Genome Sequence Analysis Reveals the Evolution of Pungency in Capsicum Spp

Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. Here, we report a high-quality genome sequence of the hot pepper (CM334, 2n=2X=24) containing predicted 34,447 protein-coding genes. A total of 86.8% (3.02 Gb) of the 3.48 Gb genome was assembled solely by WGS, and integrated as 12 chromosomes. The genome size of pepper was boosted approximately fourfold to that of the close relative, tomato, by excessive accumulation of Gypsy and Caulimoviridae family. Integrative genomic and transcriptomic analyses suggested neofunctionalization occurred at both the expression and functional levels to shape capsaicin synthase and pathway genes into roles for specialized capsaicinoid synthesis after recent gene duplication, and provided the origin of pungency after speciation from Solanaceae crop. Our analyses also unveil potential mechanisms of non-climateric ripening and pepper specific-pigmentation due to defect of ripening regulators and ethylene synthesis. The reference genome of the pepper will serve as a platform for improving the nutritional and medicinal values of Capsicum spp.