Abstract
BackgroundThe 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.ResultsThe 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.ConclusionsA 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.
Highlights
The Chinese pine (Pinus tabuliformis) is an indigenous conifer species in northern China but is relatively underdeveloped as a genomic resource; limiting gene discovery and breeding
The study of natural genetic variation in P. tabuliformis has traditionally been investigated using a common garden approach, whereas the pace of development of genomic resources has been slow, as only 288 P. tabuliformis entries are included in the NCBI database
Transcriptome sequencing and de novo assembly Prior to sequencing, the cDNA samples obtained from multiple tissues and individuals were normalised to increase the sequencing efficiency of rare transcripts
Summary
The Chinese pine (Pinus tabuliformis) is an indigenous conifer species in northern China but is relatively underdeveloped as a genomic resource; limiting gene discovery and breeding. Chinese pine (Pinus tabuliformis Carr.) is a widespread indigenous conifer species and an economically and ecologically important hard pine in northern China [4,5]. The study of natural genetic variation in P. tabuliformis has traditionally been investigated using a common garden approach, whereas the pace of development of genomic resources has been slow, as only 288 P. tabuliformis entries are included in the NCBI database. Information regarding the genetic control of many important traits and fine-scale genetic variations is extremely limited, and more is needed given the renewed emphasis to accelerate the pace of P. tabuliformis breeding and shorten the breeding cycle
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