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Open Access Research article

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

Shi-Hui Niu1, Zhe-Xin Li1, Hu-Wei Yuan1, Xiao-Yang Chen12, Yue Li1 and Wei Li1*

Author Affiliations

1 National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of the Ministry of Education, College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, People's Republic of China

2 Laboratory of Bio-technology of Tropical and Subtropical Forestry, College of Forestry, South China Agriculture University, Guangzhou, 510642, People's Republic of China

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BMC Genomics 2013, 14:263  doi:10.1186/1471-2164-14-263

Published: 18 April 2013

Abstract

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.

Keywords:
Pinus tabuliformis Carr; 454 pyrosequencing; SNPs; SSRs; Pinus phylogeny; Comparative transcriptomics