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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #322429

Research Project: Genetic and Genomic Basis of Vegetable and Fruit Biology, Quality and Nutrient Content

Location: Plant, Soil and Nutrition Research

Title: Genome sequence of the hot pepper provides insights into the evolution of pungency in Capscicum species

item KIM, SEUNGILL - Seoul National University
item PARK, MINKYU - Seoul National University
item YEOM, SEON-IN - Seoul National University
item KIM, YONG-MIN - Seoul National University
item LEE, JEMIN - Boyce Thompson Institute
item LEE, HYUN-AHN - Boyce Thompson Institute
item Giovannoni, James
item SORENSEN, IBEN - Cornell University - New York
item ROSE, JOCELYN - Cornell University - New York
item CHOI, DOIL - Seoul National University

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/24/2014
Publication Date: 12/29/2014
Citation: Kim, S., Park, M., Yeom, S., Kim, Y., Lee, J., Lee, H., Giovannoni, J.J., Sorensen, I., Rose, J., Choi, D. 2014. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capscicum species. Nature Genetics. 46:270-279.

Interpretive Summary: 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.

Technical Abstract: Hot pepper is an important spice crop the world-over and is closely related to sweet peppers that represent an important vegetable crop in many cultures. Both hot and mild peppers are important sources of dietary nutrients and hot pepper is a source of the medicinal compound capsaicin, which is widely used in topical anti-pain medications. Here we report the first genome sequence of a pepper species in addition to sequences for two cultivated varieties. We also present gene expression data for the full complement of sequenced pepper genes in multiple tissues and emphasizing fruit, as enabled by the genome sequence. Capture of the nearly complete repertoire of pepper genome sequences and their expression during fruit development reveals important genes in capsaicin synthesis and insights into the evolutionary conservation of ripening mechanisms. We also demonstrate that the pepper genome is greatly expanded as compared to its close relative tomato.