RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation and diversity. Although challenging, RNA-seq is particularly promising for research on non-model, secretive species that cannot be observed in nature easily and therefore remain comparatively understudied. Among such animals, the caecilians (order Gymnophiona) likely constitute the least known group of vertebrates, despite being an old and remarkably distinct lineage of amphibians. Here, we characterize multi-tissue transcriptomes for five species of caecilians that represent a broad level of diversity across the order. We identified vertebrate homologous elements of caecilian functional genes of varying tissue specificity that reveal a great number of unclassified gene families, especially for the skin. We annotated several protein domains for those unknown candidate gene families to investigate their function. We also conducted supertree analyses of a phylogenomic dataset of 1,955 candidate orthologous genes among five caecilian species and other major lineages of vertebrates, with the inferred tree being in agreement with current views of vertebrate evolution and systematics. Our study provides insights into the evolution of vertebrate protein-coding genes, and a basis for future research on the molecular elements underlying the particular biology and adaptations of caecilian amphibians.
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This work received financial support from the Ministry of Economy and Competitiveness of Spain (RYC-2011-09321 and CGL2012-40082 grants to DSM, BES-2013-062723 FPI predoctoral fellowship and EEBB-I-15-09665 research stay to MTS). Support was also provided by the network of research laboratories working on adaptation genomics (AdaptNET) funded by the Ministry of Economy and Competitiveness of Spain (grant CGL2015-71726-REDT).
Tissue-specific RNA-seq reads and species-specific de novo transcriptome assemblies are available from NCBI through BioProject ID number PRJNA387587. SRA database accession numbers are also provided in Supplementary Table S1.
Torres-Sánchez, María; Creevey, Christopher J.; Kornobis, Etienne; Gower, David J.; Wilkinson, Mark; and San Mauro, Diego, "Multi-Tissue Transcriptomes of Caecilian Amphibians Highlight Incomplete Knowledge of Vertebrate Gene Families" (2019). Neuroscience Faculty Publications. 51.