Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species.
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.
1] Department of Plant Science, Seoul National University, Seoul, Korea. [2].
Seungill
S
Kim
1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3].
Minkyu
M
Park
1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3].
Seon-In
SI
Yeom
1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3].
Yong-Min
YM
Kim
1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea. [3].
Je Min
JM
Lee
1] Department of Plant Science, Seoul National University, Seoul, Korea. [2].
Hyun-Ah
HA
Lee
1] Department of Plant Science, Seoul National University, Seoul, Korea. [2].
Eunyoung
E
Seo
Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
Jaeyoung
J
Choi
Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
Kyeongchae
K
Cheong
Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
Ki-Tae
KT
Kim
Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
Kyongyong
K
Jung
Department of Bioinformatics and Life Science, Soongsil University, Seoul, Korea.
Gir-Won
GW
Lee
1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea.
Sang-Keun
SK
Oh
Department of Plant Science, Seoul National University, Seoul, Korea.
Chungyun
C
Bae
Department of Plant Science, Seoul National University, Seoul, Korea.
Saet-Byul
SB
Kim
Department of Plant Science, Seoul National University, Seoul, Korea.
Hye-Young
HY
Lee
Department of Plant Science, Seoul National University, Seoul, Korea.
Shin-Young
SY
Kim
Department of Plant Science, Seoul National University, Seoul, Korea.
Myung-Shin
MS
Kim
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.
Byoung-Cheorl
BC
Kang
Department of Plant Science, Seoul National University, Seoul, Korea.
Yeong Deuk
YD
Jo
Department of Plant Science, Seoul National University, Seoul, Korea.
Hee-Bum
HB
Yang
Department of Plant Science, Seoul National University, Seoul, Korea.
Hee-Jin
HJ
Jeong
Department of Plant Science, Seoul National University, Seoul, Korea.
Won-Hee
WH
Kang
Vegetable Breeding Research Center, Seoul National University, Seoul, Korea.
Jin-Kyung
JK
Kwon
Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
Chanseok
C
Shin
Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
Jae Yun
JY
Lim
Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
June Hyun
JH
Park
Department of Plant Science, Seoul National University, Seoul, Korea.
Jin Hoe
JH
Huh
Department of Plant Science, Seoul National University, Seoul, Korea.
June-Sik
JS
Kim
Department of Plant Science, Seoul National University, Seoul, Korea.
Byung-Dong
BD
Kim
Agricultural Research Organization, Institute of Plant Science, Volcani Center, Bet Dagan, Israel.
Oded
O
Cohen
Agricultural Research Organization, Institute of Plant Science, Volcani Center, Bet Dagan, Israel.
Ilan
I
Paran
Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea.
Mi Chung
MC
Suh
Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, Korea.
Saet Buyl
SB
Lee
Genomics Genetics Institute, GreenGene BioTech, Inc., Yongin, Korea.
Yeon-Ki
YK
Kim
Codes Division, Insilicogen, Inc., Suwon, Korea.
Younhee
Y
Shin
Codes Division, Insilicogen, Inc., Suwon, Korea.
Seung-Jae
SJ
Noh
Codes Division, Insilicogen, Inc., Suwon, Korea.
Junhyung
J
Park
Ginseng Resources Research Laboratory, Korea Ginseng Corporation, Daejeon, Korea.
Young Sam
YS
Seo
Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
Suk-Yoon
SY
Kwon
Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
Hyun A
HA
Kim
Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
Jeong Mee
JM
Park
Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea.
Hyun-Jin
HJ
Kim
Division of Bioscience and Bioinformatics, Myongji University, Yongin, Korea.
Sang-Bong
SB
Choi
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.
Paul W
PW
Bosland
Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, USA.
Gregory
G
Reeves
Seeders, Inc., Daejeon, Korea.
Sung-Hwan
SH
Jo
Seeders, Inc., Daejeon, Korea.
Bong-Woo
BW
Lee
Department of Biological Sciences, Seoul National University, Seoul, Korea.
Hyung-Taeg
HT
Cho
Department of Biological Sciences, Seoul National University, Seoul, Korea.
Hee-Seung
HS
Choi
Department of Biological Sciences, Seoul National University, Seoul, Korea.
Min-Soo
MS
Lee
Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USA.
Yeisoo
Y
Yu
Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
Yang
Y
Do Choi
Agricultural Genome Center, National Academy of Agricultural Science, Rural Development Administration, Suwon, Korea.
Beom-Seok
BS
Park
Seed Biotechnology Center, University of California, Davis, Davis, California, USA.
Allen
A
van Deynze
Seed Biotechnology Center, University of California, Davis, Davis, California, USA.
Hamid
H
Ashrafi
Seed Biotechnology Center, University of California, Davis, Davis, California, USA.
Theresa
T
Hill
Department of Systems Biology, Yonsei University, Seoul, Korea.
Woo Taek
WT
Kim
Department of Systems Biology, Yonsei University, Seoul, Korea.
Hyun-Sook
HS
Pai
Department of Systems Biology, Yonsei University, Seoul, Korea.
Hee Kyung
HK
Ahn
Department of Horticulture and Breeding, Andong National University, Andong, Korea.
Inhwa
I
Yeam
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.
James J
JJ
Giovannoni
Department of Plant Biology, Cornell University, Ithaca, New York, USA.
Jocelyn K C
JK
Rose
Department of Plant Biology, Cornell University, Ithaca, New York, USA.
Iben
I
Sørensen
Biotechnology Institute, Nongwoo Bio, Yeoju, Korea.
Sang-Jik
SJ
Lee
Genome Center, University of California, Davis, Davis, California, USA.
Ryan W
RW
Kim
National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea.
Ik-Young
IY
Choi
National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea.
Beom-Soon
BS
Choi
National Instrumentation Center for Environmental Management, Seoul National University, Seoul, Korea.
Jong-Sung
JS
Lim
Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
Yong-Hwan
YH
Lee
1] Department of Plant Science, Seoul National University, Seoul, Korea. [2] Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea.
Doil
D
Choi
D002211:Capsaicin / Q000378:metabolism; D002212:Capsicum / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D019143:Evolution, Molecular; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D059646:Genome Size; D018745:Genome, Plant; D018551:Solanum lycopersicum / Q000235:genetics; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D018749:RNA, Plant / Q000235:genetics; D013045:Species Specificity
D018749:RNA, Plant; D002211:Capsaicin