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

被引：635

作者：

Qin, Cheng ^{[1
,3
]}

Yu, Changshui ^{[2
]}

Shen, Yaou ^{[1
]}

Fang, Xiaodong ^{[4
,5
]}

Chen, Lang ^{[2
]}

Min, Jiumeng ^{[4
]}

Cheng, Jiaowen ^{[3
]}

Zhao, Shancen ^{[4
]}

Xu, Meng ^{[4
]}

Luo, Yong ^{[2
]}

Yang, Yulan ^{[4
]}

Wu, Zhiming ^{[6
]}

Mao, Likai ^{[4
]}

Wu, Haiyang ^{[4
]}

Ling-Hu, Changying ^{[2
]}

Zhou, Huangkai ^{[4
]}

Lin, Haijian ^{[1
]}

Gonzalez-Morales, Sandra ^{[7
]}

Trejo-Saavedra, Diana L. ^{[8
]}

Tian, Hao ^{[2
]}

Tang, Xin ^{[3
]}

Zhao, Maojun ^{[9
]}

Huang, Zhiyong ^{[4
]}

Zhou, Anwei ^{[2
]}

Yao, Xiaoming ^{[4
]}

Cui, Junjie ^{[3
]}

Li, Wenqi ^{[4
]}

Chen, Zhe ^{[1
]}

Feng, Yongqiang ^{[2
]}

Niu, Yongchao ^{[4
]}

Bi, Shimin ^{[2
]}

Yang, Xiuwei ^{[2
]}

Li, Weipeng ^{[3
]}

Cai, Huimin ^{[4
]}

Luo, Xirong ^{[2
]}

Montes-Hernandez, Salvador ^{[10
]}

Leyva-Gonzalez, Marco A. ^{[7
]}

Xiong, Zhiqiang ^{[4
]}

He, Xiujing ^{[1
]}

Bai, Lijun ^{[4
]}

Tan, Shu ^{[3
]}

Tang, Xiangqun ^{[2
]}

Liu, Dan ^{[4
]}

Liu, Jinwen ^{[3
,4
]}

Zhang, Shangxing ^{[2
]}

Chen, Maoshan ^{[4
]}

Zhang, Lu ^{[4
,11
]}

Zhang, Li ^{[3
]}

Zhang, Yinchao

Liao, Weiqin ^{[2
]}

机构：

[1] Sichuan Agr Univ, Maize Res Inst, Key Lab Biol & Genet Improvement Maize Southwest, Minist Agr, Wenjiang 611130, Peoples R China

[2] Zunyi Acad Agr Sci, Pepper Inst, Shenzhen 563102, Peoples R China

[3] S China Agr Univ, Coll Hort, Guangzhou 510642, Guangdong, Peoples R China

[4] Beijing Genom Inst Shenzhen, Shenzhen 518083, Peoples R China

[5] Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark

[6] Zhongkai Univ Agr & Engn, Coll Hort & Landscape Architecture, Guangzhou 510225, Guangdong, Peoples R China

[7] Lab Nacl Genom Biodiversidad Langebio, Ctr Invest Estudios Avanzados Cinvestav, Irapuato 36821, Mexico

[8] Unidad Irapuato, Dept Ingn Gen, Ctr Invest & Estudios Avanzados IPN Cinvestav, Irapuato 36821, Mexico

[9] Sichuan Agr Univ, Coll Biol & Sci, Yaan 625014, Peoples R China

[10] Inst Nacl Invest Forestales Agricolas & Pecuarias, Celaya 38010, Mexico

[11] City Univ Hong Kong, Dept Comp Sci, Hong Kong 999077, Hong Kong, Peoples R China

[12] INRA Provence Alpes Cote Azur, UR1052, Unit Genet & Ameliorat Fruits & Legumes, F-84140 Montfavet, France

[13] New Mexico State Univ, Chile Pepper Inst, Las Cruces, NM 88003 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2014年 / 111卷 / 14期

关键词：

de novo genome sequence; genome expansion; Solanaceae evolution; GENETIC DIVERSITY; DRAFT GENOME; ANNUUM; FRUIT; RETROTRANSPOSONS; ACCUMULATION; SOLANACEAE; RESISTANCE; EVOLUTION; SELECTION;

D O I：

10.1073/pnas.1400975111

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页码：5135 / 5140

页数：6

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