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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, *
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 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.
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https://hal.inrae.fr/hal-02640860
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Submitted on : Thursday, May 28, 2020 - 3:31:28 PM
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Cheng Qin, Changshui Yu, Yaou Shen, Xiaodong Fang, Lang Chen, et al.. 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 , National Academy of Sciences, 2014, 111 (14), pp.5135-5140. ⟨10.1073/pnas.1400975111⟩. ⟨hal-02640860⟩

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