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

Cheng Qin; Changshui Yu; Yaou Shen; Xiaodong Fang; Lang Chen; Jiumeng Min; Jiaowen Cheng; Shancen Zhao; Meng Xu; Yong Luo; Yulan Yang; Zhiming Wu; Likai Mao; Haiyang Wu; Ling-Hu Changying; Huangkai Zhou; Haijian Lin; Sandra González-Morales; Diana L. Trejo-Saavedra; Hao Tian; Xin Tang; Maojun Zhao; Zhiyong Huang; Anwei Zhou; Xiaoming Yao; Junjie Cui; Wenqi Li; Zhe Chen; Yongqiang Feng; Yongchao Niu; Shimin Bi; Xiuwei Yang; Weipeng Li; Huimin Cai; Xirong Luo; Salvador Montes-Hernández; Marco A. Leyva-González; Zhiqiang Xiong; Xiujing He; Lijun Bai; Shu Tan; Xiangqun Tang; Dan Liu; Jinwen Liu; Shangxing Zhang; Maoshan Chen; Lu Zhang; Li Zhang; Yinchao Zhang; Weiqin Liao; Yan Zhang; Min Wang; Xiaodan Lv; Bo Wen; Hongjun Liu; Hemi Luan; Yonggang Zhang; Shuang Yang; Xiaodian Wang; Jiaohui Xu; Xueqin Li; Shuaicheng Li; Junyi Wang; Alain Palloix; Paul W. Bosland; Yingrui Li; Anders Krogh; Rafael F. Rivera-Bustamante; Luis Herrera-Estrella; Ye Yin; Jiping Yu; Kailin Hu; Zhiming Zhang

doi:10.1073/pnas.1400975111

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

Cheng Qin, Changshui Yu, Yaou Shen, Xiaodong Fang, Lang Chen, Jiumeng Min, Jiaowen Cheng, Shancen Zhao, Meng Xu, Yong Luo, Yulan Yang, Zhiming Wu, Likai Mao, Haiyang Wu, Ling-Hu Changying, Huangkai Zhou, Haijian Lin, Sandra González-Morales, Diana L. Trejo-Saavedra, Hao TianXin Tang, Maojun Zhao, Zhiyong Huang, Anwei Zhou, Xiaoming Yao, Junjie Cui, Wenqi Li, Zhe Chen, Yongqiang Feng, Yongchao Niu, Shimin Bi, Xiuwei Yang, Weipeng Li, Huimin Cai, Xirong Luo, Salvador Montes-Hernández, Marco A. Leyva-González, Zhiqiang Xiong, Xiujing He, Lijun Bai, Shu Tan, Xiangqun Tang, Dan Liu, Jinwen Liu, Shangxing Zhang, Maoshan Chen, Lu Zhang, Li Zhang, Yinchao Zhang, Weiqin Liao, Yan Zhang, Min Wang, Xiaodan Lv, Bo Wen, Hongjun Liu, Hemi Luan, Yonggang Zhang, Shuang Yang, Xiaodian Wang, Jiaohui Xu, Xueqin Li, Shuaicheng Li, Junyi Wang, Alain Palloix, Paul W. Bosland, Yingrui Li, Anders Krogh, Rafael F. Rivera-Bustamante, Luis Herrera-Estrella, Ye Yin, Jiping Yu, Kailin Hu, Zhiming Zhang

Department of Computer Science

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

723 Citations (Scopus)

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.

