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

Plant Molecular Biology
Sanna OlssonGiovanni G Vendramin

Abstract

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. 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.

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Datasets Mentioned

BETA
GACG01000000
PRJNA393771

Methods Mentioned

BETA
RNA-Seq
RNAseq

Software Mentioned

evobiR R
STAR
FullLengtherNext
HMMER
Primer3
MrBayes
PhyDE®
SeqTrimNext
GATK
Trimal

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