Kosch Tiffany A, Torres-Sánchez María, Liedtke H Christoph, Summers Kyle, Yun Maximina H, Crawford Andrew J, Maddock Simon T, Ahammed Md Sabbir, Araújo Victor L N, Bertola Lorenzo V, Bucciarelli Gary M, Carné Albert, Carneiro Céline M, Chan Kin O, Chen Ying, Crottini Angelica, da Silva Jessica M, Denton Robert D, Dittrich Carolin, Themudo Gonçalo Espregueira, Farquharson Katherine A, Forsdick Natalie J, Gilbert Edward, Che Jing, Katzenback Barbara A, Kotharambath Ramachandran, Levis Nicholas A, Márquez Roberto, Mazepa Glib, Mulder Kevin P, Müller Hendrik, O'Connell Mary J, Orozco-terWengel Pablo, Palomar Gemma, Petzold Alice, Pfennig David W, Pfennig Karin S, Reichert Michael S, Robert Jacques, Scherz Mark D, Siu-Ting Karen, Snead Anthony A, Stöck Matthias, Stuckert Adam M M, Stynoski Jennifer L, Tarvin Rebecca D, Wollenberg Valero Katharina C
One Health Research Group, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Werribee, Victoria, Australia.
Department of Biodiversity, Ecology, and Evolution, Complutense University of Madrid, 28040 Madrid, Spain.
bioRxiv. 2024 Oct 3:2024.06.27.601086. doi: 10.1101/2024.06.27.601086.
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, antipredator 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.
两栖动物是四足动物中的一个多样化群体，其三个系统目和科之间的分化时间很深。通过基因组学视角研究两栖动物生物学，能增进我们对这一动物类群以及其他陆地脊椎动物特征的理解。由于该类群面临的威胁日益增加，对两栖动物基因组资源的需求比以往任何时候都更加迫切。两栖动物是最濒危的分类群体之一，约41%的物种因栖息地丧失、土地利用模式变化、疾病、气候变化及其协同效应而面临灭绝威胁。两栖动物基因组资源有助于更好地理解个体发育多样性、组织再生、多样的生活史和繁殖模式、反捕食策略以及恢复力和适应性反应。它们也是研究广泛基因组特征（如进化基因组的扩张和收缩）的重要模型，因为它们在所有动物类群中展现出最广泛的基因组大小范围，并且拥有多种遗传性别决定机制。尽管具有这些特征，但两栖动物的基因组测序仍显著落后于其他脊椎动物，主要原因是组装其庞大且富含重复序列的基因组存在挑战，以及相对缺乏社会支持。长读长测序技术的出现，结合先进的分子和计算技术，这些技术可改善支架搭建并减少计算工作量，现在使得应对其中一些挑战成为可能。为通过国际协调与合作促进并加速两栖动物基因组学研究的产出与应用，我们于2023年初发起了两栖动物基因组学联盟（AGC，https://mvs.unimelb.edu.au/amphibian-genomics-consortium）。这个新兴的群体已经有来自41个国家的282多名成员。AGC旨在利用其成员的多样能力，推进两栖动物的基因组资源，并弥合生物学家、生物信息学家和保护从业者之间的实施差距。在此，我们评估两栖动物基因组学领域的现状，突出以往的研究，提出需要克服的挑战，并呼吁研究和保护界作为AGC的一部分团结起来，使两栖动物基因组学研究能够“跃”上新台阶。
