BMC Genomics (Nov 2024)
The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation
- Tiffany A. Kosch,
- María Torres-Sánchez,
- H. Christoph Liedtke,
- Kyle Summers,
- Maximina H. Yun,
- Andrew J. Crawford,
- Simon T. Maddock,
- Md. Sabbir Ahammed,
- Victor L. N. Araújo,
- Lorenzo V. Bertola,
- Gary M. Bucciarelli,
- Albert Carné,
- Céline M. Carneiro,
- Kin O. Chan,
- Ying Chen,
- Angelica Crottini,
- Jessica M. da Silva,
- Robert D. Denton,
- Carolin Dittrich,
- Gonçalo Espregueira Themudo,
- Katherine A. Farquharson,
- Natalie J. Forsdick,
- Edward Gilbert,
- Jing Che,
- Barbara A. Katzenback,
- Ramachandran Kotharambath,
- Nicholas A. Levis,
- Roberto Márquez,
- Glib Mazepa,
- Kevin P. Mulder,
- Hendrik Müller,
- Mary J. O’Connell,
- Pablo Orozco-terWengel,
- Gemma Palomar,
- Alice Petzold,
- David W. Pfennig,
- Karin S. Pfennig,
- Michael S. Reichert,
- Jacques Robert,
- Mark D. Scherz,
- Karen Siu-Ting,
- Anthony A. Snead,
- Matthias Stöck,
- Adam M. M. Stuckert,
- Jennifer L. Stynoski,
- Rebecca D. Tarvin,
- Katharina C. Wollenberg Valero,
- The Amphibian Genomics Consortium
Affiliations
- Tiffany A. Kosch
- One Health Research Group, Melbourne Veterinary School, Faculty of Science, University of Melbourne
- María Torres-Sánchez
- Department of Biodiversity, Ecology, and Evolution, Complutense University of Madrid
- H. Christoph Liedtke
- Eco-Evo-Devo Group, Estación Biológica de Doñana CSIC
- Kyle Summers
- Biology Department, East Carolina University
- Maximina H. Yun
- CRTD/Center for Regenerative Therapies Dresden, Technische Universität Dresden
- Andrew J. Crawford
- Department of Biological Sciences, Universidad de los Andes
- Simon T. Maddock
- School of Natural and Environmental Sciences, Newcastle University
- Md. Sabbir Ahammed
- Department of Zoology, Jagannath University
- Victor L. N. Araújo
- Department of Biological Sciences, Universidad de los Andes
- Lorenzo V. Bertola
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University
- Gary M. Bucciarelli
- Department of Wildlife, Fish, and Conservation Biology, University of California
- Albert Carné
- Museo Nacional de Ciencias Naturales-CSIC
- Céline M. Carneiro
- Department of Integrative Biology, The University of Texas at Austin
- Kin O. Chan
- University of Kansas Biodiversity Institute and Natural History Museum
- Ying Chen
- Biology Department, Queen’s University
- Angelica Crottini
- Centro de Investigação Em Biodiversidade E Recursos Genéticos, CIBIOInBIO Laboratório AssociadoUniversidade Do Porto
- Jessica M. da Silva
- Evolutionary Genomics and Wildlife Management, Foundational Biodiversity Science, Kirstenbosch Research Centre, South African National Biodiversity Institute
- Robert D. Denton
- Department of Biology, Marian University
- Carolin Dittrich
- Rojas Lab, Department of Life Science, Konrad-Lorenz-Institute of Ethology, University of Veterinary Medicine
- Gonçalo Espregueira Themudo
- CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto
- Katherine A. Farquharson
- School of Life and Environmental Sciences, The University of Sydney
- Natalie J. Forsdick
- Manaaki Whenua – Landcare Research
- Edward Gilbert
- School of Natural Sciences, The University of Hull
- Jing Che
- Key Laboratory of Genetic Evolution and Animal Models, and Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences
- Barbara A. Katzenback
- Department of Biology, University of Waterloo
- Ramachandran Kotharambath
- Herpetology Lab, Dept. of Zoology, Central University of Kerala, Tejaswini Hills
- Nicholas A. Levis
- Department of Biology, Indiana University
- Roberto Márquez
- Department of Biological Sciences, Virginia Tech
- Glib Mazepa
- Department of Ecology and Evolution, University of Lausanne
- Kevin P. Mulder
- Faculty of Veterinary Medicine, Wildlife Health Ghent, Ghent University
- Hendrik Müller
- Central Natural Science Collections, Martin Luther University Halle-Wittenberg
- Mary J. O’Connell
- School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham
- Pablo Orozco-terWengel
- School of Biosciences, Cardiff University
- Gemma Palomar
- Department of Genetics, Physiology, and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid
- Alice Petzold
- Institute of Biochemistry and Biology, University of Potsdam
- David W. Pfennig
- Department of Biology, University of North Carolina
- Karin S. Pfennig
- Department of Biology, University of North Carolina
- Michael S. Reichert
- Department of Integrative Biology, Oklahoma State University
- Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center
- Mark D. Scherz
- Natural History Museum of Denmark, University of Copenhagen
- Karen Siu-Ting
- School of Biological Sciences, Queen’s University Belfast
- Anthony A. Snead
- Department of Biology, New York University
- Matthias Stöck
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB)
- Adam M. M. Stuckert
- Department of Biology and Biochemistry, University of Houston
- Jennifer L. Stynoski
- Instituto Clodomiro Picado, Universidad de Costa Rica
- Rebecca D. Tarvin
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California
- Katharina C. Wollenberg Valero
- School of Biology and Environmental Science, University College Dublin, Belfield Campus
- The Amphibian Genomics Consortium
- DOI
- https://doi.org/10.1186/s12864-024-10899-7
- Journal volume & issue
-
Vol. 25,
no. 1
pp. 1 – 19
Abstract
Abstract 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.
Keywords
