title: De novo transcriptome analysis of the Siberian apricot (Prunus sibirica L.) and search for potential SSR markers by 454 pyrosequencing.
abstract: 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 425 bp in a single run, totaling 528.4 Mb of sequence data using 454 GS FLX Titanium sequencing. All reads were assembled de novo into 46,940 unigenes with a mean size of 651 bp (range: 45-5566 bp). 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.
authors.affiliation: Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China.
authors.forename: Shubin
authors.initials: S
authors.lastname: Dong
authors.affiliation: Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
authors.forename: Yulin
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Niu
authors.affiliation: Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Ning
authors.affiliation: Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
authors.forename: Shanzhi
authors.initials: S
authors.lastname: Lin
authors.affiliation: Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China. Electronic address: zxzhang@bjfu.edu.cn.
authors.forename: Zhixiang
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics; D044943:Fatty Acid Desaturases / Q000235:genetics*; D005227:Fatty Acids / Q000096:biosynthesis* / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D050356:Lipid Metabolism / Q000235:genetics; D018895:Microsatellite Repeats / Q000235:genetics*; D027861:Prunus / Q000235:genetics*; D012639:Seeds / Q000235:genetics; D017422:Sequence Analysis, DNA; D013230:Stearoyl-CoA Desaturase / Q000235:genetics; D059467:Transcriptome / Q000235:genetics
chemical_list: D018744:DNA, Plant; D005227:Fatty Acids; D044943:Fatty Acid Desaturases; D013230:Stearoyl-CoA Desaturase
keywords: 454 pyrosequencing; SSR markers; Siberian apricot (Prunus sibirica L.); Transcriptome