BIOSFERA, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Diego Batallas
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
- Departamento de Biodiversidad, Ecología y Evolución de la Facultad de Ciencias Biológicas, Programa de Doctorado en Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan P. Reyes-Puig
- Unidad de Investigación, Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador
- Fundación Oscar Efrén Reyes, Departamento de Ambiente, Fundación EcoMinga, Baños, Ecuador
| | - Diego F. Cisneros-Heredia
- Unidad de Investigación, Instituto Nacional de Biodiversidad (INABIO), Quito, Ecuador
- Laboratorio de Zoología Terrestre & Museo de Zoología, Instituto de Biodiversidad Tropical IBIOTROP, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Khristian Venegas-Valencia
- Centro de Colecciones y Gestión de Especies, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Villa de Leyva, Boyacá, Colombia
| | - Sandra P. Galeano
- Centro de Colecciones y Gestión de Especies, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Villa de Leyva, Boyacá, Colombia
| | - Jaime Culebras
- Photo Wildlife Tours, Quito, Ecuador
- Fundación Cóndor Andino, Quito, Ecuador
| | - Juan M. Guayasamin
- Laboratorio de Biología Evolutiva, Instituto BIOSFERA, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
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181
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Fayos M, Sacristán C, Velarde R, Ewbank AC, Sastre N, de la Torre A, Iglesias I, Gonzalez B, Sacristán I. Detection and characterization of hemotropic Mycoplasmas in Iberian wolves (Canis lupus signatus) of Cantabria, Spain. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 124:105659. [PMID: 39173940 DOI: 10.1016/j.meegid.2024.105659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 08/13/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024]
Abstract
Hemoplasmas (hemotropic mycoplasmas) are uncultivable wall-less bacteria able to infect mammalian erythrocytes. Hemoplasmas can cause anemia, especially in immunocompromised hosts, predisposing to secondary infections and even leading to death. Between 2017 and 2023, spleen samples of 131 wild Iberian wolves (Canis lupus signatus) of Cantabria (Spain) were screened for Mycoplasma spp. using a real-time PCR able to amplify a 360 bp fragment of the 16S rRNA gene and confirmed by direct Sanger sequencing. Additional conventional PCRs were performed to screen for coinfections by different Mycoplasma species and to discriminate between Mycoplasma haemocanis/haemofelis (Mhc/Mhf). Overall, 24/131 (18.3%) animals were PCR-positive. Biological and environmental factors potentially promoting hemoplasma infection in this species were analyzed. Two different hemoplasma species were detected: Mhc/Mhf (18/131; 13.7%) and Candidatus Mycoplasma haematoparvum (CMhp) (3/131; 2.3%), each with one nucleotide sequence type (ntST); three other sequences were not classified. No Mhc/Mhf and CMhp coinfection were observed. The 12 Mhc/Mhf suitable for ribonuclease P RNA sequencing were confirmed as Mhc. Mhc ntST was 100% identical to a Mhc sequence previously obtained in domestic dogs (Canis lupus familiaris), and in wild Iberian wolves of northwestern Spain (Asturias and Galicia) at a similar prevalence to the one found herein, suggesting a high Mhc genetic homogeneity in this wild population. CMhp ntST was 100% identical to CMhp sequences from domestic dogs. To our knowledge, this is the first description of CMhp in the Iberian wolf. The high genetic similarity observed in Mhc and CMhp sequences, as well as their high similarity with domestic dog sequences, suggest its recent introduction, a high level of intraspecific transmission within the wild wolf population, and likely, interspecific transmission between wolves and domestic dogs.
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Affiliation(s)
- Manena Fayos
- Centro de Recuperación de Fauna Silvestre de Cantabria, Obregón 39690, Spain; Escuela de Doctorado de la UNED, Madrid 28015, Spain.
| | - Carlos Sacristán
- Centro de Investigación en Sanidad Animal, INIA-CSIC, Carretera Algete el Casar s/n, Valdeolmos, Madrid 28130, Spain
| | - Roser Velarde
- Wildlife Ecology and Health Group & Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona 08193, Spain
| | - Ana Carolina Ewbank
- Centro de Investigación en Sanidad Animal, INIA-CSIC, Carretera Algete el Casar s/n, Valdeolmos, Madrid 28130, Spain.
| | - Natalia Sastre
- Servei Veterinari de Genètica Molecular (SVGM), Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona 08193, Spain
| | - Ana de la Torre
- Wildlife Ecology and Health Group & Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona 08193, Spain
| | - Irene Iglesias
- Wildlife Ecology and Health Group & Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona 08193, Spain
| | - Beatriz Gonzalez
- Asistencia Técnica de TRAGSA Para la Dirección General de Montes y Biodiversidad de la Consejería de Desarrollo Rural, Ganadería, Pesca y Alimentación del Gobierno de Cantabria, C/ Albert Einstein, 2 Parque Científico y Tecnológico de Cantabria, Santander 39011, Spain
| | - Irene Sacristán
- Centro de Investigación en Sanidad Animal, INIA-CSIC, Carretera Algete el Casar s/n, Valdeolmos, Madrid 28130, Spain
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182
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Alexander N, de Flamingh A, Cosentino BJ, Schooley RL. Phylogenetic assessment within a species complex of a subterranean rodent (Geomys bursarius) with conservation implications for isolated subspecies. J Hered 2024; 115:565-574. [PMID: 38982643 PMCID: PMC11334213 DOI: 10.1093/jhered/esae035] [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: 02/19/2024] [Accepted: 07/08/2024] [Indexed: 07/11/2024] Open
Abstract
Range contraction and expansion from glaciation have led to genetic divergence that may be particularly pronounced in fossorial species with low dispersal. The plains pocket gopher (Geomys bursarius) is a fossorial species that ranges widely across North America but has a poorly understood phylogeny. We used mitogenomes (14,996 base pairs) from 56 individuals across seven subspecies, plus two outgroup species, to assess genetic divergence from minimum spanning trees, measure genetic distances, and infer phylogenetic trees using BEAST. We found G. b. wisconsinensis was monophyletic with recent divergence. Further assessment is needed for G. b. major because it was paraphyletic and exhibited inconsistent groupings with other clades. Importantly, we identified G. b. illinoensis as being genetically distinct and monophyletic likely due to a unique colonization event eastward across the Mississippi River. Because G. b. illinoensis faces continued pressures from niche reduction and habitat loss, we recommend that G. b. illinoensis be considered an evolutionary significant unit warranting conservation actions to promote connectivity and restore suitable habitat. Such conservation efforts should benefit other grassland species including those originating from clades west of the Mississippi River that may also be evolutionary significant units.
