Perspectives on studying molecular adaptations of amphibians in the genomic era

Abstract

Understanding the genetic mechanisms underlying particular adaptations/phenotypes of organisms is one of the core issues of evolutionary biology. The use of genomic data has greatly advanced our understandings on this issue, as well as other aspects of evolutionary biology, including molecular adaptation, speciation, and even conservation of endangered species. Despite the well-recognized advantages, usages of genomic data are still limited to non-mammal vertebrate groups, partly due to the difficulties in assembling large or highly heterozygous genomes. Although this is particularly the case for amphibians, nonetheless, several comparative and population genomic analyses have shed lights into the speciation and adaptation processes of amphibians in a complex landscape, giving a promising hope for a wider application of genomics in the previously believed challenging groups of organisms. At the same time, these pioneer studies also allow us to realize numerous challenges in studying the molecular adaptations and/or phenotypic evolutionary mechanisms of amphibians. In this review, we first summarize the recent progresses in the study of adaptive evolution of amphibians based on genomic data, and then we give perspectives regarding how to effectively identify key pathways underlying the evolution of complex traits in the genomic era, as well as directions for future research.

Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

“…Genome assemblies are essential resources for further work to exploit the experimental possibilities of these diverse animals. The new high quality X. tropicalis genome upgrades previous draft assemblies 18,19 and our new genomes complement draft chromosome-scale sequences for the African clawed frog 20 (Xenopus laevis), the African bullfrog 21 (Pyxicephalus adspersus), the Leishan moustache toad 22 (Leptobrachium leishanense), the Ailao moustache toad 23 (Leptobrachium [Vibrissaphora] ailaonicum), and Asiatic toad 24 (Bufo gargarizans), as well as scaffold-and contig-scale assemblies for other species 25 . The rapidly increasing number of chromosome-scale genome assemblies makes anurans ripe for comparative genomic and evolutionary analysis.…”

Genomic data is missing for many highly invasive species, restricting our preparedness for escalating incursion rates

“… 47 , 48 ); rather, taxon-specific idiosyncrasies likely play a role for some groups. For example, ploidy in plants can increase the complexity and challenge of genomic analysis compared to other taxonomic groups 49 and amphibians have large and highly heterozygous genomes 50 . Fortunately, recent technological advancements, especially relating to long-read sequencing, are making genomic research more accessible and accurate, particularly for organisms with large and/or complex genomes 51 .…”

State of the Amphibia 2020: A Review of Five Years of Amphibian Research and Existing Resources

“…Challenges and opportunities in amphibian research.-Large amphibian genome sizes remain one of the greatest challenges in amphibian research. The size and repetitive content of amphibian genomes has hindered whole-genome sequencing efforts (Sun et al, 2020). For comparison, .500 fish genomes (Randhawa and Pawar, 2021; average size of 808 Mb) and .300 bird genomes have been sequenced (Feng et al, 2020;average size of 1.13 Gb [Randhawa and Pawar, 2021]), yet only 28 amphibian genomes are available.…”