Comparative analysis of amphibian genomes: an emerging resource for basic and applied research

Abstract

ABSTRACTAmphibians are the most threatened group of vertebrates and are in dire need of conservation intervention to ensure their continued survival. They have many unique features including a high diversity of reproductive strategies, permeable and specialized skin capable of producing toxins and antimicrobial compounds, multiple genetic mechanisms of sex determination, and in some lineages even the ability to regenerate limbs and internal organs. Although genomics approaches would shed light on these unique phenotypic traits and aid in conservation management, sequencing and assembly of amphibian genomes has lagged far behind other taxa due to their comparatively large genome sizes. Fortunately, the development of long-read sequencing technologies and initiatives has led to a recent burst of new amphibian genome assemblies. Although growing, the field of amphibian genomics suffers from the lack of annotation resources, tools for working with challenging genomes, and lack of high-quality assemblies in multiple clades of amphibians. Here we analyze 32 publicly available amphibian genomes to evaluate their usefulness for functional genomics analysis. We report considerable variation in assembly quality and completeness, and report some of the highest transposable element and repeat contents of any vertebrate, which is associated with climate. We also provide evidence of conserved genome synteny despite the long divergence times of this group but show that chromosome naming and orientation have been inconsistent across genome assemblies. Additionally, we discuss sequencing gaps in the phylogeny and suggest key targets for future sequencing endeavors. Lastly, we propose increased investment in amphibian genomics research to promote their conservation.