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Affiliation(s)
- Nathan Alexander
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, United States
| | - Alida de Flamingh
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States
| | - Bradley J Cosentino
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, United States
| | - Robert L Schooley
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, United States
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183
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Wu Y, Linan AG, Hoban S, Hipp AL, Ricklefs RE. Divergent ecological selection maintains species boundaries despite gene flow in a rare endemic tree, Quercus acerifolia (maple-leaf oak). J Hered 2024; 115:575-587. [PMID: 38881254 DOI: 10.1093/jhered/esae033] [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: 10/06/2023] [Accepted: 06/11/2024] [Indexed: 06/18/2024] Open
Abstract
Strong gene flow from outcrossing relatives tends to blur species boundaries, while divergent ecological selection can counteract gene flow. To better understand how these two forces affect the maintenance of species boundaries, we focused on a species complex including a rare species, maple-leaf oak (Quercus acerifolia), which is found in only four disjunct ridges in Arkansas. Its limited range and geographic proximity to co-occurring close relatives create the possibility for genetic swamping. In this study, we gathered genome-wide single nucleotide polymorphisms (SNPs) using restriction-site-associated DNA sequencing (RADseq) from 190 samples of Q. acerifolia and three of its close relatives, Q. shumardii, Q. buckleyi, and Q. rubra. We found that Q. shumardii and Q. acerifolia are reciprocally monophyletic with low support, suggesting incomplete lineage sorting, introgression between Q. shumardii and Q. acerifolia, or both. Analyses that model allele distributions demonstrate that admixture contributes strongly to this pattern. Populations of Q. acerifolia experience gene flow from Q. shumardii and Q. rubra, but we found evidence that divergent selection is likely maintaining species boundaries: 1) ex situ collections of Q. acerifolia have a higher proportion of hybrids compared to the mature trees of the wild populations, suggesting ecological selection against hybrids at the seed/seedling stage; 2) ecological traits co-vary with genomic composition; and 3) Q. acerifolia shows genetic differentiation at loci hypothesized to influence tolerance of radiation, drought, and high temperature. Our findings strongly suggest that in maple-leaf oak, selection results in higher divergence at regions of the genome despite gene flow from close relatives.
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Affiliation(s)
- Yingtong Wu
- Biology Department, University of Missouri-St. Louis, St. Louis, MO, United States
- Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, St. Louis, MO, United States
| | - Alexander G Linan
- Center for Conservation and Sustainable Development, Missouri Botanical Garden, St. Louis, MO, United States
| | - Sean Hoban
- Center for Tree Science, The Morton Arboretum, Lisle, IL, United States
| | - Andrew L Hipp
- Center for Tree Science, The Morton Arboretum, Lisle, IL, United States
- The Field Museum, Integrative Research Center, Chicago, IL, United States
| | - Robert E Ricklefs
- Biology Department, University of Missouri-St. Louis, St. Louis, MO, United States
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184
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Daru BH. Predicting undetected native vascular plant diversity at a global scale. Proc Natl Acad Sci U S A 2024; 121:e2319989121. [PMID: 39133854 PMCID: PMC11348117 DOI: 10.1073/pnas.2319989121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 06/28/2024] [Indexed: 08/29/2024] Open
Abstract
Vascular plants are diverse and a major component of terrestrial ecosystems, yet their geographic distributions remain incomplete. Here, I present a global database of vascular plant distributions by integrating species distribution models calibrated to species' dispersal ability and natural habitats to predict native range maps for 201,681 vascular plant species into unsurveyed areas. Using these maps, I uncover unique patterns of native vascular plant diversity, endemism, and phylogenetic diversity revealing hotspots in underdocumented biodiversity-rich regions. These hotspots, based on detailed species-level maps, show a pronounced latitudinal gradient, strongly supporting the theory of increasing diversity toward the equator. I trained random forest models to extrapolate diversity patterns under unbiased global sampling and identify overlaps with modeled estimations but unveiled cryptic hotspots that were not captured by modeled estimations. Only 29% to 36% of extrapolated plant hotspots are inside protected areas, leaving more than 60% outside and vulnerable. However, the unprotected hotspots harbor species with unique attributes that make them good candidates for conservation prioritization.
