Identification of Stress-Induced Biosynthetic Gene Clusters in Plants

Phytoalexins are specialized metabolites that play a crucial role in plant defense response. Similarly to other plant specialized metabolites, their biosynthetic pathways are in some cases encoded by co-localized genes that form biosynthetic gene clusters (BGCs). Discovery of BGCs responsible for phytoalexin production can significantly facilitate delineation of their biosynthesis and function. Here we describe an experimental approach for systematic identification of stress-induced BGCs, potentially involved in phytoalexin biosynthesis. Plants are treated with methyl jasmonate (MeJA) to induce stress-responsive metabolic pathways, and RNA sequencing (RNA-seq) of treated plants is applied to identify genes upregulated in response to MeJA treatment. The resulting transcriptomic data is next integrated with BGC prediction tools to identify co-localized genes, together leading to the identification of stress-induced BGC candidates. This approach provides a pipeline that serves to facilitate the discovery of novel phytoalexin biosynthetic pathways, thus providing insight into defense-related plant specialized metabolism and its underlying genetic basis.