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Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families
- Source :
- DNA Research, DNA Research, 2019, 26 (1), pp.13-20. ⟨10.1093/dnares/dsy034⟩, Torres-Sánchez, M, Creevey, C J, Kornobis, E, Gower, D J, Wilkinson, M & San Mauro, D 2018, ' Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families ', DNA Research . https://doi.org/10.1093/dnares/dsy034, DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, DNA Research, Oxford University Press (OUP), 2019, 26 (1), pp.13-20. ⟨10.1093/dnares/dsy034⟩, E-Prints Complutense: Archivo Institucional de la UCM, Universidad Complutense de Madrid, E-Prints Complutense. Archivo Institucional de la UCM, instname
- Publication Year :
- 2019
- Publisher :
- HAL CCSD, 2019.
-
Abstract
- International audience; 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.
- Subjects :
- 0106 biological sciences
Candidate gene
gene families
MESH: Amphibians / genetics
MESH: Sequence Analysis, Protein
Lineage (evolution)
[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
01 natural sciences
Sequence Analysis, Protein
Phylogenomics
MESH: Sequence Analysis, RNA
MESH: Animals
MESH: Phylogeny
Phylogeny
MESH: Evolution, Molecular
0303 health sciences
MESH: Transcriptome
Vertebrate
phylogenomics
MESH: Multigene Family
General Medicine
Full Papers
Supertree
Multigene Family
Caecilian
MESH: Amphibian Proteins / genetics
Biology
Anfibios
Amphibian Proteins
Amphibians
Evolution, Molecular
03 medical and health sciences
biology.animal
Genetics
Gene family
Animals
Gymnophiona
Molecular Biology
030304 developmental biology
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE]
Sequence Analysis, RNA
Ecología
biology.organism_classification
Genética
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics
Evolutionary biology
MESH: Amphibians / metabolism
RNA-seq
Transcriptome
010606 plant biology & botany
skin-specific genes
Subjects
Details
- Language :
- English
- ISSN :
- 13402838
- Database :
- OpenAIRE
- Journal :
- DNA Research, DNA Research, 2019, 26 (1), pp.13-20. ⟨10.1093/dnares/dsy034⟩, Torres-Sánchez, M, Creevey, C J, Kornobis, E, Gower, D J, Wilkinson, M & San Mauro, D 2018, ' Multi-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families ', DNA Research . https://doi.org/10.1093/dnares/dsy034, DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, DNA Research, Oxford University Press (OUP), 2019, 26 (1), pp.13-20. ⟨10.1093/dnares/dsy034⟩, E-Prints Complutense: Archivo Institucional de la UCM, Universidad Complutense de Madrid, E-Prints Complutense. Archivo Institucional de la UCM, instname
- Accession number :
- edsair.doi.dedup.....7564752ac0dc69a324965c5f122b0489