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

De novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and... Key message We 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. Abstract 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. Keywords Transcriptome · Phylogenomics · SSR · SNP · Orthologous genes Introduction elements, transposable elements, large intron sizes, big gene families and abundance of pseudogenes as well as With c. 615 species (Farjon 2010), conifers are ecologi- polyploidy (Ahuja and Neale http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Plant Molecular Biology Springer Journals

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

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Publisher
Springer Journals
Copyright
Copyright © 2018 by Springer Science+Business Media B.V., part of Springer Nature
Subject
Life Sciences; Plant Sciences; Biochemistry, general; Plant Pathology
ISSN
0167-4412
eISSN
1573-5028
D.O.I.
10.1007/s11103-018-0742-9
Publisher site
See Article on Publisher Site

Abstract

Key message We 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. Abstract 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. Keywords Transcriptome · Phylogenomics · SSR · SNP · Orthologous genes Introduction elements, transposable elements, large intron sizes, big gene families and abundance of pseudogenes as well as With c. 615 species (Farjon 2010), conifers are ecologi- polyploidy (Ahuja and Neale

Journal

Plant Molecular BiologySpringer Journals

Published: May 30, 2018

References

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