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 Jo; Hee 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

doi:10.1038/ng.2877

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

Department of Environmental Horticulture

Research output: Contribution to journal › Article › peer-review

797 Scopus citations

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 language	English
Pages (from-to)	270-278
Number of pages	9
Journal	Nature Genetics
Volume	46
Issue number	3
DOIs	https://doi.org/10.1038/ng.2877
State	Published - Mar 2014

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Kim, S., Park, M., Yeom, S. I., Kim, Y. M., Lee, J. M., Lee, H. A., Seo, E., Choi, J., Cheong, K., Kim, K. T., Jung, K., Lee, G. W., Oh, S. K., Bae, C., Kim, S. B., Lee, H. Y., Kim, S. Y., Kim, M. S., Kang, B. C., ... 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

@article{4bbaf4e60bef4a28a588917442360205,

title = "Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species",

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.",

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

year = "2014",

month = mar,

doi = "10.1038/ng.2877",

language = "English",

volume = "46",

pages = "270--278",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

number = "3",

}

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

TY - JOUR

T1 - Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

AU - Kim, Seungill

AU - Park, Minkyu

AU - Yeom, Seon In

AU - Kim, Yong Min

AU - Lee, Je Min

AU - Lee, Hyun Ah

AU - Seo, Eunyoung

AU - Choi, Jaeyoung

AU - Cheong, Kyeongchae

AU - Kim, Ki Tae

AU - Jung, Kyongyong

AU - Lee, Gir Won

AU - Oh, Sang Keun

AU - Bae, Chungyun

AU - Kim, Saet Byul

AU - Lee, Hye Young

AU - Kim, Shin Young

AU - Kim, Myung Shin

AU - Kang, Byoung Cheorl

AU - Jo, Yeong Deuk

AU - Yang, Hee Bum

AU - Jeong, Hee Jin

AU - Kang, Won Hee

AU - Kwon, Jin Kyung

AU - Shin, Chanseok

AU - Lim, Jae Yun

AU - Park, June Hyun

AU - Huh, Jin Hoe

AU - Kim, June Sik

AU - Kim, Byung Dong

AU - Cohen, Oded

AU - Paran, Ilan

AU - Suh, Mi Chung

AU - Lee, Saet Buyl

AU - Kim, Yeon Ki

AU - Shin, Younhee

AU - Noh, Seung Jae

AU - Park, Junhyung

AU - Seo, Young Sam

AU - Kwon, Suk Yoon

AU - Kim, Hyun A.

AU - Park, Jeong Mee

AU - Kim, Hyun Jin

AU - Choi, Sang Bong

AU - Bosland, Paul W.

AU - Reeves, Gregory

AU - Jo, Sung Hwan

AU - Lee, Bong Woo

AU - Cho, Hyung Taeg

AU - Choi, Hee Seung

AU - Lee, Min Soo

AU - Yu, Yeisoo

AU - Do Choi, Yang

AU - Park, Beom Seok

AU - Van Deynze, Allen

AU - Ashrafi, Hamid

AU - Hill, Theresa

AU - Kim, Woo Taek

AU - Pai, Hyun Sook

AU - Ahn, Hee Kyung

AU - Yeam, Inhwa

AU - Giovannoni, James J.

AU - Rose, Jocelyn K.C.

AU - Sørensen, Iben

AU - Lee, Sang Jik

AU - Kim, Ryan W.

AU - Choi, Ik Young

AU - Choi, Beom Soon

AU - Lim, Jong Sung

AU - Lee, Yong Hwan

AU - Choi, Doil

PY - 2014/3

Y1 - 2014/3

N2 - 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.

AB - 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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U2 - 10.1038/ng.2877

DO - 10.1038/ng.2877

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AN - SCOPUS:84895880054

SN - 1061-4036

VL - 46

SP - 270

EP - 278

JO - Nature Genetics

JF - Nature Genetics

IS - 3

ER -

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

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