The Hot and the Colorful: Understanding the Metabolism, Genetics and Evolution of Consumer Preferred Metabolic Traits in Pepper and Related Species

Recent advances in genomics and metabolomics have made the study of specialized metabolism far more tractable than it was previously. Here we evaluate specialized metabolite pathways of <i>Capsicum</i> spp. (peppers), focusing mainly on carotenoids, flavonoids, and capsaicinoids as examples of classes of secondary metabolites. To place these data in the context of the evolution of metabolic pathways, we compare the extent of genomic and chemical diversity in several species of the nightshades (Solanaceae), the family to which pepper belongs. We further discuss the genetic mechanisms known to underly metabolic diversity prior to carrying out a detailed genomic study of the enzymes active in the pathways influencing fruit color and pungency. Using large-scale comparative analyses across 25 sequenced plant genomes, we identify orthologs of structural metabolic genes and discuss the data in terms of variation of gene family size and its impact on the diversity of secondary metabolites. BCAA: branched-chain amino acid; K-Pg: Cretaceous-Paleogene; ROS: reactive oxygen species; TE: transposable element; WGD: whole genome duplication