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

Kosch, T. A.; Torres-Sanchez, M.; Liedtke, H. C.; Summers, K.; Yun, M. H.; Crawford, A. J.; Maddock, S. T.; Ahammed, M. S.; Araujo, V. L. N.; Vincenzo Bertola, L.; Bucciarelli, G.; Carne, A.; Carneiro, C. M.; Chan, K. O.; Chen, Y.; Crottini, A.; da Silva, J. M.; Denton, R. D.; Dittrich, C.; Espregueira Themudo, G.; Farquharson, K. A.; Forsdick, N. J.; Gilbert, E.; Che, J.; Katzenback, B. A.; Kotharambath, R.; Levis, N. A.; Marquez, R.; Mazepa, G.; Mulder, K. P.; Muller, H.; O'Connell, M. J.; Orozco-terWengel, P.; Palomar, G.; Petzold, A.; Pfennig, D. W.; Pfennig, K. S.; Reichert, M. S.; Robert

doi:10.1101/2024.06.27.601086

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bioRxiv · 10.1101/2024.06.27.601086

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

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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.

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Kosch, T. A., Torres-Sanchez, M., Liedtke, H. C., Summers, K., Yun, M. H., Crawford, A. J., Maddock, S. T., Ahammed, M. S., Araujo, V. L. N., Vincenzo Bertola, L., Bucciarelli, G., Carne, A., Carneiro, C. M., Chan, K. O., Chen, Y., Crottini, A., da Silva, J. M., Denton, R. D., Dittrich, C., Espregueira Themudo, G., Farquharson, K. A., Forsdick, N. J., Gilbert, E., Che, J., Katzenback, B. A., Kotharambath, R., Levis, N. A., Marquez, R., Mazepa, G., Mulder, K. P., Muller, H., O'Connell, M. J., Orozco-terWengel, P., Palomar, G., Petzold, A., Pfennig, D. W., Pfennig, K. S., Reichert, M. S., Robert. 2024-07-01. The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation. https://doi.org/10.1101/2024.06.27.601086

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