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185
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Roberts JR, Bernstein JM, Austin CC, Hains T, Mata J, Kieras M, Pirro S, Ruane S. Whole snake genomes from eighteen families of snakes (Serpentes: Caenophidia) and their applications to systematics. J Hered 2024; 115:487-497. [PMID: 38722259 DOI: 10.1093/jhered/esae026] [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: 03/08/2024] [Accepted: 05/08/2024] [Indexed: 08/21/2024] Open
Abstract
We present genome assemblies for 18 snake species representing 18 families (Serpentes: Caenophidia): Acrochordus granulatus, Aparallactus werneri, Boaedon fuliginosus, Calamaria suluensis, Cerberus rynchops, Grayia smithii, Imantodes cenchoa, Mimophis mahfalensis, Oxyrhabdium leporinum, Pareas carinatus, Psammodynastes pulverulentus, Pseudoxenodon macrops, Pseudoxyrhopus heterurus, Sibynophis collaris, Stegonotus admiraltiensis, Toxicocalamus goodenoughensis, Trimeresurus albolabris, and Tropidonophis doriae. From these new genome assemblies, we extracted thousands of loci commonly used in systematic and phylogenomic studies on snakes, including target-capture datasets composed of ultraconserved elements (UCEs) and anchored hybrid enriched loci (AHEs), as well as traditional Sanger loci. Phylogenies inferred from the two target-capture loci datasets were identical with each other and strongly congruent with previously published snake phylogenies. To show the additional utility of these non-model genomes for investigative evolutionary research, we mined the genome assemblies of two New Guinea island endemics in our dataset (S. admiraltiensis and T. doriae) for the ATP1a3 gene, a thoroughly researched indicator of resistance to toad toxin ingestion by squamates. We find that both these snakes possess the genotype for toad toxin resistance despite their endemism to New Guinea, a region absent of any toads until the human-mediated introduction of Cane Toads in the 1930s. These species possess identical substitutions that suggest the same bufotoxin resistance as their Australian congenerics (Stegonotus australis and Tropidonophis mairii) which forage on invasive Cane Toads. Herein, we show the utility of short-read high-coverage genomes, as well as improving the deficit of available squamate genomes with associated voucher specimens.
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Affiliation(s)
- Jackson R Roberts
- Division of Zoology, Sternberg Museum of Natural History, Fort Hays State University, Hays, KS 67601, United States
- Division of Herpetology, Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, United States
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States
| | - Justin M Bernstein
- Center for Genomics, University of Kansas, Lawrence, KS 66045, United States
- Department of Biology, University of Texas at Arlington, Arlington, TX 76010, United States
| | - Christopher C Austin
- Division of Herpetology, Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, United States
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States
| | - Taylor Hains
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, United States
- Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, Chicago, IL 60637, United States
| | - Joshua Mata
- Amphibian and Reptile Collection, The Field Museum of Natural History, Chicago, IL 60605, United States
| | - Michael Kieras
- Iridian Genomes, Inc., Bethesda, MD 20817, United States
| | - Stacy Pirro
- Iridian Genomes, Inc., Bethesda, MD 20817, United States
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center, The Field Museum of Natural History, Chicago, IL 60637, United States
- Amphibian and Reptile Collection, The Field Museum of Natural History, Chicago, IL 60605, United States
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186
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Machado AB, Simões RO, Maldonado A, Santos MAJ, Luque JL. Morphological and Molecular Analyses of Aponurus laguncula Looss, 1907 (Digenea: Lecithasteridae) Parasitic in Atlantic Spadefish Chaetodipterus faber (Broussonet, 1782) (Acanthuriformes: Ephippidae) from Brazilian Coastal Zone. Acta Parasitol 2024:10.1007/s11686-024-00878-z. [PMID: 39162922 DOI: 10.1007/s11686-024-00878-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/30/2024] [Indexed: 08/21/2024]
Abstract
OBJECTIVES An integrative taxonomic description of Aponurus laguncula (Lecithasteridae), a digenean parasitic species of Chaetodipterus faber (Acanthuriformes) from Brazilian Southeast, is provided. Morphological techniques, as whole mounted slides, histology and scanning electron microscopy, and molecular analyses supported that integrative description. METHODS Fifteen digenean specimens were stained in hydrochloric carmine and mounted on permanent slides. Two specimens were stained in hematoxylin and eosin following histological routine processing. Four parasites were dehydrated through a graded ethanol series, critical point dried with carbon dioxide and coated with gold to scanning electron microscopy analysis. Sequence of the large ribosomal subunit (28S rDNA) gene was generated and used to construct a phylogeny based on maximum likelihood and Bayesian inference analyses. RESULTS Morphological description and morphometric data obtained in present study were in accordance with previous studies of the species. Use of another morphological techniques, as scanning electron microscopy and histology, corroborated the observed features of whole mounted slides. Also, they provided a better observation of previous reported characteristics and new features reporting, such as an elongated hermaphroditic duct, a smooth tegument and cells that compose the prostatic gland. The molecular sequence obtained in the present study formed a robust clade with available sequences of species of Aponurus. CONCLUSIONS The integrative taxonomic approach successfully combined morphological observations, including both previously reported features and new descriptions from histological and electron microscopy analyses, with molecular data to identify these specimens as A. laguncula. Moreover, the detailed characterization of structures, such as the gonads in A. laguncula, that would be challenging to analyze using a single technique, was possible. Further molecular studies with less conserved genetic markers should be conducted to understand phylogenetic relationships between Aponurus species.
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Affiliation(s)
- A B Machado
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - R O Simões
- Departamento de Parasitologia Animal, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - A Maldonado
- Laboratório de Biologia e Parasitologia de Mamíferos Silvestres Reservatórios, Fundação Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - M A J Santos
- Departamento de Biologia Animal, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil
| | - J L Luque
- Departamento de Parasitologia Animal, Universidade Federal Rural do Rio de Janeiro, Seropédica, Brazil.
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187
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Cavalcante KS, Rodrigues BL, Posada-López L, Peniche T, Saraiva JF, Galardo AKR, Galati EAB. Description of Trichophoromyia jariensis, a new species of phlebotomine sand fly (Diptera: Psychodidae) from the eastern Amazon. JOURNAL OF MEDICAL ENTOMOLOGY 2024:tjae095. [PMID: 39159937 DOI: 10.1093/jme/tjae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/26/2024] [Accepted: 07/18/2024] [Indexed: 08/21/2024]
Abstract
A new sand fly species, Trichophoromyia jariensis n. sp. Cavalcante, Rodrigues, & Galati, from the state of Amapá, Brazil, is described based on both male and female morphology and cytochrome c oxidase subunit I DNA barcodes. The DNA barcoding analysis clearly associated males and females of this new species.
