Genome Sequence Analysis Reveals the Evolution of Pungency in Capsicum Species

Hot pepper (Capsicum annuum L.) is one of the oldest domesticated crops in the Americas and the most widely grown spice crop in the world. Here, we report a high-quality genome sequence of hot pepper (CM334, 2n=2x=24) containing a 34,914 predicted protein-coding gene. A total of 87.9% (3.06 Gb) of the 3.48-Gb genome was assembled solely by whole-genome shotgun (WGS) and integrated as 12 chromosomes. Resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense provided the landscape of genomic variations among Capsicum species. The genome size of pepper was boosted approximately fourfold compared to that of the close relative tomato. This was mediated by excessive accumulation of long terminal repeat (LTR) retrotransposons, primarily of the Gypsy family. A unique feature of the pepper genome was the high copy number of a DNA pararetrovirus, the Caulimoviridae family. Integrative genomic and transcriptomic analyses suggested that the change of gene expression and neofunctionalization of the capsaicin synthase gene shaped the capsaicinoid biosynthetic pathway. Our analyses also unveiled differential molecular patterns of ripening regulators and ethylene synthesis in pepper and tomato. The reference genome of pepper will serve as a platform for improving the nutritional and medicinal values of Capsicum species.