Comparative transcriptomics of a complex of four European pine species

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Wachowiak, W.; Trivedi, U.; Telford, A.; Cavers, S. (2014)

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

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

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.


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

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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


Centre for Ecology & Hydrology
The University of Edinburgh
Centre for Ecology & Hydrology
Centre for Ecology & Hydrology

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Centre for Ecology & Hydrology


Spatial Reference System
WGS 84


Topic Categories
Other keywords
Pinus sylvestris
Scots pine
Pinus mugo
Dwarf mountain pine
Pinus uliginosa
Mountain pine
Pinus uncinata
Peat-bog pine
pine complex
nucleotide divergence
Local adaption
next-generation sequencing
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Ecological Processes and Resilience
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Evolutionary ecology
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Centre for Ecology & Hydrology
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NERC profile of ISO19115:2003 version 1.0