De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients

Medicinal Salvia miltiorrhiza is a Chinese herb commonly used for treating cardiovascular diseases and neuroasthenic insomnia. However, little is known at the genetics level about how its compounds are synthesized in that plant. Here, we obtained 56,774 unigenes (average length = 467 bases) in its transcriptome by performing Solexa deep sequencing over the entire growing cycle. Unigenes (34,340; 60.49%) were annotated and 2545 unigenes were assigned to specific pathways. Unigenes (1539) were identified as part of five major, secondary-metabolite pathways, covering almost all nodes in the phenylpropanoid and terpenoid pathways. Using Blast search against AGRIS, 1341 unigenes were found homologous to 686 Arabidopsis transcription factor genes. Real-time PCR was also used to verify the spatio-temporal expression patterns of several novel transcripts related to biosynthesis of active ingredients in that species. These results not only enrich the gene resource but also benefit research into its molecular genetics and functional genomics.