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Affiliation(s)
- Keison S Cavalcante
- Laboratório de Entomologia Médica (LABENMED), Instituto de Pesquisas Científicas e Tecnológicas do Amapá (IEPA), Macapá, Brazil
- Faculdade de Saúde Pública, Programa de Pós-graduação em Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
| | - Bruno L Rodrigues
- Faculdade de Saúde Pública, Programa de Pós-graduação em Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
| | - Laura Posada-López
- Faculdade de Saúde Pública, Programa de Pós-graduação em Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
- PECET (Programa de Estudio y Control de Enfermedades Tropicales), Facultad de Medicina, Universidad de Antioquia UdeA, Calle, Medellín, Colombia
| | - Taires Peniche
- Laboratório de Entomologia Médica (LABENMED), Instituto de Pesquisas Científicas e Tecnológicas do Amapá (IEPA), Macapá, Brazil
- Faculdade de Saúde Pública, Programa de Pós-graduação em Saúde Pública, Universidade de São Paulo, São Paulo, Brazil
| | - José F Saraiva
- Laboratório de Entomologia Médica (LABENMED), Instituto de Pesquisas Científicas e Tecnológicas do Amapá (IEPA), Macapá, Brazil
| | - Allan Kardec R Galardo
- Laboratório de Entomologia Médica (LABENMED), Instituto de Pesquisas Científicas e Tecnológicas do Amapá (IEPA), Macapá, Brazil
| | - Eunice A B Galati
- Departamento de Epidemiologia, Universidade de São Paulo São Paulo, Brazil
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188
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Weary TE, Mehta KPM, Goldberg TL. Novel Gammapapillomavirus type in the nasal cavity of a wild red colobus (Piliocolobus tephrosceles). Access Microbiol 2024; 6:000866.v3. [PMID: 39165252 PMCID: PMC11334581 DOI: 10.1099/acmi.0.000866.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 08/01/2024] [Indexed: 08/22/2024] Open
Abstract
Papillomaviruses (PVs) are double-stranded, circular, epitheliotropic DNA viruses causing benign warts (papillomas) or inducing dysplasia that can progress to cancer. Although they have been identified in all vertebrate taxa, most classified types are human PVs (HPVs); relatively little is known about PVs in other species. Here we characterize a novel Gammapapillomavirus type, PtepPV1, from a nasal swab of a wild red colobus (Piliocolobus tephrosceles) in Kibale National Park, Uganda. The virus has a genome of 6576 bases, encoding the seven canonical early (E) ORFs (E6, E7, E1, E2, E4, E1^E4 and E8^E2) and two late (L) ORFs (L1 and L2) of the gammapapillomaviruses, and is 81.0% similar to HPV-mSK_118, detected in a cutaneous wart from an immunocompromised human patient, in the L1 gene at the amino acid level. Alphapapillomaviruses (genus Alphapapillomavirus) cause anogenital carcinomas such as cervical cancer and have been described previously in several nonhuman primates. However, the first gammapapillomavirus (genus Gammapapillomavirus), which cause transient cutaneous infections, was not described until 2019 in a healthy rhesus macaque (Macaca mulatta) genital swab. The new virus from red colobus, PtepPV1, has many genomic features encoded by high-risk oncogenic PVs, such as the E7 gene LXSXE and CXXC motifs, suggesting potential for pRb and zinc-finger binding, respectively. To our knowledge, PtepPV1 is also the first reported nonhuman primate PV found in the nasal cavity. PtepPV1 expands the known host range, geographical distribution, tissue tropism and biological characteristics of nonhuman primate PVs.
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Affiliation(s)
- Taylor E. Weary
- Department of Pathobiological Sciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, WI, USA
| | - Kavi P. M. Mehta
- Department of Comparative Biosciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, WI, USA
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison School of Veterinary Medicine, Madison, WI, USA
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Jonika MM, Wilhoit KT, Chin M, Arekere A, Blackmon H. Drift drives the evolution of chromosome number II: The impact of range size on genome evolution in Carnivora. J Hered 2024; 115:524-531. [PMID: 38712909 PMCID: PMC11334210 DOI: 10.1093/jhered/esae025] [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: 06/30/2023] [Revised: 01/03/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024] Open
Abstract
Chromosome number is a fundamental genomic trait that is often the first recorded characteristic of a genome. Across large clades, a common pattern emerges: many or even most lineages exhibit relative stasis, while a handful of lineages or species exhibit striking variation. Despite recent developments in comparative methods, most of this heterogeneity is still poorly understood. It is essential to understand why some lineages have rapid rates of chromosome number evolution, as it can impact a variety of other traits. Previous research suggests that biased female meiotic drive may shape rates of karyotype evolution in some mammals. However, Carnivora exhibits variation that this female meiotic drive model cannot explain. We hypothesize that variation in effective population size may underlie rate variation in Carnivora. To test this hypothesis, we estimated rates of fusions and fissions while accounting for range size, which we use as a proxy for effective population size. We reason fusions and fissions are deleterious or underdominant and that only in lineages with small range sizes will these changes be able to fix due to genetic drift. In this study, we find that the rates of fusions and fissions are elevated in taxa with small range sizes relative to those with large range sizes. Based on these findings, we conclude that 1) naturally occurring structural mutations that change chromosome number are underdominant or mildly deleterious, and 2) when population sizes are small, structural rearrangements may play an important role in speciation and reduction in gene flow among populations.
