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.
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Acknowledgements
Funding was provided by the Spanish Ministry of Economy and Competitiveness (MINECO) under AdapCon grant (CGL2011-30182-C02-01/02), as well as by the project INIA-MAPAMA EG17-048 co-financed by FEADER (75%) according to EU Regulation 1305/2013. GGV was supported by a grant of the Italian Ministry of Education and Scientific Research (‘Biodiversitalia’, RBAP10A2T4). SO received funding from the Spanish Ministry of Economy and Competitiveness (MINECO) under PTA2015-10836-I contract. We acknowledge Supercomputing Centre of Galicia (CESGA) as well as CSC—Finnish IT Center and the Finnish grid infrastructure (FGI) for Science for the allocation of computational resources.
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SCGM, DG, MM and GGV conceived the study. SCGM, SP and GGV designed and produced the sequence data sets. SO and SP analyzed the data with input from FA and DG. DG and SO drafted the manuscript. All the authors contributed to editing and revising the manuscript.
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Online Resource 1
Annotations of 16,810 putative Taxus baccata genes. Predicted ORFs for 15,289 genes having an ortholog in the searched databases are presented in the table ESM_1.xlsx (FullLengtherNext_ortholog sheet). Additional 1,521 putative new genes are listed in the table ESM_1.xlsx (FullLengtherNext_new sheet). The annotations of all the 16,810 putative genes are presented in the table ESM_1.xlsx (16810_annotation sheet). (XLSX 8084 KB)
Online Resource 2
Sequences of 16,810 predicted Taxus baccata cds. (ZIP 4402 KB)
Online Resource 3
Distribution of all Gene ontology (GO) terms in the three GO categories assigned to putative genes of Taxus baccata. (TXT 4196 KB)
Online Resource 4
Results of SSR screening in the Taxus baccata transcriptome. Only SSR motifs composed of at least four contiguous repeated units are reported; contig name with start and end positions of the repeat are given in the table ESM_4.xlsx (microsatellites sheet). Identified 2,330 perfect SSR motifs in the putative coding Taxus baccata sequences for which primers were successfully designed are given in the table ESM_4.xlsx (primers sheet). (XLSX 485 KB)
Online Resource 5
59,513 SNPs after filtering in coding regions and UTRs in Taxus baccata. (ZIP 2245 KB)
Online Resource 6
1,320 orthologous groups for the four species: Picea sitchensis, Taxus baccata (Tbac), Taxus cuspidata (Tcus), and Taxus wallichiana (Twal). (ZIP 2557 KB)
Online Resource 7
1,418 orthologous groups present in Taxus baccata, Taxus cuspidata, and Taxus wallichiana. (ZIP 1208 KB)
Online Resource 8
Concatenated data matrix of 914 orthologous groups filtered for possible misalignments and paralogues present in Taxus baccata, Taxus cuspidata, and Taxus wallichiana. Frame shifts in alignments are indicated by exclamation marks. (NEXUS 3700 KB)
Online Resource 9
Concatenated data matrix used for phylogenetic analyses based on 981 orthologous groups filtered for possible misalignments and paralogues present in the four species: Picea sitchensis, Taxus baccata, Taxus cuspidata, and Taxus wallichiana. Exclamation marks generated by frame shifts in alignments were replaced with question marks to be compatible with phylogenetic programs. (NEXUS 3332 KB)
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Olsson, S., Pinosio, S., González-Martínez, S.C. et al. De novo assembly of English yew (Taxus baccata) transcriptome and its applications for intra- and inter-specific analyses. Plant Mol Biol 97, 337–345 (2018). https://doi.org/10.1007/s11103-018-0742-9
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DOI: https://doi.org/10.1007/s11103-018-0742-9