Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization
Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization
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栽培辣椒和野生辣椒的全基因组测序为辣椒驯化和专业化提供了见解
DOI：
10.1073/pnas.1400975111
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发表时间：
2014-04-08
影响因子：
11.1
通讯作者：
Zhang, Zhiming
中科院分区：
文献类型：
--
作者：
Qin, Cheng;Yu, Changshui;Zhang, Zhiming
意义 这两个辣椒基因组与 20 个重测序材料（包括 3 个被归类为半野生/野生的材料）一起，可以更好地了解各种辣椒物种的进化、驯化和分化，并最终将增强这一重要的全球作物的未来遗传改良。辣椒作为一种经济作物，满足了人们的辛辣口味，在世界范围内都有药用价值。为了更好地了解辣椒的进化、驯化和特化，我们在此展示了栽培辣椒 Zunla-1 (C. annuum L.) 及其野生祖先 Chiltepin (C. annuum var. glabriusculum) 的基因组序列。我们估计，通过逆转录转座子元件的快速扩增，辣椒基因组扩展了~0.3 Mya（相对于其他茄科植物的基因组），导致基因组由~81%的重复序列组成。大约 79% 的 3.48-Gb 支架包含 34,476 个蛋白质编码基因，通过高密度遗传图谱锚定在染色体上。将栽培辣椒和野生辣椒基因组与 20 个重测序材料进行比较，揭示了人工选择的分子足迹，为我们提供了候选驯化基因的列表。我们还发现串联重复基因的剂量补偿效应可能有助于辣椒的辛辣多样化。辣椒参考基因组不仅为研究辣椒基因组的进化提供了重要信息，而且为茄科家族的进化研究提供了重要信息，并将有助于建立更有效的辣椒育种计划。
Significance The two pepper genomes together with 20 resequencing accessions, including 3 accessions that are classified as semiwild/wild, provide a better understanding of the evolution, domestication, and divergence of various pepper species and ultimately, will enhance future genetic improvement of this important worldwide crop. 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.