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Affiliation(s)
- Michelle M Jonika
- Department of Biology, Texas A&M University, College Station, TX, United States
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
| | - Kayla T Wilhoit
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Maximos Chin
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Abhimanyu Arekere
- Department of Biology, Texas A&M University, College Station, TX, United States
- Department of Biomedical Engineering, University of Texas, Austin, TX, United States
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX, United States
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
- Ecology and Evolutionary Biology Interdepartmental Program, Texas A&M University, College Station, TX, United States
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190
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Cheng X, Jiang L, Zhao X, Wang S, Li J, Luo C, Zhang G. Synergism of endophytic microbiota and plants promotes the removal of polycyclic aromatic hydrocarbons from the Alfalfa rhizosphere. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135513. [PMID: 39178770 DOI: 10.1016/j.jhazmat.2024.135513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/12/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024]
Abstract
Endophytic bacteria can promote plant growth and accelerate pollutant degradation. However, it is unclear whether endophytic consortia (Consortium_E) can stabilize colonisation and degradation. We inoculated Consortium_E into the rhizosphere to enhance endophytic bacteria survival and promote pollutant degradation. Rhizosphere-inoculated Consortium_E enhanced polycyclic aromatic hydrocarbon (PAH) degradation rates by 11.5-13.1 % compared with sole bioaugmentation and plant treatments. Stable-isotope-probing (SIP) showed that the rhizosphere-inoculated Consortium_E had the largest number of degraders (8 amplicon sequence variants). Furthermore, only microbes from Consortium_E were identified among the degraders in bioaugmentation treatments, indicating that directly participated in phenanthrene metabolism. Interestingly, Consortium_E reshaped the community structure of degraders without significantly altering the rhizosphere community structure, and strengthened the core position of degraders in the network, facilitating close interactions between degraders and non-degraders in the rhizosphere, which were crucial for ensuring stable functionality. The synergistic effect between plants and Consortium_E significantly enhanced the upregulation of aromatic hydrocarbon degradation and auxiliary degradation pathways in the rhizosphere. These pathways showed a non-significant increasing trend in the uninoculated rhizosphere compared with the control, indicating that Consortium_E primarily promotes rhizosphere effects. Our results explore the Consortium_E bioaugmentation mechanism, providing a theoretical basis for the ecological restoration of contaminated soils.
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Affiliation(s)
- Xianghui Cheng
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Longfei Jiang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Xuan Zhao
- College of Architecture and Civil Engineering, Kunming University, Kunming 650214, China
| | - Shuang Wang
- School of Materials and Environmental Engineering, Chengdu Technological University, Chengdu 610000, China
| | - Jibing Li
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Chunling Luo
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China.
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry and Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100039, China
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191
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André BLO, Montoya QV, Martiarena MJS, Rodrigues A. Culture-dependent methods revel the diversity of endophytic fungi of Psidium cattleianum leaves (Myrtales: Myrtaceae). Braz J Microbiol 2024:10.1007/s42770-024-01481-0. [PMID: 39155340 DOI: 10.1007/s42770-024-01481-0] [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: 04/15/2024] [Accepted: 08/03/2024] [Indexed: 08/20/2024] Open
Abstract
Endophytic fungi are a diverse group of microorganisms that reside within plant tissues and play a crucial ecological role in the development of their hosts. Psidium cattleianum (Myrtales: Myrtaceae: 'Cattley guava') is a Brazilian native species with economic potential due to the diverse applications of its fruits, wood, and essential oils. Despite their significance, the diversity of endophytic fungi associated with P. cattleianum remains unexplored. Here, we investigated the diversity of endophytic fungi in the leaves of this plant using cultivation-dependent isolation methods, analysis of the macroscopic characters of the isolates, and phylogenetic analyses employing the ITS barcode marker. A total of 396 isolates, classified into 25 fungal taxa, were obtained, namely, Alternaria, Aspergillus, Cladosporium, Colletotrichum, Coprinellus, Coriolopsis, Diaporthe, Induratia, Mycosphaerella, Muyocoprom, Myrmecridium, Neofusicoccum, Pantospora, Paracamarosporium, Parapallidocercospora, Paraphaeosphaeria, Penicillium, Perenniporia, Phaeophleospora, Phyllosticta, Pseudofusicoccum, Talaromyces, Xylaria, Sordariomycetes, and Xylariomycetes. Our findings reveal a significant diversity of fungi associated with P. cattleianum leaves; however, our study suggests an even greater diversity of fungi associated with this plant species. Interestingly, although P. cattleianum shares endophytic fungi with other plants in the Myrtaceae family, this plant species harbors a unique fungal community. This distinction is evidenced by certain fungal genera and seven potentially new phylogenetic species, isolated in this study.
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Affiliation(s)
- Bianca Lariza Oliveira André
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Quimi Vidaurre Montoya
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Maria Jesus Sutta Martiarena
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil
| | - Andre Rodrigues
- Department of General and Applied Biology, Institute of Biosciences, São Paulo State University (UNESP), Avenida 24-A, n. 1515, Bela Vista, Rio Claro, SP, 13506-900, Brazil.
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192
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Baron-Ortiz DA, Rodriguez-Cruz FA, Santos-Amaya OF. First Record of Conotrachelus quadrilineatus Champion, 1904 (Coleoptera: Curculionidae: Molytinae) Damaging Beans in South America. NEOTROPICAL ENTOMOLOGY 2024:10.1007/s13744-024-01187-w. [PMID: 39158772 DOI: 10.1007/s13744-024-01187-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 07/06/2024] [Indexed: 08/20/2024]
Abstract
Common bean (Phaseolus vulgaris L.) is the most important legume used for direct human consumption in Latin America, with an increasing expansion of cultivated areas in recent years. Here, we report the first occurrence of Conotrachelus quadrilineatus Champion, 1904 (Coleoptera: Curculionidae: Molytinae) feeding on bean in South America. Larvae and adults of C. quadrilineatus were observed during the first half of 2022, severely affecting the plantations of 20 bean farmers in the municipality of Garcia-Rovira, Santander Colombia. It is necessary to describe and quantify the damage of C. quadrilineatus in bean crops, as well as to study its bioecology.
