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De novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and inter-specific analyses

hal.structure.identifierDepartment of Forest Ecology and GeneticsForest Research Centre
dc.contributor.authorOLSSON, Sanna
hal.structure.identifierIstituto di Genomica Applicata [IGA]
hal.structure.identifierNational Research Council of Italy | Consiglio Nazionale delle Ricerche [CNR]
dc.contributor.authorPINOSIO, Sara
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierSustainable Forest Management Research Institute
hal.structure.identifierCentre for Ecological Research and Forestry Applications [CREAF]
dc.contributor.authorGONZÁLEZ-MARTÍNEZ, Santiago C.
hal.structure.identifierThe Wellcome Trust Sanger Institute [Cambridge]
dc.contributor.authorABASCAL, Federico
hal.structure.identifierCentre for Ecological Research and Forestry Applications [CREAF]
dc.contributor.authorMAYOL, Maria
hal.structure.identifierDepartment of Forest Ecology and GeneticsForest Research Centre
hal.structure.identifierSustainable Forest Management Research Institute
dc.contributor.authorGRIVET, Delphine
hal.structure.identifierNational Research Council of Italy | Consiglio Nazionale delle Ricerche [CNR]
dc.contributor.authorVENDRAMIN, Giovanni G.
dc.date.issued2018
dc.identifier.issn0167-4412
dc.description.abstractEnWe provide novel genomic resources for Taxus baccata in the form of a reference transcriptome, SSR and SNP markers, and orthologous single-copy genes, useful for phylogenomic and population genomic applications. English yew (T. baccata) is the only European representative of the Taxaceae family, a conifer group originated in the Jurassic period. The wide extent of environmental heterogeneity within the species' range, together with its long presence in Europe, make English yew an ideal species to investigate adaptive evolution in conifers. To enlarge the genomic resources available for this species, we used Illumina short read sequencing followed by de novo assembly to build the transcriptome of English yew. In addition to a fully annotated transcriptome as well as large sets of new potential SSR and SNP markers for T. baccata, we provide a data set of orthologous single-copy genes across three Taxus species using Picea sitchensis as outgroup, and discuss ortholog uses and limitations for phylogenomic and population genomic applications.
dc.language.isoen
dc.publisherSpringer Verlag (Germany)
dc.subjectPhylogenomics
dc.subjectTranscriptome
dc.subject.enOrthologous genes
dc.subject.enSNP
dc.subject.enSSR
dc.title.enDe novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and inter-specific analyses
dc.typeArticle de revue
dc.identifier.doi10.1007/s11103-018-0742-9
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalPlant Molecular Biology
bordeaux.page337–345
bordeaux.volume97
bordeaux.issue4-5
bordeaux.peerReviewedoui
hal.identifierhal-02622882
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-02622882v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Plant%20Molecular%20Biology&rft.date=2018&rft.volume=97&rft.issue=4-5&rft.spage=337%E2%80%93345&rft.epage=337%E2%80%93345&rft.eissn=0167-4412&rft.issn=0167-4412&rft.au=OLSSON,%20Sanna&PINOSIO,%20Sara&GONZ%C3%81LEZ-MART%C3%8DNEZ,%20Santiago%20C.&ABASCAL,%20Federico&MAYOL,%20Maria&rft.genre=article


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