Original language	English
Pages (from-to)	5135-5140
Journal	PNAS: Proceedings of the National Academy of Sciences of the United States of America
Volume	111
Issue number	14
Online published	3 Mar 2014
DOIs	https://doi.org/10.1073/pnas.1400975111
Publication status	Published - 8 Apr 2014

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 2 Zero Hunger

Research Keywords

De novo genome sequence
Genome expansion
Solanaceae evolution

Policy Impact

Cited in Policy Documents

Access Output

10.1073/pnas.1400975111

Other Access Options

Check CityUHK Library

Permanent Link

Right click to copy link

Cite this

Qin, C., Yu, C., Shen, Y., Fang, X., Chen, L., Min, J., Cheng, J., Zhao, S., Xu, M., Luo, Y., Yang, Y., Wu, Z., Mao, L., Wu, H., Changying, L.-H., Zhou, H., Lin, H., González-Morales, S., Trejo-Saavedra, D. L., ... Zhang, Z. (2014). Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. PNAS: Proceedings of the National Academy of Sciences of the United States of America, 111(14), 5135-5140. https://doi.org/10.1073/pnas.1400975111

@article{546dd5aeae2445a6ab667850b70ef425,

title = "Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization",

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.",

keywords = "De novo genome sequence, Genome expansion, Solanaceae evolution",

author = "Cheng Qin and Changshui Yu and Yaou Shen and Xiaodong Fang and Lang Chen and Jiumeng Min and Jiaowen Cheng and Shancen Zhao and Meng Xu and Yong Luo and Yulan Yang and Zhiming Wu and Likai Mao and Haiyang Wu and Ling-Hu Changying and Huangkai Zhou and Haijian Lin and Sandra Gonz{\'a}lez-Morales and Trejo-Saavedra, {Diana L.} and Hao Tian and Xin Tang and Maojun Zhao and Zhiyong Huang and Anwei Zhou and Xiaoming Yao and Junjie Cui and Wenqi Li and Zhe Chen and Yongqiang Feng and Yongchao Niu and Shimin Bi and Xiuwei Yang and Weipeng Li and Huimin Cai and Xirong Luo and Salvador Montes-Hern{\'a}ndez and Leyva-Gonz{\'a}lez, {Marco A.} and Zhiqiang Xiong and Xiujing He and Lijun Bai and Shu Tan and Xiangqun Tang and Dan Liu and Jinwen Liu and Shangxing Zhang and Maoshan Chen and Lu Zhang and Li Zhang and Yinchao Zhang and Weiqin Liao and Yan Zhang and Min Wang and Xiaodan Lv and Bo Wen and Hongjun Liu and Hemi Luan and Yonggang Zhang and Shuang Yang and Xiaodian Wang and Jiaohui Xu and Xueqin Li and Shuaicheng Li and Junyi Wang and Alain Palloix and Bosland, {Paul W.} and Yingrui Li and Anders Krogh and Rivera-Bustamante, {Rafael F.} and Luis Herrera-Estrella and Ye Yin and Jiping Yu and Kailin Hu and Zhiming Zhang",

year = "2014",

month = apr,

day = "8",

doi = "10.1073/pnas.1400975111",

language = "English",

volume = "111",

pages = "5135--5140",

journal = "PNAS: Proceedings of the National Academy of Sciences of the United States of America",

issn = "0027-8424",

publisher = "National Academy of Sciences",

number = "14",

}

Qin, C, Yu, C, Shen, Y, Fang, X, Chen, L, Min, J, Cheng, J, Zhao, S, Xu, M, Luo, Y, Yang, Y, Wu, Z, Mao, L, Wu, H, Changying, L-H, Zhou, H, Lin, H, González-Morales, S, Trejo-Saavedra, DL, Tian, H, Tang, X, Zhao, M, Huang, Z, Zhou, A, Yao, X, Cui, J, Li, W, Chen, Z, Feng, Y, Niu, Y, Bi, S, Yang, X, Li, W, Cai, H, Luo, X, Montes-Hernández, S, Leyva-González, MA, Xiong, Z, He, X, Bai, L, Tan, S, Tang, X, Liu, D, Liu, J, Zhang, S, Chen, M, Zhang, L, Zhang, L, Zhang, Y, Liao, W, Zhang, Y, Wang, M, Lv, X, Wen, B, Liu, H, Luan, H, Zhang, Y, Yang, S, Wang, X, Xu, J, Li, X, Li, S, Wang, J, Palloix, A, Bosland, PW, Li, Y, Krogh, A, Rivera-Bustamante, RF, Herrera-Estrella, L, Yin, Y, Yu, J, Hu, K & Zhang, Z 2014, 'Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization', PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 14, pp. 5135-5140. https://doi.org/10.1073/pnas.1400975111

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. / Qin, Cheng; Yu, Changshui; Shen, Yaou et al.
In: PNAS: Proceedings of the National Academy of Sciences of the United States of America, Vol. 111, No. 14, 08.04.2014, p. 5135-5140.