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Affiliation(s)
- Daniel A Baron-Ortiz
- Federación Nacional de Cultivadores de Cereales, Leguminosas y Soya, Fenalce, Yopal, Colombia
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193
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Lin H, Song W, Ma D, Yang C, Yao Y, Liu R, Hao L, Wu D, Wang S, Jiang J, Xiong J, Ma R, Xiao J, Zhuang Z. Screening and Characterization of a New Iflavirus Virus in the Fruit Tree Pest Pyrops candelaria. INSECTS 2024; 15:625. [PMID: 39194829 DOI: 10.3390/insects15080625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 08/29/2024]
Abstract
Pyrops candelaria is one of the common pests of fruit trees, but the research on the pathogenic microorganisms it may carry is very limited. Therefore, it is essential to reveal the pathogenic microbes it carries and their potential hazards. This study found a new virus from the transcriptome of P. candelaria, which was first reported in P. candelaria and named PyCaV (Pyrops candelaria associated virus). RACE and bioinformatics assay revealed that the full length of PyCaV is 10,855 bp with the polyA tail, containing a single open-reading frame (ORF) encoding a polyprotein consisting of 3171 amino acid (aa). The virus has a typical iflavirus structure, including two rhv domains, an RNA helicase domain (HEL), a 3C cysteine protease domain (Pro), and an RNA-dependent RNA polymerase domain (RdRp). Further phylogenetic analysis revealed that this virus belongs to family Iflaviridae and sequence alignments analysis suggested PyCaV is a new member in an unassigned genus of family Iflaviridae. Further in-depth analysis of the virus infection showed that PyCaV is distributed throughout the whole P. candelaria, including its head, chest, and abdomen, but more PyCaV was identified in the chest. The distribution of PyCaV in different parts of P. candelaria was further explored, which showed that more PyCaV was detected in its piercing-sucking mouthparts and chest viscera. Statistical analysis showed that the PyCaV infection was affected by time and location.
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Affiliation(s)
- Hong Lin
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weitao Song
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongmei Ma
- College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chi Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanfang Yao
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Renyi Liu
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ling Hao
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dandan Wu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jimou Jiang
- Fruit Research Institute, Fujian Academy of Agricultural Science, Fuzhou 350013, China
| | - Jun Xiong
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Rui Ma
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiajing Xiao
- Center for Agroforestry Mega Data Science, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenhong Zhuang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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194
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Wang Y, Hu Z, Wei L, Wan F, Wei F, Hao J, Su C. Complete mitochondrial genome of Colias sifanica Grum-Grshimailo, 1891 (Lepidoptera: Pieridae) from montane region in northwestern China. Mitochondrial DNA B Resour 2024; 9:1107-1111. [PMID: 39165383 PMCID: PMC11334738 DOI: 10.1080/23802359.2024.2392760] [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: 12/26/2023] [Accepted: 08/09/2024] [Indexed: 08/22/2024] Open
Abstract
Colias sifanica Grum-Grshimailo, 1891, is a typical montane butterfly species which occurs on the Qinghai-Tibet Plateau (QTP) and adjacent regions in China. In this study, the complete mitochondrial genome of this species was assembled from data generated by next-generation sequencing. The mitogenome was 15,151 bp in length and comprised 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The base composition of the C. sifanica mitogenome was 39.7% A, 41.3% T, 11.3% C and 7.7% G, significantly AT biased as commonly found in other Pieridae mitogenomes. Phylogenetic analyses based on all PCGs using both the maximum likelihood and Bayesian inference methods indicated that C. sifanica is closely related to C. fieldii with high support values, and the phylogenetic relationship of (Dercas + ((Gandaca + Gonepteryx) + (Phoebis + (Anteos + (Catopsilia + (Zerene + Colias))))))) was shown for the tribe Coliadini. Though both the mitogenomic gene order and overall base composition were found to be conserved, different Ka/Ks ratios for several mitogenomic PCGs were detected between Colias and other species in the tribe Coliadini.
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Affiliation(s)
- Ying Wang
- College of Physical Education, Anhui Normal University, Wuhu, China
| | - Zeyu Hu
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Liufang Wei
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | | | - Fanyu Wei
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Chengyong Su
- College of Life Sciences, Anhui Normal University, Wuhu, China
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195
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Zheng X, Lin X, Zhang X, Huang X, Yue X, Pu J. Complete mitochondrial genome of Penicillidia dufourii (Diptera: Hippoboscoidea: Nycteribiidae) and phylogenetic relationship. Parasitol Res 2024; 123:302. [PMID: 39158739 DOI: 10.1007/s00436-024-08321-y] [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: 05/31/2024] [Accepted: 08/08/2024] [Indexed: 08/20/2024]
Abstract
Penicillidia dufourii (Westwood 1834) is a specialized parasite categorized under family Nycteribiidae that prefers to parasitize the body surface of various bats under the genus Myotis. Many species of the family Nycteribiidae are carriers of various pathogens; however, research on P. dufourii remains scarce, and studies on its molecular identification and population genetic structure are still lacking. In this study, the complete mitochondrial genome of P. dufourii was elucidated for the first time using Illumina sequencing. The mitochondrial genome is 15,354 bp in size and encodes approximately 37 genes, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. Analysis of 13 protein-coding genes revealed that UUA, UCA, CGA, and GGA were the most common codons, while nad4L had the fastest evolutionary rate and cox1 the slowest. Phylogenetic analysis based on the mitochondrial genome indicated that P. dufourii is clustered with other species of the family Nycteribiidae and is most closely related to Nycteribia parvula and Phthiridium szechuanum.
