De novo transcriptome analysis of the Siberian apricot (Prunus sibirica L.) and search for potential SSR markers by 454 pyrosequencing

The Siberian apricot, an economically and ecologically important plant in China, contains seeds high in oil and can grow on marginal land. Although this species has multiple purposes and may be a feedstock of biofuel in China, transcriptome information and molecular research on this species remain limited. RNA-Seq technology has been widely applied to transcriptomics, genomics and the development of molecular markers, and functional gene studies. In this study, we obtained 1,243,067 high-quality reads with a mean size of 425bp in a single run, totaling 528.4Mb of sequence data using 454 GS FLX Titanium sequencing. All reads were assembled de novo into 46,940 unigenes with a mean size of 651bp (range: 45-5566bp). Assembled unigenes were annotated in multiple public databases based on similarity alignments to genes and proteins. 191 unigenes involving in lipid biosynthesis and metabolism were found, among them, expression patterns of two desaturase enzymes were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), based on six tissues from Siberian apricot, the seeds had the highest expression. 7304 simple sequence repeats (SSR) were identified from 6509 unigenes, a total of 9930 primer pairs were designed, 50 primer pairs were randomly selected to validate of the usefulness, and 24 (48%) primer pairs produced bands of the expected size. These data provide a base of sequence information to improve agronomic characters and molecular marker-assisted breeding to alter the composition of fatty acids in seeds from this plant, and hence, facilitate its utilization as a future biodiesel feedstock.