Computational identification of cis-regulatory elements associated with pungency of chili peppers

In silico characterization of promoter or regulatory regions of genomes is an important aspect of understanding gene expression regulation. Plant secondary metabolism represents an opportunity to discover promoter elements among coordinately transcribed genes on these complex pathways. We used CisFind, a software tool we developed, for finding un-extendable conserved matches among multiple DNA sequences. The underlying algorithm for this tool is a modified suffix tree. We used CisFind to detect unknown common regulatory elements in the 5' proximal regions of four genes on the capsaicinoid biosynthetic pathway. These DNA sequences were retrieved by genome walking from eight different chili peppers differing in pungency levels; tomato DNA was included as an outgroup. Nine unique candidate promoter elements were identified among these sequences. Their distribution is consistent with a role in regulating these genes for expression related to chili pungency. These candidate promoter elements were also predicted by other online software tools with different algorithms, increasing the probability that these elements are in fact biologically relevant.