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Affiliation(s)
- Xiaoyan Zheng
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Xiaoxia Lin
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Xianzheng Zhang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
| | - Xiaobin Huang
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China.
| | - Xinke Yue
- School of Life Sciences, Yunnan Normal University, Kunming, 650000, China.
| | - Ju Pu
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, 671000, Yunnan, China
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196
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Olarte-Castillo XA, Goodman LB, Whittaker GR. Molecular detection using hybridization capture and next-generation sequencing reveals cross-species transmission of feline coronavirus type-1 between a domestic cat and a captive wild felid. Microbiol Spectr 2024:e0006124. [PMID: 39158411 DOI: 10.1128/spectrum.00061-24] [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: 01/09/2024] [Accepted: 06/12/2024] [Indexed: 08/20/2024] Open
Abstract
Feline coronavirus (FCoV) infection normally causes mild or subclinical signs and is common in domestic cats. However, in some cats, FCoV infection can also lead to the development of feline infectious peritonitis (FIP)-a typically lethal disease. FCoV has two serotypes or genotypes, FCoV-1 and FCoV-2, both of which can cause FIP. The main difference between the genotypes is the viral spike (S) protein that determines tropism and pathogenicity, crucial mechanisms in the development of FIP. Subclinical infection and FIP have both been reported in wild felids, including in threatened species. Due to the high genetic variability of the S gene and the technical challenges to sequencing it, detection and characterization of FCoV in wild felids have mainly centered on other more conserved genes. Therefore, the genotype causing FIP in most wild felids remains unknown. Here, we report a retrospective molecular epidemiological investigation of FCoV in a zoological institution in the U.Ss. In 2008, a domestic cat (Felis catus) and a Pallas' cat (Otocolobus manul) sharing the same room succumbed to FIP. Using in situ hybridization, we detected FCoV RNA in different tissues of both felids. Using hybridization capture and next-generation sequencing, we detected, sequenced, and characterized the whole genome of the FCoV infecting both felids. Our data show for the first time that FCoV-1 can be transmitted between domestic and wild felids and extends the known host range of FCoV-1. Our findings highlight the importance of identifying the genotype causing FIP, to develop effective control measures. IMPORTANCE Feline coronavirus (FCoV) is highly prevalent in domestic cats worldwide and has also been reported in wild felids, including endangered species, in which it has caused substantial population declines. Characterizing the genetic diversity of FCoV is crucial due to recent reports of novel pathogenic recombinant variants causing high mortality in feral cats in Cyprus. In this retrospective molecular epidemiology study, we used archived samples collected in a zoological institution in the U.S. in which a domestic and a wild felid succumbed to FCoV. Using hybridization capture (HC) and next-generation sequencing, we show for the first time that FCoV can be naturally transmitted between domestic and wild felids. We demonstrate the efficacy of HC for detecting and sequencing the whole genome of FCoV, which is essential to characterize its different genotypes.
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Affiliation(s)
- Ximena A Olarte-Castillo
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
| | - Laura B Goodman
- James A. Baker Institute for Animal Health, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Gary R Whittaker
- Department of Microbiology & Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
- Cornell Feline Health Center, Ithaca, New York, USA
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197
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Moreira D, Blaz J, Kim E, Eme L. A gene-rich mitochondrion with a unique ancestral protein transport system. Curr Biol 2024; 34:3812-3819.e3. [PMID: 39084221 DOI: 10.1016/j.cub.2024.07.017] [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: 11/26/2023] [Revised: 05/03/2024] [Accepted: 07/02/2024] [Indexed: 08/02/2024]
Abstract
Mitochondria originated from an ancient endosymbiosis involving an alphaproteobacterium.1,2,3 Over time, these organelles reduced their gene content massively, with most genes being transferred to the host nucleus before the last eukaryotic common ancestor (LECA).4 This process has yielded varying gene compositions in modern mitogenomes, including the complete loss of this organellar genome in some extreme cases.5,6,7,8,9,10,11,12,13,14 At the other end of the spectrum, jakobids harbor the most gene-rich mitogenomes, encoding 60-66 proteins.8 Here, we introduce the mitogenome of Mantamonas sphyraenae, a protist from the deep-branching CRuMs supergroup.15,16 Remarkably, it boasts the most gene-rich mitogenome outside of jakobids, by housing 91 genes, including 62 protein-coding ones. These include rare homologs of the four subunits of the bacterial-type cytochrome c maturation system I (CcmA, CcmB, CcmC, and CcmF) alongside a unique ribosomal protein S6. During the early evolution of mitochondria, gene transfer from the proto-mitochondrial endosymbiont to the nucleus became possible thanks to systems facilitating the transport of proteins synthesized in the host cytoplasm back to the mitochondrion. In addition to the universally found eukaryotic protein import systems, jakobid mitogenomes were reported to uniquely encode the SecY transmembrane protein of the Sec general secretory pathway, whose evolutionary origin was however unclear. The Mantamonas mitogenome not only encodes SecY but also SecA, SecE, and SecG, making it the sole eukaryote known to house a complete mitochondrial Sec translocation system. Furthermore, our phylogenetic and comparative genomic analyses provide compelling evidence for the alphaproteobacterial origin of this system, establishing its presence in LECA.
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Affiliation(s)
- David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91190 Gif-sur-Yvette, France.
| | - Jazmin Blaz
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91190 Gif-sur-Yvette, France
| | - Eunsoo Kim
- Division of EcoScience, Ewha Womans University, Seoul, South Korea; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Laura Eme
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91190 Gif-sur-Yvette, France.
