. 2014 Mar;46(3):270-8.

doi: 10.1038/ng.2877. Epub 2014 Jan 19.

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

Seungill Kim¹, Minkyu Park², Seon-In Yeom², Yong-Min Kim², Je Min Lee², Hyun-Ah Lee¹, Eunyoung Seo¹, Jaeyoung Choi³, Kyeongchae Cheong³, Ki-Tae Kim³, Kyongyong Jung³, Gir-Won Lee⁴, Sang-Keun Oh⁵, Chungyun Bae⁶, Saet-Byul Kim⁶, Hye-Young Lee⁶, Shin-Young Kim⁶, Myung-Shin Kim⁶, Byoung-Cheorl Kang⁷, Yeong Deuk Jo⁶, Hee-Bum Yang⁶, Hee-Jin Jeong⁶, Won-Hee Kang⁶, Jin-Kyung Kwon⁸, Chanseok Shin³, Jae Yun Lim³, June Hyun Park³, Jin Hoe Huh⁶, June-Sik Kim⁶, Byung-Dong Kim⁶, Oded Cohen⁹, Ilan Paran⁹, Mi Chung Suh¹⁰, Saet Buyl Lee¹⁰, Yeon-Ki Kim¹¹, Younhee Shin¹², Seung-Jae Noh¹², Junhyung Park¹², Young Sam Seo¹³, Suk-Yoon Kwon¹⁴, Hyun A Kim¹⁴, Jeong Mee Park¹⁴, Hyun-Jin Kim¹⁴, Sang-Bong Choi¹⁵, Paul W Bosland¹⁶, Gregory Reeves¹⁷, Sung-Hwan Jo¹⁸, Bong-Woo Lee¹⁸, Hyung-Taeg Cho¹⁹, Hee-Seung Choi¹⁹, Min-Soo Lee¹⁹, Yeisoo Yu²⁰, Yang Do Choi³, Beom-Seok Park²¹, Allen van Deynze²², Hamid Ashrafi²², Theresa Hill²², Woo Taek Kim²³, Hyun-Sook Pai²³, Hee Kyung Ahn²³, Inhwa Yeam²⁴, James J Giovannoni²⁵, Jocelyn K C Rose²⁶, Iben Sørensen²⁶, Sang-Jik Lee²⁷, Ryan W Kim²⁸, Ik-Young Choi²⁹, Beom-Soon Choi²⁹, Jong-Sung Lim²⁹, Yong-Hwan Lee³, Doil Choi⁵

Affiliations

¹ 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2].
² 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3].
³ Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
⁴ Department of Bioinformatics and Life Science, Soongsil University, Seoul, Korea.
⁵ 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea.
⁶ Department of Plant Science, Seoul National University, Seoul, Korea.
⁷ 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3] Vegetable Breeding Research Center, Seoul National University, Seoul, Korea.
⁸ Vegetable Breeding Research Center, Seoul National University, Seoul, Korea.
⁹ Agricultural Research Organization, Institute of Plant Science, Volcani Center, Bet Dagan, Israel.
¹⁰ Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea.
¹¹ Genomics Genetics Institute, GreenGene BioTech, Inc., Yongin, Korea.
¹² Codes Division, Insilicogen, Inc., Suwon, Korea.
¹³ Ginseng Resources Research Laboratory, Korea Ginseng Corporation, Daejeon, Korea.
¹⁴ Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
¹⁵ Division of Bioscience and Bioinformatics, Myongji University, Yongin, Korea.
¹⁶ 1] Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA. [2] Chile Pepper Institute, New Mexico State University, Las Cruces, New Mexico, USA.
¹⁷ Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA.
¹⁸ Seeders, Inc., Daejeon, Korea.
¹⁹ Department of Biological Sciences, Seoul National University, Seoul, Korea.
²⁰ Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USA.
²¹ Agricultural Genome Center, National Academy of Agricultural Science, Rural Development Administration, Suwon, Korea.
²² Seed Biotechnology Center, University of California, Davis, Davis, California, USA.
²³ Department of Systems Biology, Yonsei University, Seoul, Korea.
²⁴ Department of Horticulture and Breeding, Andong National University, Andong, Korea.
²⁵ 1] US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Ithaca, New York, USA. [2] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA.
²⁶ Department of Plant Biology, Cornell University, Ithaca, New York, USA.
²⁷ Biotechnology Institute, Nongwoo Bio, Yeoju, Korea.
²⁸ Genome Center, University of California, Davis, Davis, California, USA.
²⁹ National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea.

PMID: 24441736
DOI: 10.1038/ng.2877

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

Seungill Kim et al. Nat Genet. 2014 Mar.

. 2014 Mar;46(3):270-8.

doi: 10.1038/ng.2877. Epub 2014 Jan 19.

Authors

Affiliations

¹ 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2].
² 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3].
³ Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
⁴ Department of Bioinformatics and Life Science, Soongsil University, Seoul, Korea.
⁵ 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea.
⁶ Department of Plant Science, Seoul National University, Seoul, Korea.
⁷ 1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3] Vegetable Breeding Research Center, Seoul National University, Seoul, Korea.
⁸ Vegetable Breeding Research Center, Seoul National University, Seoul, Korea.
⁹ Agricultural Research Organization, Institute of Plant Science, Volcani Center, Bet Dagan, Israel.
¹⁰ Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea.
¹¹ Genomics Genetics Institute, GreenGene BioTech, Inc., Yongin, Korea.
¹² Codes Division, Insilicogen, Inc., Suwon, Korea.
¹³ Ginseng Resources Research Laboratory, Korea Ginseng Corporation, Daejeon, Korea.
¹⁴ Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
¹⁵ Division of Bioscience and Bioinformatics, Myongji University, Yongin, Korea.
¹⁶ 1] Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA. [2] Chile Pepper Institute, New Mexico State University, Las Cruces, New Mexico, USA.
¹⁷ Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA.
¹⁸ Seeders, Inc., Daejeon, Korea.
¹⁹ Department of Biological Sciences, Seoul National University, Seoul, Korea.
²⁰ Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USA.
²¹ Agricultural Genome Center, National Academy of Agricultural Science, Rural Development Administration, Suwon, Korea.
²² Seed Biotechnology Center, University of California, Davis, Davis, California, USA.
²³ Department of Systems Biology, Yonsei University, Seoul, Korea.
²⁴ Department of Horticulture and Breeding, Andong National University, Andong, Korea.
²⁵ 1] US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Ithaca, New York, USA. [2] Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA.
²⁶ Department of Plant Biology, Cornell University, Ithaca, New York, USA.
²⁷ Biotechnology Institute, Nongwoo Bio, Yeoju, Korea.
²⁸ Genome Center, University of California, Davis, Davis, California, USA.
²⁹ National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea.

PMID: 24441736
DOI: 10.1038/ng.2877

Abstract

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.

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

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

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