Wachowiak, W.; Trivedi, U.; Telford, A.; Cavers, S.

Comparative transcriptomics of a complex of four European pine species

Data from whole transcriptome sequencing of the four European pine species - Pinus sylvestris (Scots pine), P. mugo (Dwarf mountain pine), P. uliginosa (Mountain pine) and P. uncinata (Peat-bog pine). Those data include
1) transcriptome sequence of a reference Scots pine sample generated using Illumina paired-end sequencing technology and
2) information about single nucleotide polymorphisms (SNPs) in 17 samples collected across the European range, compared to the reference Scots pine sample.

These genomic resources were produced to advance the study of the genetic basis of adaptive variation and speciation in pines.

Publication date: 2014-10-10

Get the data

This dataset is made available under the terms of the Open Government Licence

Format of the data: Variant Call Format (VCF)

You must cite: Wachowiak, W.; Trivedi, U.; Telford, A.; Cavers, S. (2014). Comparative transcriptomics of a complex of four European pine species. NERC Environmental Information Data Centre. https://doi.org/10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1

 

© UK Centre for Ecology & Hydrology

Where/When

Study area
Temporal extent
2006-01-01    to    2008-12-31

Provenance & quality

1.Lineage of the reference transcriptome sequence of Scots pine samples from Glen Tanar (Scotland). Total Ribonucleic acid (RNA) was extracted from needles using Spectrum (TM) Plant Total RNA Kit (Sigma). A template complementary DNA (cDNA) library was prepared using ®TruSeq RNA Sample Preparation Kit (Illumina). The cDNA library was sequenced using Illumina HiSeq 2000 platform at Edinburgh Genomics, the University of Edinburgh, Scotland (Illumina, San Diego, California). 100 base, paired-end reads were generated and assembled de novo into contigs using Trinity (version r2012-06-08). The reference transcript sequence contains 40798 contigs in total. 2.The single nucleotide polymorphism (SNP) data file was prepared by aligning 16 samples to the reference, a sample set that included P. sylvestris (4 samples), P. mugo (5 samples), P. uncinata (4 samples) and P. uliginosa (3 samples). Samples collected between 2006 and 2010

Citations

Wachowiak, W., Trivedi, U., Perry, A., & Cavers, S. (2015). Comparative transcriptomics of a complex of four European pine species. BMC Genomics, 16(1). https://doi.org/10.1186/s12864-015-1401-z
Liu, J.-J., Schoettle, A. W., Sniezko, R. A., Sturrock, R. N., Zamany, A., Williams, H., … Kegley, A. (2016). Genetic mapping of Pinus flexilis major gene (Cr4) for resistance to white pine blister rust using transcriptome-based SNP genotyping. BMC Genomics, 17(1). https://doi.org/10.1186/s12864-016-3079-2

Correspondence/contact details

Witold Wachowiak
UK Centre for Ecology & Hydrology
Bush Estate
Penicuik
Midlothian
EH26 0QB
UNITED KINGDOM
 enquiries@ceh.ac.uk

Authors

Wachowiak, W.
Centre for Ecology & Hydrology
Trivedi, U.
The University of Edinburgh
Telford, A.
Centre for Ecology & Hydrology
Cavers, S.
Centre for Ecology & Hydrology

Other contacts

Custodian
NERC EDS Environmental Information Data Centre
 info@eidc.ac.uk
Publisher
NERC Environmental Information Data Centre
 info@eidc.ac.uk
Rights Holder
UK Centre for Ecology & Hydrology
 enquiries@ceh.ac.uk

Additional metadata

Topic categories
Biota
Keywords
Dwarf mountain pine,  Europe,  Evolutionary ecology Local adaption,  Mountain pine,  next-generation sequencing,  nucleotide divergence,  Peat-bog pine,  pine complex,  Pinus mugo Pinus sylvestris Pinus uliginosa Pinus uncinata Scots pine,  speciation,  transcriptomics
INSPIRE Theme
Environmental Monitoring Facilities
Spatial representation type
Tabular (text)
Spatial reference system
WGS 84
Last updated
20 May 2022 10:40