Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion

doi:10.1016/j.pld.2020.07.008

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	Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion
	Yusupov,Ziyoviddin ; Deng,Tao; Volis,Sergei ; Khassanov,Furkat ; Makhmudjanov,Dilmurod ; Tojibaev,Komiljon ; Sun,Hang
	2021
发表期刊	PLANT DIVERSITY
ISSN	2096-2703
卷号	43 期号:2 页码:102-110
摘要	Allium sect. Cepa (Amaryllidaceae) comprises economically important plants, yet resolving the phylogenetic relationships within the section has been difficult as nuclear and chloroplast-based phylogenetic trees have been incongruent. Until now, phylogenetic studies of the section have been based on a few genes. In this study, we sequenced the complete chloroplast genome (plastomes) of four central Asian species of sect. Cepa: Allium oschaninii, A. praemixtum, A. pskemense and A. galanthum. Their chloroplast (cp) genomes included 114 unique genes of which 80 coded proteins. Seven protein-coding genes were highly variable and therefore promising for future phylogenetic and phylogeographic studies. Our plastome-based phylogenetic tree of Allium sect. Cepa revealed two separate clades: one comprising the central Asian species A. oschaninii, A. praemixtum, and A. pskemense, and another comprising A. galanthum, A. altaicum, and two cultivated species, A. cepa and A. fistulosum. These findings contradict previously reported phylogenies that relied on ITS and morphology. Possible explanations for this discrepancy are related to interspecific hybridization of species ancestral to A. galanthum and A. cepa followed by chloroplast capture; however, this is impossible to prove without additional data. Our results suggest that the central Asian Allium species did not play a role in the domestication of the common onion. Among the chloroplast genes, rpoC2 was identified as a gene of choice in further phylogeographical studies of the genus Allium. Copyright (C) 2020 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co., Ltd.
关键词	Chloroplast genome SNP Phylogeny Chloroplast capture PHYLOGENETIC ANALYSIS CHLOROPLAST GENOME WILD DNA
DOI	10.1016/j.pld.2020.07.008
WOS记录号	WOS:000644759700002
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73305
专题	中国科学院昆明植物研究所
作者单位	1.Chinese Acad Sci, Kunming Inst Bot, CAS Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China 2.Acad Sci Uzbek, Inst Bot, Int Joint Lab Mol Phylogeny & Biogeog, Tashkent 100125, Uzbekistan 3.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Yusupov,Ziyoviddin,Deng,Tao,Volis,Sergei,et al. Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion[J]. PLANT DIVERSITY,2021,43(2):102-110.
APA	Yusupov,Ziyoviddin.,Deng,Tao.,Volis,Sergei.,Khassanov,Furkat.,Makhmudjanov,Dilmurod.,...&Sun,Hang.(2021).Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion.PLANT DIVERSITY,43(2),102-110.
MLA	Yusupov,Ziyoviddin,et al."Phylogenomics of Allium section Cepa (Amaryllidaceae) provides new insights on domestication of onion".PLANT DIVERSITY 43.2(2021):102-110.

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