Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

TLDR

The hot pepper, Capsicum annuum, is a widely cultivated spice crop whose genome was sequenced, and comparative genomics across Solanaceae reveals insights into genome expansion, pungency, ripening, and disease resistance. The study aims to sequence and assemble the hot pepper genome and resequence two cultivated peppers and the wild species Capsicum chinense. The authors performed high‑coverage (186.6×) whole‑genome sequencing and de novo assembly of the Mexican landrace CM334, and resequenced two cultivated peppers and the wild species Capsicum chinense. The hot pepper genome is about four times larger than tomato’s, enriched in Gypsy and Caulimoviridae repeats, and its gene‑expression changes and capsaicin‑synthase neofunctionalization drive capsaicinoid biosynthesis, while distinct ripening regulators differentiate it from tomato, and the reference genome will aid breeding for nutrition and medicine.

Abstract

Doil Choi and colleagues report the genome sequence of the hot pepper, Capsicum annuum, as well as the resequencing of two cultivated peppers and a wild species, Capsicum chinense. Comparative genomic analysis across Solanaceae provides insights into genome expansion, pungency, ripening and disease resistance in hot peppers. Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.