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
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