title: Comparative transcriptomics of a complex of four European pine species.
abstract: BACKGROUND
  Pinus sylvestris, P. mugo, P. uliginosa and P. uncinata are closely related but phenotypically and ecologically very distinct European pine species providing an excellent study system for analysis of the genetic basis of adaptive variation and speciation. For comparative genomic analysis of the species, transcriptome sequence was generated for 17 samples collected across the European distribution range using Illumina paired-end sequencing technology.
  
  
  RESULTS
  De novo transcriptome assembly of a reference sample of P. sylvestris contained 40968 unigenes, of which fewer than 0.5% were identified as putative retrotransposon sequences. Based on gene annotation approaches, 19659 contigs were identified and assigned to unique genes covering a broad range of gene ontology categories. About 80% of the reads from each sample were successfully mapped to the reference transcriptome of P. sylvestris. Single nucleotide polymorphisms were identified in 22041-24096 of the unigenes providing a set of ~220-262 k SNPs identified for each species. Very similar levels of nucleotide polymorphism were observed across species (π=0.0044-0.0053) and highest pairwise nucleotide divergence (0.006) was found between P. mugo and P. sylvestris at a common set of unigenes.
  
  
  CONCLUSIONS
  The study provides whole transcriptome sequence and a large set of SNPs to advance population and association genetic studies in pines. Our study demonstrates that transcriptome sequencing can be a very useful approach for development of novel genomic resources in species with large and complex genomes.
authors.affiliation: Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK. witcho@ceh.ac.uk.|Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland. witcho@ceh.ac.uk.
authors.forename: Witold
authors.initials: W
authors.lastname: Wachowiak
authors.affiliation: Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JT, UK. urmi.trivedi@ed.ac.uk.
authors.forename: Urmi
authors.initials: U
authors.lastname: Trivedi
authors.affiliation: Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK. annt@ceh.ac.uk.
authors.forename: Annika
authors.initials: A
authors.lastname: Perry
authors.affiliation: Centre for Ecology and Hydrology Edinburgh, Bush Estate, Penicuik, Midlothian, EH26 0QB, UK. scav@ceh.ac.uk.
authors.forename: Stephen
authors.initials: S
authors.lastname: Cavers
mesh_terms: D055028:Comparative Genomic Hybridization; D005060:Europe; D005819:Genetic Markers; D018745:Genome, Plant; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D028223:Pinus / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D040641:Quantitative Trait Loci; D018749:RNA, Plant / Q000032:analysis / Q000302:isolation & purification / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D005819:Genetic Markers; D018749:RNA, Plant