Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

Qin, Cheng, Yu, Changshui, Shen, Yaou, Fang, Xiaodong, Chen, Lang, Min, Jiumeng, Cheng, Jiaowen, Zhao, Shancen, Xu, Meng, Luo, Yong, Yang, Yulan, Wu, Zhiming, Mao, Likai, Wu, Haiyang, Ling-Hu, Changying, Zhou, Huangkai, Lin, Haijian, Gonzalez-Morales, Sandra, Trejo-Saavedra, Diana L., Tian, Hao, Tang, Xin, Zhao, Maojun, Huang, Zhiyong, Zhou, Anwei, Yao, Xiaoming, Cui, Junjie, Li, Wenqi, Chen, Zhe, Feng, Yongqiang, Niu, Yongchao, Bi, Shimin, Yang, Xiuwei, Li, Weipeng, Cai, Huimin, Luo, Xirong, Montes-Hernandez, Salvador, Leyva-Gonzalez, Marco A., Xiong, Zhiqiang, He, Xiujing, Bai, Lijun, Tan, Shu, Tang, Xiangqun, Liu, Dan, Liu, Jinwen, Zhang, Shangxing, Chen, Maoshan, Zhang, Lu, Zhang, Li, Zhang, Yinchao, Liao, Weiqin, Zhang, Yan, Wang, Min, Lv, Xiaodan, Wen, Bo, Liu, Hongjun, Luan, Hemi, Zhang, Yonggang, Yang, Shuang, Wang, Xiaodian, Xu, Jiaohui, Li, Xueqin, Li, Shuaicheng, Wang, Junyi, Palloix, Alain, Bosland, Paul W., Li, Yingrui, Krogh, Anders, Rivera-Bustamante, Rafael F., Herrera-Estrella, Luis, Yin, Ye, Yu, Jiping, Hu, Kailin and Zhang, Zhiming (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proceedings of the National Academy of Sciences of the United States of America, 111 14: 5135-5140. doi:10.1073/pnas.1400975111

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Author Qin, Cheng
Yu, Changshui
Shen, Yaou
Fang, Xiaodong
Chen, Lang
Min, Jiumeng
Cheng, Jiaowen
Zhao, Shancen
Xu, Meng
Luo, Yong
Yang, Yulan
Wu, Zhiming
Mao, Likai
Wu, Haiyang
Ling-Hu, Changying
Zhou, Huangkai
Lin, Haijian
Gonzalez-Morales, Sandra
Trejo-Saavedra, Diana L.
Tian, Hao
Tang, Xin
Zhao, Maojun
Huang, Zhiyong
Zhou, Anwei
Yao, Xiaoming
Cui, Junjie
Li, Wenqi
Chen, Zhe
Feng, Yongqiang
Niu, Yongchao
Bi, Shimin
Yang, Xiuwei
Li, Weipeng
Cai, Huimin
Luo, Xirong
Montes-Hernandez, Salvador
Leyva-Gonzalez, Marco A.
Xiong, Zhiqiang
He, Xiujing
Bai, Lijun
Tan, Shu
Tang, Xiangqun
Liu, Dan
Liu, Jinwen
Zhang, Shangxing
Chen, Maoshan
Zhang, Lu
Zhang, Li
Zhang, Yinchao
Liao, Weiqin
Zhang, Yan
Wang, Min
Lv, Xiaodan
Wen, Bo
Liu, Hongjun
Luan, Hemi
Zhang, Yonggang
Yang, Shuang
Wang, Xiaodian
Xu, Jiaohui
Li, Xueqin
Li, Shuaicheng
Wang, Junyi
Palloix, Alain
Bosland, Paul W.
Li, Yingrui
Krogh, Anders
Rivera-Bustamante, Rafael F.
Herrera-Estrella, Luis
Yin, Ye
Yu, Jiping
Hu, Kailin
Zhang, Zhiming
Title Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization
Formatted title
Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization
Journal name Proceedings of the National Academy of Sciences of the United States of America   Check publisher's open access policy
ISSN 1091-6490
0027-8424
Publication date 2014-04-08
Sub-type Article (original research)
DOI 10.1073/pnas.1400975111
Open Access Status File (Publisher version)
Volume 111
Issue 14
Start page 5135
End page 5140
Total pages 6
Place of publication Washington, DC United States
Publisher National Academy of Sciences
Language eng
Formatted abstract
As an economic crop, pepper satisfies people’s spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.
Keyword De novo genome sequence
Genome expansion
Solanaceae evolution
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
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