ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2019
Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 32 citations in OpenAlex.
- Evolution of an amphibian-specific family of epidermal differentiation-associated genes.Molecular biology and evolution · 2026Article
- Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.Evolution; international journal of organic evolution · 2025Article
- Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.bioRxiv : the preprint server for biology · 2025Article
- A cloud-based training module for efficient de novo transcriptome assembly using Nextflow and Google cloud.Briefings in bioinformatics · 2024Article
- Caspase-1 activates gasdermin A in non-mammals.eLife · 2024Article
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- Transcriptome mining extends the host range of theVirus evolution · 2023Article
- Evolutionary diversification of epidermal barrier genes in amphibians.Scientific reports · 2022Article
- The gastrin-releasing peptide/bombesin system revisited by a reverse-evolutionary study considering Xenopus.Scientific reports · 2021Article
- Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models.Genomics, proteomics & bioinformatics · 2021Article
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- Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics.Molecular biology and evolution · 2019Article
- What lies beneath? Molecular evolution during the radiation of caecilian amphibians.BMC genomics · 2019Article
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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