Comparative transcriptomics of a complex of four European pine species
Cite this dataset as:
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
Download/Access
PLEASE NOTE: By accessing or using this dataset, you agree to the terms of the relevant licence agreement(s). You will ensure that this dataset is cited in any publication that describes research in which the data have been used.
This dataset is made available under the terms of the Open Government Licence 
https://doi.org/10.5285/b6900166-ded6-4f7a-8734-484b6f77b2f1
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.
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
View numbers valid from 01 June 2023 Download numbers valid from 20 June 2024 (information prior to this was not collected)
Format
Variant Call Format (VCF)
Spatial information
Study area
Spatial representation type
Tabular (text)
Spatial reference system
WGS 84
Temporal information
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 sixteen samples to the reference, a sample set that included P. sylvestris (four samples), P. mugo (five samples), P. uncinata (four samples) and P. uliginosa (three samples). Samples collected between 2006 and 2010.
2. The single nucleotide polymorphism (SNP) data file was prepared by aligning sixteen samples to the reference, a sample set that included P. sylvestris (four samples), P. mugo (five samples), P. uncinata (four samples) and P. uliginosa (three samples). Samples collected between 2006 and 2010.
Licensing and constraints
This dataset is made available under the terms of the Open Government Licence
Cite this dataset as:
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
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
Penicuik
Midlothian
EH26 0QB
UNITED KINGDOM
Authors
Wachowiak, W.
Centre for Ecology & Hydrology
Trivedi, U.
The University of Edinburgh
Telford, A.
Centre for Ecology & Hydrology
https://orcid.org/0000-0003-2139-9236 Other contacts
Rights holder
UK Centre for Ecology & Hydrology
Custodian
NERC EDS Environmental Information Data Centre
info@eidc.ac.uk
Publisher
NERC Environmental Information Data Centre
info@eidc.ac.uk