The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

被引：1

作者：

Tiffany A. Kosch ^{[1
]}

María Torres-Sánchez ^{[2
]}

H. Christoph Liedtke ^{[3
]}

Kyle Summers ^{[4
]}

Maximina H. Yun ^{[5
]}

Andrew J. Crawford ^{[6
]}

Simon T. Maddock ^{[7
]}

Md. Sabbir Ahammed ^{[8
]}

Victor L. N. Araújo ^{[9
]}

Lorenzo V. Bertola ^{[10
]}

Gary M. Bucciarelli ^{[11
]}

Albert Carné ^{[7
]}

Céline M. Carneiro ^{[12
]}

Kin O. Chan ^{[13
]}

Ying Chen ^{[14
]}

Angelica Crottini ^{[15
]}

Jessica M. da Silva ^{[16
]}

Robert D. Denton ^{[17
]}

Carolin Dittrich ^{[18
]}

Gonçalo Espregueira Themudo ^{[19
]}

Katherine A. Farquharson ^{[20
]}

Natalie J. Forsdick ^{[21
]}

Edward Gilbert ^{[22
]}

Jing Che ^{[23
]}

Barbara A. Katzenback ^{[24
]}

Ramachandran Kotharambath ^{[25
]}

Nicholas A. Levis ^{[26
]}

Roberto Márquez ^{[27
]}

Glib Mazepa ^{[28
]}

Kevin P. Mulder ^{[29
]}

Hendrik Müller ^{[30
]}

Mary J. O’Connell ^{[31
]}

Pablo Orozco-terWengel ^{[32
]}

Gemma Palomar ^{[33
]}

Alice Petzold ^{[34
]}

David W. Pfennig ^{[35
]}

Karin S. Pfennig ^{[36
]}

Michael S. Reichert ^{[37
]}

Jacques Robert ^{[38
]}

Mark D. Scherz ^{[39
]}

Karen Siu-Ting ^{[40
]}

Anthony A. Snead ^{[41
]}

Matthias Stöck ^{[42
]}

Adam M. M. Stuckert ^{[43
]}

Jennifer L. Stynoski ^{[44
]}

Rebecca D. Tarvin ^{[45
]}

Katharina C. Wollenberg Valero ^{[46
]}

机构：

[1] University of Melbourne,One Health Research Group, Melbourne Veterinary School, Faculty of Science

[2] Complutense University of Madrid,Department of Biodiversity, Ecology, and Evolution

[3] Estación Biológica de Doñana CSIC,Eco

[4] East Carolina University,Evo

[5] Technische Universität Dresden,Devo Group

[6] Max Planck Institute for Molecular Cell Biology and Genetics,Biology Department

[7] Universidad de los Andes,CRTD/Center for Regenerative Therapies Dresden

[8] Historia Natural C.J. Marinkelle,Department of Biological Sciences

[9] Universidad de los Andes,School of Natural and Environmental Sciences

[10] Newcastle University,Island Biodiversity and Conservation Centre

[11] University of Seychelles,Department of Zoology

[12] Jagannath University,Centre for Tropical Bioinformatics and Molecular Biology

[13] James Cook University,Department of Wildlife, Fish, and Conservation Biology

[14] University of California,Department of Integrative Biology

[15] Museo Nacional de Ciencias Naturales-CSIC,Biology Department

[16] The University of Texas at Austin,Centro de Investigação Em Biodiversidade E Recursos Genéticos

[17] University of Kansas Biodiversity Institute and Natural History Museum,Department of Biology

[18] Queen’s University,Evolutionary Genomics and Wildlife Management

[19] CIBIOInBIO Laboratório AssociadoUniversidade Do Porto,Centre for Evolutionary Genomics and Wildlife Conservation, Department of Zoology

[20] University of Florence,Department of Biology

[21] BIOPOLIS Program in Genomics,Rojas Lab, Department of Life Science

[22] Biodiversity and Land Planning,CIIMAR Interdisciplinary Centre of Marine and Environmental Research

[23] CIBIO,School of Life and Environmental Sciences

[24] Foundational Biodiversity Science,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science

[25] Kirstenbosch Research Centre,School of Natural Sciences

[26] South African National Biodiversity Institute,Energy and Environment Institute

[27] University of Johannesburg,Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain

[28] Auckland Park,Department of Biology

[29] Marian University,Herpetology Lab, Dept. of Zoology

[30] Konrad-Lorenz-Institute of Ethology,Department of Biology

[31] University of Veterinary Medicine,Department of Biological Sciences

[32] University of Porto,Department of Ecology and Evolution

[33] The University of Sydney,Faculty of Veterinary Medicine

[34] The University of Sydney,School of Life Sciences, Faculty of Medicine and Health Sciences

[35] Manaaki Whenua – Landcare Research,School of Biosciences

[36] The University of Hull,Department of Genetics, Physiology, and Microbiology, Faculty of Biological Sciences

[37] The University of Hull,Institute of Environmental Sciences, Faculty of Biology

[38] Kunming Institute of Zoology,Institute of Biochemistry and Biology

[39] Chinese Academy of Sciences,Department of Biology

[40] Southeast Asia Biodiversity Research Institute,Department of Integrative Biology

[41] Chinese Academy of Sciences,Department of Microbiology and Immunology

[42] University of Waterloo,School of Biological Sciences

[43] Central University of Kerala,Herpetology Lab

[44] Tejaswini Hills,Department of Biology

[45] Indiana University,Department of Biology and Biochemistry

[46] Virginia Tech,Museum of Vertebrate Zoology and Department of Integrative Biology

[47] University of Lausanne,School of Biology and Environmental Science

[48] Department of Ecology and Genetics,undefined

[49] Evolutionary Biology,undefined

[50] ,undefined

来源：

BMC Genomics | / 25卷 / 1期

关键词：

Amphibians; Biodiversity conservation; Comparative genomics; Genomics; Lissamphibia; Metagenomics; Phylogenomics; Population genomics; Taxonomy; Transcriptomics;

D O I：

10.1186/s12864-024-10899-7

中图分类号：

学科分类号：

摘要：

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to “leap” to the next level.

引用

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