Transcriptome Analysis and SNP Marker Identification in Vicia amurensis Oett. using 454 Pyrosequencing

Vicia amurensis Oett. is a perennial plant found in northern China, Japan, Korea, and Manchuria, which are contained flavonol glycosides, and used against the infection caused by tick-borne encephalitis and respiratory impairments. We used 454 sequencing technology to sequence the V.amurensis transcriptome, which yielded 26.59 Mb. A total of 71,228 raw sequence reads were obtained and assembled by de novo sequence assembly. The assembled sequences resulted in 39,295 completely assembled and 3,738 partially assembled contigs, 26,707 singletons, and 71 repeat sequences. The contig distributions in three non-mutually exclusive gene ontology classifications and clusters of orthologous gene classes showed that differentially expressed genes were over represented in classes J (translation, ribosomal structure, and biogenesis), O (posttranslational modifications, protein turnover, chaperones), R (general function and prediction only) and C (energy production and conversion) which were also used in the identification of genes related to nitrogen fixation.  In total, 12656 SNP types were detected in which the variants contained 11143 SNps and 1513InDels. The higher confidence differences were composed of 2311 SNPs and 72 Indels respectively. We present the first and broad extensive survey on transcriptome characterization and SNP marker identification in V. amurensis, since, availability of the previous genomic information is limited or scanty.  Our study provides broad range of functional categories as well as provides resources for functional genomics studies and the development of SNP marker, which will certainly lead to the crop improvement in the coming days.