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

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dc.contributor.authorTorres-Sánchez, María
dc.contributor.authorCreevey, Christopher J.
dc.contributor.authorKornobis, Etienne
dc.contributor.authorGower, David J.
dc.contributor.authorWilkinson, Mark
dc.contributor.authorSan Mauro, Diego
dc.date.accessioned2023-06-17T13:27:51Z
dc.date.available2023-06-17T13:27:51Z
dc.date.issued2019-02-01
dc.description.abstractRNA 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.
dc.description.departmentDepto. de Biodiversidad, Ecología y Evolución
dc.description.facultyFac. de Ciencias Biológicas
dc.description.refereedTRUE
dc.description.sponsorshipMinisterio de Economía y Competitividad (MINECO)
dc.description.sponsorshipNetwork of research laboratories working on adaptation genomics (AdaptNET)
dc.description.statuspub
dc.eprint.idhttps://eprints.ucm.es/id/eprint/56966
dc.identifier.doi10.1093/dnares/dsy034
dc.identifier.issn1756-1663
dc.identifier.officialurlhttps://www.ncbi.nlm.nih.gov/pubmed/30351380
dc.identifier.urihttps://hdl.handle.net/20.500.14352/13548
dc.issue.number1
dc.journal.titleDNA Research
dc.language.isoeng
dc.page.final20
dc.page.initial13
dc.publisherOxford University Press
dc.relation.projectID(RYC-2011-09321); (CGL2012-40082); (BES-2013-062723); (EEBB-I-15-09665); (CGL2015-71726-REDT)
dc.rightsAtribución-NoComercial 3.0 España
dc.rights.accessRightsopen access
dc.rights.urihttps://creativecommons.org/licenses/by-nc/3.0/es/
dc.subject.cdu574
dc.subject.cdu575
dc.subject.cdu597.6
dc.subject.keywordGymnophiona
dc.subject.keywordRNA-seq
dc.subject.keywordgene families
dc.subject.keywordphylogenomics
dc.subject.keywordskin-specific genes
dc.subject.ucmAnfibios
dc.subject.ucmEcología (Biología)
dc.subject.ucmGenética
dc.subject.unesco2401.17 Invertebrados
dc.subject.unesco2401.06 Ecología animal
dc.subject.unesco2409 Genética
dc.titleMulti-tissue transcriptomes of caecilian amphibians highlight incomplete knowledge of vertebrate gene families
dc.typejournal article
dc.volume.number26
dspace.entity.typePublication
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