Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization
Cheng Qin
(1, 2, 3)
,
Changshui Yu
(2)
,
Yaou Shen
(1)
,
Xiaodong Fang
(4, 5)
,
Lang Chen
(2)
,
Jiumeng Min
(4)
,
Jiaowen Cheng
(3)
,
Shancen Zhao
(4)
,
Meng Xu
(4)
,
Yong Luo
(2)
,
Yulan Yang
(4)
,
Zhiming Wu
(6)
,
Likai Mao
(4)
,
Haiyang Wu
(4)
,
Changying Ling-Hu
(2)
,
Huangkai Zhou
(4)
,
Haijian Lin
(1)
,
Sandra Gonzalez-Morales
(7)
,
Diana L. Trejo-Saavedra
(8)
,
Hao Tian
(2)
,
Xin Tang
(3)
,
Maojun Zhao
(9)
,
Zhiyong Huang
(4)
,
Anwei Zhou
(2)
,
Xiaoming Yao
(4)
,
Junjie Cui
(3)
,
Wenqi Li
(4)
,
Zhe Chen
(1)
,
Yongqiang Feng
(2)
,
Yongchao Niu
(4)
,
Shimin Bi
(2)
,
Xiuwei Yang
(2)
,
Weipeng Li
(3)
,
Huimin Cai
(4)
,
Xirong Luo
(2)
,
Salvador Montes-Hernandez
(10)
,
Marco A. Leyva-Gonzalez
(7)
,
Zhiqiang Xiong
(4)
,
Xiujing He
(1)
,
Lijun Bai
(4)
,
Shu Tan
(3)
,
Xiangqun Tang
(2)
,
Dan Liu
(4)
,
Jinwen Liu
(4)
,
Shangxing Zhang
(2)
,
Maoshan Chen
(4)
,
Lu Zhang
(4, 11)
,
Li Zhang
(3)
,
Yinchao Zhang
(1)
,
Weiqin Liao
(2)
,
Yan Zhang
(4)
,
Min Wang
(2)
,
Xiaodan Lv
(4)
,
Bo Wen
(4)
,
Hongjun Liu
(1)
,
Hemi Luan
(4)
,
Yonggang Zhang
(2)
,
Shuang Yang
(4)
,
Xiaodian Wang
(2)
,
Jiaohui Xu
(4)
,
Xueqin Li
(2)
,
Shuaicheng Li
(11)
,
Junyi Wang
(4)
,
Alain Palloix
(12)
,
Paul W. Bosland
(13)
,
Yingrui Li
(4)
,
Anders Krogh
(5)
,
Rafael F. Rivera-Bustamante
(8)
,
Luis Herrera-Estrella
(7)
,
Ye Yin
(4)
,
Jiping Yu
(2)
,
Kailin Hu
(3)
,
Zhiming Zhang
(1)
1
Ministry of Agriculture
2 Zunyi Academy of Agricultural Sciences
3 College of Horticulture
4 BGI - Beijing Genomics Institute [Shenzhen]
5 Department of Biology
6 Zhongkai University of Agriculture and Engineering
7 CINVESTAV - Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional
8 Instituto Politécnico Nacional
9 Sichuan Agricultural University
10 INIFAP - Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias [Mexico]
11 CUHK - City University of Hong Kong [Hong Kong]
12 GAFL - Génétique et Amélioration des Fruits et Légumes
13 New Mexico State University
2 Zunyi Academy of Agricultural Sciences
3 College of Horticulture
4 BGI - Beijing Genomics Institute [Shenzhen]
5 Department of Biology
6 Zhongkai University of Agriculture and Engineering
7 CINVESTAV - Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional
8 Instituto Politécnico Nacional
9 Sichuan Agricultural University
10 INIFAP - Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias [Mexico]
11 CUHK - City University of Hong Kong [Hong Kong]
12 GAFL - Génétique et Amélioration des Fruits et Légumes
13 New Mexico State University
Cheng Qin
- Fonction : co premier-auteur
Xiaodong Fang
- Fonction : co premier-auteur
Lang Chen
- Fonction : co premier-auteur
- PersonId : 801049
- ORCID : 0000-0002-2118-5601
Dan Liu
- Fonction : Auteur
- PersonId : 774383
- ORCID : 0000-0001-5888-7933
Yan Zhang
- Fonction : Auteur
- PersonId : 756469
- ORCID : 0000-0003-0744-6198
Luis Herrera-Estrella
Connectez-vous pour contacter l'auteur
- Fonction : Auteur correspondant
- PersonId : 959713
Connectez-vous pour contacter l'auteur
Résumé
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 similar to 0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of similar to 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.