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198
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Niu KY, He J, Tang SM, Su XJ, Luo ZL. Morphological and Phylogenetic Analyses Reveal Three Novel Species of Sanguinoderma ( Ganodermataceae, Basidiomycota) from Yunnan Province, China. J Fungi (Basel) 2024; 10:589. [PMID: 39194914 DOI: 10.3390/jof10080589] [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: 07/22/2024] [Revised: 08/14/2024] [Accepted: 08/16/2024] [Indexed: 08/29/2024] Open
Abstract
Sanguinoderma (Ganodermataceae) is recognized as a valuable medicinal resource in Taiwan, China. Additionally, it serves as a traditional folk medicine for treating neurotic epilepsy in Malaysia. This study involved the collection of six specimens of Sanguinoderma from Yunnan Province, China. Employing multigene phylogenetic analysis of DNA sequences, including internal transcribed spacer (ITS), nuclear large subunit (LSU), RNA polymerase II second largest subunit (rpb2), translation elongation factor 1-alpha (tef1-α), mitochondrial small subunit (mtSSU), nuclear small subunit (nSSU) and morphological examinations, three new species, viz. Sanguinoderma concentricum, S. dehongense and S. ovisporum, are introduced. Sanguinoderma concentricum is characterized by a central stipe basidiomata, an orbicular to suborbicular pileus, a grayish-yellow surface with alternating concentric zones and wavy margin-like petals and regular pileipellis cells (4-8 × 17-28 μm). Sanguinoderma dehongense is characterized by a long stipe and flabelliform basidiomata, a dark-grayish yellow-to-dark-yellow pileus surface, irregular pileipellis cells and wavy margin and ellipsoid basidia (8-11 × 9-13 μm). Sanguinoderma ovisporum is characterized by a reniform basidiomata, a heterogeneous context and ovoid basidiospores (7.5-8.6 × 5.5-7.2 µm). A detailed description and illustrations of these new species are provided, as well as a morphological comparison with similar taxa.
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Affiliation(s)
- Kai-Yang Niu
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Jun He
- College of Biotechnology and Engineering, West Yunnan University, Lincang 677000, China
| | - Song-Ming Tang
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Xi-Jun Su
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
| | - Zong-Long Luo
- College of Agriculture and Biological Science, Dali University, Dali 671003, China
- Cangshan Forest Ecosystem Observation and Research Station of Yunnan Province, Dali University, Dali 671003, China
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199
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Kuhl H, Strassert JFH, Čertnerová D, Varga E, Kreuz E, Lamatsch DK, Wuertz S, Köhler J, Monaghan MT, Stöck M. The haplotype-resolved Prymnesium parvum (type B) microalga genome reveals the genetic basis of its fish-killing toxins. Curr Biol 2024; 34:3698-3706.e4. [PMID: 38986615 DOI: 10.1016/j.cub.2024.06.033] [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: 03/29/2024] [Revised: 05/13/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024]
Abstract
The catastrophic loss of aquatic life in the Central European Oder River in 2022, caused by a toxic bloom of the haptophyte microalga Prymnesium parvum (in a wide sense, s.l.), underscores the need to improve our understanding of the genomic basis of the toxin. Previous morphological, phylogenetic, and genomic studies have revealed cryptic diversity within P. parvum s.l. and uncovered three clade-specific (types A, B, and C) prymnesin toxins. Here, we used state-of-the-art long-read sequencing and assembled the first haplotype-resolved diploid genome of a P. parvum type B from the strain responsible for the Oder disaster. Comparative analyses with type A genomes uncovered a genome-size expansion driven by repetitive elements in type B. We also found conserved synteny but divergent evolution in several polyketide synthase (PKS) genes, which are known to underlie toxin production in combination with environmental cues. We identified an approximately 20-kbp deletion in the largest PKS gene of type B that we link to differences in the chemical structure of types A and B prymnesins. Flow cytometry and electron microscopy analyses confirmed diploidy in the Oder River strain and revealed differences to closely related strains in both ploidy and morphology. Our results provide unprecedented resolution of strain diversity in P. parvum s.l. and a better understanding of the genomic basis of toxin variability in haptophytes. The reference-quality genome will enable us to better understand changes in microbial diversity in the face of increasing environmental pressures and provides a basis for strain-level monitoring of invasive Prymnesium in the future.
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Affiliation(s)
- Heiner Kuhl
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Jürgen F H Strassert
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Dora Čertnerová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic; Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Elisabeth Varga
- Department of Food Chemistry and Toxicology, University of Vienna, Vienna, Austria; Unit Food Hygiene and Technology, Centre for Food Science and Veterinary Public Health, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine, Vienna, Austria
| | - Eva Kreuz
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Dunja K Lamatsch
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Sven Wuertz
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Jan Köhler
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany.
| | - Matthias Stöck
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.
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200
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Li Y, Moritz C, Brennan IG, Zwick A, Nicholls J, Grealy A, Slipinski A. Evolution across the adaptive landscape in a hyperdiverse beetle radiation. Curr Biol 2024; 34:3685-3697.e6. [PMID: 39067451 DOI: 10.1016/j.cub.2024.06.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/30/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]
Abstract
The extraordinary diversification of beetles on Earth is a textbook example of adaptive evolution. Yet, the tempo and drivers of this super-radiation remain largely unclear. Here, we address this problem by investigating macroevolutionary dynamics in darkling beetles (Coleoptera: Tenebrionidae), one of the most ecomorphologically diverse beetle families (with over 30,000 species). Using multiple genomic datasets and analytical approaches, we resolve the long-standing inconsistency over deep relationships in the family. In conjunction with a landmark-based dataset of body shape morphology, we show that the evolutionary history of darkling beetles is marked by ancient rapid radiations, frequent ecological transitions, and rapid bursts of morphological diversification. On a global scale, our analyses uncovered a significant pulse of phenotypic diversification proximal to the Cretaceous-Palaeogene (K/Pg) mass extinction and convergence of body shape associated with recurrent ecological specializations. On a regional scale, two major Australasian radiations, the Adeliini and the Heleine clade, exhibited contrasting patterns of ecomorphological diversification, representing phylogenetic niche conservatism versus adaptive radiation. Our findings align with the Simpsonian model of adaptive evolution across the macroevolutionary landscape and highlight a significant role of ecological opportunity in driving the immense ecomorphological diversity in a hyperdiverse beetle group.
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Affiliation(s)
- Yun Li
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia.
| | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Ian G Brennan
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - James Nicholls
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
| | - Alicia Grealy
- Australian National Herbarium, CSIRO, Canberra, ACT 2601, Australia
| | - Adam Slipinski
- Australian National Insect Collection, CSIRO, Canberra, ACT 2601, Australia
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