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. 2015 Mar 25;16(1):234.
doi: 10.1186/s12864-015-1401-z.

Comparative transcriptomics of a complex of four European pine species

Witold Wachowiak  1   2 , Urmi Trivedi  3 , Annika Perry  4 , Stephen Cavers  5
Affiliations

Comparative transcriptomics of a complex of four European pine species

Witold Wachowiak et al. BMC Genomics. .

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.

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Figures

Figure 1
Figure 1
Locations of the populations of the four pine species sampled for the study. Populations labelled PS - P. sylvestris, M - P. mugo, UN - P. uncinata, UG - P. uliginosa.
Figure 2
Figure 2
Gene ontology classification of the unigenes.
Figure 3
Figure 3
Shared and unique SNPs in pairwise comparisons between P. sylvestris (S), P. mugo (M), P. uncinata (UN) and P. uliginosa (UG). SNPs total: P. sylvestris (225544), P. mugo (262582), P. uncinata (220365), P. uliginosa (232822).
Figure 4
Figure 4
Principal Coordinates Analysis (PCoA) based on pairwise nucleotide difference matrix at 676 contigs (>1.3Mbp, 27929 SNPs) showing genetic relationships between P. sylvestris (●), P. mugo (■), P. uncinata (♦) and P. uliginosa (▲) samples.
See this image and copyright information in PMC

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