Discovery of genes related to steroidal alkaloid biosynthesis in Fritillaria cirrhosa by generating and mining a dataset of expressed sequence tags (ESTs)

Fritillaria cirrhosa D. Don is an endangered species in the Liliaceae family, the bulb of which is the primary plant source for the Chinese traditional medicine "Chuan-beimu", having activities that relieve coughs and eliminates phlegm. The major pharmacologically active constituents of F. cirrhosa are steroidal alkaloids. Two thousand one hundred and fifty-eight high-quality expressed sequence tags (ESTs) were generated from a cDNA library of F. cirrhosa bulbs and assembled to total 1343 unique transcripts. After removing ribosomal RNA sequences, 1330 putative protein coding sequences were obtained; among these, 765 (57.5%) had at least one significant match to the Swiss-Prot protein database via a BLASTX similarity search. The 1330 unique transcripts were further functionally classified for gene discovery purposes using the gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases. More than ten transcripts that are likely involved in the biosynthesis of F. cirrhosa alkaloids and corresponding regulatory activities were discovered in this EST dataset, including HMGR, FPSs, CYP450s and aminotransferases. This report describes the first example of EST analysis from the Fritillaria genus and lays the foundation for further cloning and identification of candidate genes related to steroidal alkaloid biosynthesis in F. cirrhosa.