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

Seungill Kim, Minkyu Park, Seon In Yeom, Yong Min Kim, Je Min Lee, Hyun Ah Lee, Eunyoung Seo, Jaeyoung Choi, Kyeongchae Cheong, Ki Tae Kim, Kyongyong Jung, Gir Won Lee, Sang Keun Oh, Chungyun Bae, Saet Byul Kim, Hye Young Lee, Shin Young Kim, Myung Shin Kim, Byoung Cheorl Kang, Yeong Deuk JoHee Bum Yang, Hee Jin Jeong, Won Hee Kang, Jin Kyung Kwon, Chanseok Shin, Jae Yun Lim, June Hyun Park, Jin Hoe Huh, June Sik Kim, Byung Dong Kim, Oded Cohen, Ilan Paran, Mi Chung Suh, Saet Buyl Lee, Yeon Ki Kim, Younhee Shin, Seung Jae Noh, Junhyung Park, Young Sam Seo, Suk Yoon Kwon, Hyun A. Kim, Jeong Mee Park, Hyun Jin Kim, Sang Bong Choi, Paul W. Bosland, Gregory Reeves, Sung Hwan Jo, Bong Woo Lee, Hyung Taeg Cho, Hee Seung Choi, Min Soo Lee, Yeisoo Yu, Yang Do Choi, Beom Seok Park, Allen Van Deynze, Hamid Ashrafi, Theresa Hill, Woo Taek Kim, Hyun Sook Pai, Hee Kyung Ahn, Inhwa Yeam, James J. Giovannoni, Jocelyn K C Rose, Iben Sørensen, Sang Jik Lee, Ryan W. Kim, Ik Young Choi, Beom Soon Choi, Jong Sung Lim, Yong Hwan Lee, Doil Choi

Research output: Contribution to journalArticle

333 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)270-278
Number of pages9
JournalNature Genetics
Volume46
Issue number3
DOIs
StatePublished - 2014

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Capsicum
Genome
Lycopersicon esculentum
Caulimoviridae
Roma
Genome Size
Spices
Capsaicin
Nutritive Value
Gene Expression

ASJC Scopus subject areas

  • Genetics

Cite this

Kim, S., Park, M., Yeom, S. I., Kim, Y. M., Lee, J. M., Lee, H. A., ... Choi, D. (2014). Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nature Genetics, 46(3), 270-278. https://doi.org/10.1038/ng.2877

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. / Kim, Seungill; Park, Minkyu; Yeom, Seon In; Kim, Yong Min; Lee, Je Min; Lee, Hyun Ah; Seo, Eunyoung; Choi, Jaeyoung; Cheong, Kyeongchae; Kim, Ki Tae; Jung, Kyongyong; Lee, Gir Won; Oh, Sang Keun; Bae, Chungyun; Kim, Saet Byul; Lee, Hye Young; Kim, Shin Young; Kim, Myung Shin; Kang, Byoung Cheorl; Jo, Yeong Deuk; Yang, Hee Bum; Jeong, Hee Jin; Kang, Won Hee; Kwon, Jin Kyung; Shin, Chanseok; Lim, Jae Yun; Park, June Hyun; Huh, Jin Hoe; Kim, June Sik; Kim, Byung Dong; Cohen, Oded; Paran, Ilan; Suh, Mi Chung; Lee, Saet Buyl; Kim, Yeon Ki; Shin, Younhee; Noh, Seung Jae; Park, Junhyung; Seo, Young Sam; Kwon, Suk Yoon; Kim, Hyun A.; Park, Jeong Mee; Kim, Hyun Jin; Choi, Sang Bong; Bosland, Paul W.; Reeves, Gregory; Jo, Sung Hwan; Lee, Bong Woo; Cho, Hyung Taeg; Choi, Hee Seung; Lee, Min Soo; Yu, Yeisoo; Do Choi, Yang; Park, Beom Seok; Van Deynze, Allen; Ashrafi, Hamid; Hill, Theresa; Kim, Woo Taek; Pai, Hyun Sook; Ahn, Hee Kyung; Yeam, Inhwa; Giovannoni, James J.; Rose, Jocelyn K C; Sørensen, Iben; Lee, Sang Jik; Kim, Ryan W.; Choi, Ik Young; Choi, Beom Soon; Lim, Jong Sung; Lee, Yong Hwan; Choi, Doil.

