Pepper Genome Sequencing
The Capsicum annuum cv. CM334 genome was sequenced in 2014 and published in Nature Genetics, revealing a 3.5-Gb genome (comparable to the human genome) with 34,476 protein-coding genes. The genome illuminated the genetic basis of pungency, the expansion of disease-resistance gene families, and the metabolic origins of Capsicum's unusual secondary metabolite diversity.
Pungency Locus
The Pun1 gene cluster encodes the acyltransferase AT3 (capsaicin synthase). Bell peppers carry a 2.5-kb transposable element insertion in the first intron of Pun1 that disrupts expression and abolishes capsaicin production. The insertion is a relatively recent event in Capsicum domestication — wild Capsicum species are almost all pungent.
Genome-Scale Insights
Sequencing revealed that pungent and non-pungent cultivars differ primarily in Pun1 expression, not pathway enzyme copy number. It also showed that the phenylpropanoid and fatty acid branches of capsaicin biosynthesis are each regulated by distinct MYB and bHLH transcription factors — targets that allow CRISPRa-based upregulation of heat production in naturally mild varieties.