Generation and analysis of expressed sequence tags from the medicinal plant Salvia miltiorrhiza

• Published in: Science China. Life sciences Vol. 53; no. 2; pp. 273 - 285
• Main Authors: Yan, YaPing, Wang, ZheZhi, Tian, Wei, Dong, ZhongMin, Spencer, David F.
• Format: Journal Article
• Language: English
• Published: Beijing Science China Press 01.02.2010; Springer Nature B.V
• Subjects: Base Sequence; Biomedical and Life Sciences; DNA, Complementary - genetics; DNA, Complementary - metabolism; Expressed Sequence Tags; Gene Expression Profiling; Gene Library; Life Sciences; Microsatellite Repeats; Oligonucleotide Array Sequence Analysis; Plant Roots - genetics; Plant Roots - metabolism; Plants, Medicinal - genetics; Research Paper; Salvia miltiorrhiza; Salvia miltiorrhiza - genetics; Software; microsatellite; Bge; gene identification; expressed sequence tags
• ISSN: 1674-7305; 1869-1889
• DOI: 10.1007/s11427-010-0005-8

Salvia miltiorrhiza Bge. is a well-known traditional Chinese herb. Its roots have been formulated and used clinically for the treatment of various diseases. However, little genetic information has so far been available and this fact has become a major obstacle for molecular studies. To address this lack of genetic information, an Expressed Sequence Tag (EST) library from whole plantlets of S. miltiorrhiza was generated. From the 12959 cDNA clones that were randomly selected and subjected to single-pass sequencing from their 5′ ends, 10288 ESTs (with sizes⩾100 bp) were selected and assembled into 1288 contigs, leaving 2937 singletons, for a total of 4225 unigenes. These were analyzed using BLASTX (against protein databases), RPS-BLAST (against a conserved domain database) as well as the web-based KEGG Automatic Annotation Server for metabolic enzyme assignment. Based on the metabolic enzyme assignment, expression patterns of 14 secondary metabolic enzyme genes in different organs and under different treatments were verified using real-time PCR analysis. Additionally, a total of 122 microsatellites were identified from the ESTs, with 89 having sufficient flanking sequences for primer design. This set of ESTs represents a significant proportion of the S. miltiorrhiza transcriptome, and gives preliminary insights into the gene complement of S. miltiorrhiza. They will prove useful for uncovering secondary metabolic pathways, analyzing cDNA-array based gene expression, genetic manipulation to improve yield of desirable secondary products, and molecular marker identification.