In: Nature Genetics, Vol. 46, No. 3, 2014, p. 270-278.

Research output: Contribution to journalArticle

Kim, S, Park, M, Yeom, SI, Kim, YM, Lee, JM, Lee, HA, Seo, E, Choi, J, Cheong, K, Kim, KT, Jung, K, Lee, GW, Oh, SK, Bae, C, Kim, SB, Lee, HY, Kim, SY, Kim, MS, Kang, BC, Jo, YD, Yang, HB, Jeong, HJ, Kang, WH, Kwon, JK, Shin, C, Lim, JY, Park, JH, Huh, JH, Kim, JS, Kim, BD, Cohen, O, Paran, I, Suh, MC, Lee, SB, Kim, YK, Shin, Y, Noh, SJ, Park, J, Seo, YS, Kwon, SY, Kim, HA, Park, JM, Kim, HJ, Choi, SB, Bosland, PW, Reeves, G, Jo, SH, Lee, BW, Cho, HT, Choi, HS, Lee, MS, Yu, Y, Do Choi, Y, Park, BS, Van Deynze, A, Ashrafi, H, Hill, T, Kim, WT, Pai, HS, Ahn, HK, Yeam, I, Giovannoni, JJ, Rose, JKC, Sørensen, I, Lee, SJ, Kim, RW, Choi, IY, Choi, BS, Lim, JS, Lee, YH & Choi, D 2014, 'Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species', Nature Genetics, vol. 46, no. 3, pp. 270-278. https://doi.org/10.1038/ng.2877
Kim, Seungill ; Park, Minkyu ; Yeom, Seon In ; Kim, Yong Min ; Lee, Je Min ; Lee, Hyun Ah ; Seo, Eunyoung ; Choi, Jaeyoung ; Cheong, Kyeongchae ; Kim, Ki Tae ; Jung, Kyongyong ; Lee, Gir Won ; Oh, Sang Keun ; Bae, Chungyun ; Kim, Saet Byul ; Lee, Hye Young ; Kim, Shin Young ; Kim, Myung Shin ; Kang, Byoung Cheorl ; Jo, Yeong Deuk ; Yang, Hee Bum ; Jeong, Hee Jin ; Kang, Won Hee ; Kwon, Jin Kyung ; Shin, Chanseok ; Lim, Jae Yun ; Park, June Hyun ; Huh, Jin Hoe ; Kim, June Sik ; Kim, Byung Dong ; Cohen, Oded ; Paran, Ilan ; Suh, Mi Chung ; Lee, Saet Buyl ; Kim, Yeon Ki ; Shin, Younhee ; Noh, Seung Jae ; Park, Junhyung ; Seo, Young Sam ; Kwon, Suk Yoon ; Kim, Hyun A. ; Park, Jeong Mee ; Kim, Hyun Jin ; Choi, Sang Bong ; Bosland, Paul W. ; Reeves, Gregory ; Jo, Sung Hwan ; Lee, Bong Woo ; Cho, Hyung Taeg ; Choi, Hee Seung ; Lee, Min Soo ; Yu, Yeisoo ; Do Choi, Yang ; Park, Beom Seok ; Van Deynze, Allen ; Ashrafi, Hamid ; Hill, Theresa ; Kim, Woo Taek ; Pai, Hyun Sook ; Ahn, Hee Kyung ; Yeam, Inhwa ; Giovannoni, James J. ; Rose, Jocelyn K C ; Sørensen, Iben ; Lee, Sang Jik ; Kim, Ryan W. ; Choi, Ik Young ; Choi, Beom Soon ; Lim, Jong Sung ; Lee, Yong Hwan ; Choi, Doil. / Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. In: Nature Genetics. 2014 ; Vol. 46, No. 3. pp. 270-278.
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AU - Seo, Eunyoung

AU - Choi, Jaeyoung

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AU - Lim, Jong Sung

AU - Lee, Yong Hwan

AU - Choi, Doil

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