Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families



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Torres-Sánchez, María and Creevey, Christopher J. and Kornobis, Etienne and Gower, David J. and Wilkinson, Mark and San Mauro, Diego (2019) Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families. DNA Research, 26 (1). pp. 13-20. ISSN 1756-1663

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RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation & 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.

Item Type:Article
Uncontrolled Keywords:Gymnophiona, RNA-seq, gene families, phylogenomics, skin-specific genes
Subjects:Medical sciences > Biology > Amphibians
Medical sciences > Biology > Ecology
Medical sciences > Biology > Genetics
ID Code:56966
Deposited On:10 Sep 2019 14:20
Last Modified:10 Sep 2019 14:20

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