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Background  The Chinese pine ( Pinus tabuliformis ) is an indigenous conifer species in northern China but is relatively underdeveloped as a genomic resource; thus, limiting gene discovery and breeding. Large-scale transcriptome data were obtained using a next-generation sequencing platform to compensate for the lack of  P. tabuliformis  genomic information.    Results  The increasing amount of transcriptome data on  Pinus  provides an excellent resource for multi-gene phylogenetic analysis and studies on how conserved genes and functions are maintained in the face of species divergence. The first  P. tabuliformis  transcriptome from a normalised cDNA library of multiple tissues and individuals was sequenced in a full 454 GS-FLX run, producing 911,302 sequencing reads. The high quality overlapping expressed sequence tags (ESTs) were assembled into 46,584 putative transcripts, and more than 700 SSRs and 92,000 SNPs/InDels were characterised. Comparative analysis of the transcriptome of six conifer species yielded 191 orthologues, from which we inferred a phylogenetic tree, evolutionary patterns and calculated rates of gene diversion. We also identified 938 fast evolving sequences that may be useful for identifying genes that perhaps evolved in response to positive selection and might be responsible for speciation in the  Pinus  lineage.    Conclusions  A large collection of high-quality ESTs was obtained,  de novo  assembled and characterised, which represents a dramatic expansion of the current transcript catalogues of  P. tabuliformis  and which will gradually be applied in breeding programs of  P. tabuliformis . Furthermore, these data will facilitate future studies of the comparative genomics of  P. tabuliformis  and other related species.

Transcriptome characterisation of Pinus tabuliformis and evolution of genes in the Pinusphylogeny