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

Research output: Preprint/Documentation/ReportPreprint

Contributors

  • Complutense University
  • Doñana Biological Station (EBD-CSIC)
  • CSIC - National Museum of Natural Sciences (MNCN)
  • BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
  • Marian University
  • University of Porto
  • Manaaki Whenua - Landcare Research
  • CAS - Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences
  • Martin Luther University Halle-Wittenberg
  • Columbia University
  • University of Melbourne
  • East Carolina University
  • Universidad de los Andes Colombia
  • University of Seychelles
  • Jagannath University
  • James Cook University Queensland
  • University of California at Davis
  • University of Texas at Austin
  • University of Kansas
  • Queen's University Kingston
  • University of Johannesburg
  • University of Veterinary Medicine Vienna
  • University of Sydney
  • University of Hull
  • University of Waterloo
  • Central University of Kerala
  • Indiana University Bloomington
  • Virginia Polytechnic Institute and State University
  • Uppsala University
  • Ghent University
  • University of Nottingham
  • Cardiff University
  • Jagiellonian University in Kraków
  • University of Potsdam
  • University of North Carolina at Chapel Hill
  • Oklahoma State University
  • University of Rochester Medical Center
  • University of Copenhagen
  • The Natural History Museum, London
  • Leibniz-Institute of Freshwater Ecology and Inland Fisheries
  • University of Houston
  • University of Costa Rica
  • University of California at Berkeley
  • University College Dublin

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 genomics 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 genomics resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, antipredator strategies, and resilience and adaptive responses. They also serve as critical models for understanding widespread genomic characteristics, including evolutionary genome expansions and contractions given they have the largest range in genome sizes of any animal taxon and 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 advent of long-read sequencing technologies, along with computational techniques that enhance scaffolding capabilities and streamline computational workload is now enabling the ability to overcome 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) in early 2023. This burgeoning community already has more than 282 members from 41 countries (6 in Africa, 131 in the Americas, 27 in Asia, 29 in Australasia, and 89 in Europe). 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 outline how the AGC can enable amphibian genomics research to "leap" to the next level.

Details

Original languageEnglish
Publication statusPublished - 1 Jul 2024

Publication series

SeriesbioRxiv : the preprint server for biology
ISSN2692-8205
No renderer: customAssociatesEventsRenderPortal,dk.atira.pure.api.shared.model.researchoutput.WorkingPaper

External IDs

PubMedCentral PMC11244923
unpaywall 10.1101/2024.06.27.601086

Keywords