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

TY - JOUR

T1 - Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

AU - Qin, Cheng

AU - Yu, Changshui

AU - Shen, Yaou

AU - Fang, Xiaodong

AU - Chen, Lang

AU - Min, Jiumeng

AU - Cheng, Jiaowen

AU - Zhao, Shancen

AU - Xu, Meng

AU - Luo, Yong

AU - Yang, Yulan

AU - Wu, Zhiming

AU - Mao, Likai

AU - Wu, Haiyang

AU - Changying, Ling-Hu

AU - Zhou, Huangkai

AU - Lin, Haijian

AU - González-Morales, Sandra

AU - Trejo-Saavedra, Diana L.

AU - Tian, Hao

AU - Tang, Xin

AU - Zhao, Maojun

AU - Huang, Zhiyong

AU - Zhou, Anwei

AU - Yao, Xiaoming

AU - Cui, Junjie

AU - Li, Wenqi

AU - Chen, Zhe

AU - Feng, Yongqiang

AU - Niu, Yongchao

AU - Bi, Shimin

AU - Yang, Xiuwei

AU - Li, Weipeng

AU - Cai, Huimin

AU - Luo, Xirong

AU - Montes-Hernández, Salvador

AU - Leyva-González, Marco A.

AU - Xiong, Zhiqiang

AU - He, Xiujing

AU - Bai, Lijun

AU - Tan, Shu

AU - Tang, Xiangqun

AU - Liu, Dan

AU - Liu, Jinwen

AU - Zhang, Shangxing

AU - Chen, Maoshan

AU - Zhang, Lu

AU - Zhang, Li

AU - Zhang, Yinchao

AU - Liao, Weiqin

AU - Zhang, Yan

AU - Wang, Min

AU - Lv, Xiaodan

AU - Wen, Bo

AU - Liu, Hongjun

AU - Luan, Hemi

AU - Zhang, Yonggang

AU - Yang, Shuang

AU - Wang, Xiaodian

AU - Xu, Jiaohui

AU - Li, Xueqin

AU - Li, Shuaicheng

AU - Wang, Junyi

AU - Palloix, Alain

AU - Bosland, Paul W.

AU - Li, Yingrui

AU - Krogh, Anders

AU - Rivera-Bustamante, Rafael F.

AU - Herrera-Estrella, Luis

AU - Yin, Ye

AU - Yu, Jiping

AU - Hu, Kailin

AU - Zhang, Zhiming

PY - 2014/4/8

Y1 - 2014/4/8

N2 - 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.

AB - 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.

KW - De novo genome sequence

KW - Genome expansion

KW - Solanaceae evolution

UR - http://www.scopus.com/inward/record.url?scp=84898022114&partnerID=8YFLogxK

UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-84898022114&origin=recordpage

UR - https://app-overton-io.ezproxy.cityu.edu.hk/articles.php?query=10.1073/pnas.1400975111

U2 - 10.1073/pnas.1400975111

DO - 10.1073/pnas.1400975111

M3 - RGC 21 - Publication in refereed journal

C2 - 24591624

SN - 0027-8424

VL - 111

SP - 5135

EP - 5140

JO - PNAS: Proceedings of the National Academy of Sciences of the United States of America

JF - PNAS: Proceedings of the National Academy of Sciences of the United States of America

IS - 14

ER -

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

Abstract

UN SDGs

Research Keywords

Policy Impact

Access Output

Other Access Options

Permanent Link

Other Files and Links

Fingerprint

Cite this