Comparative biology needs de novo transcriptome assemblies: drawing attention towards amphibians

The study of transcriptomics across amphibians opens a window to understand how species have adapted to and cope with their environment, diseases, and new challenges. Transcriptomics can accelerate comparative studies across the amphibian tree of life because they capture diverse biological information at a fraction of the cost of genomics. Currently, 337 amphibians (3.82% of the described species) have transcriptomic data available, and 60 of them (0.68% of the described amphibian species) have reconstructed de novo assemblies readily accessible on public repositories. Here, we summarise taxonomic gaps for amphibian transcriptomics, highlighting studies that have used these resources in a multi-species comparative framework to uncover the genetic variation and gene expression patterns that underlie phenotypes across different aspects of amphibian biology. Given the particularities of amphibians, including their complex life cycles, we provide some guidelines to generate reference transcriptomes while identifying challenges that researchers might encounter. We explore the developmental and tissue-specific transcriptome divergence across the three amphibian orders to aid in identifying suitable target samples for reference transcriptomes (e.g., developmental stages, brain, kidney, reproductive tissues). Since annotations for amphibians are very limited, we recommend researchers to be critical of annotations assigned through homology. We encourage the availability of transcriptome assemblies in public repositories, sparing computational efforts and costs to advance multi-species research. Comparative studies should expand taxonomic and ecological breadth to unveil the molecular bases of evolution, adaptation, and resilience mechanisms for one of the most imperilled groups of vertebrates.