干旱区生态环境知识资源中心(Arid): Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae)

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DOI	10.1038/s41598-021-82692-5
	Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae)
	Namgung, Ju; Hoang Dang Khoa Do; Kim, Changkyun; Choi, Hyeok Jae; Kim, Joo-Hwan
通讯作者	Kim, JH (corresponding author), Gachon Univ, Dept Life Sci, Seongnam 13120, South Korea.
来源期刊	SCIENTIFIC REPORTS
ISSN	2045-2322
出版年	2021
卷号	11 期号:1
英文摘要	Allioideae includes economically important bulb crops such as garlic, onion, leeks, and some ornamental plants in Amaryllidaceae. Here, we reported the complete chloroplast genome (cpDNA) sequences of 17 species of Allioideae, five of Amaryllidoideae, and one of Agapanthoideae. These cpDNA sequences represent 80 protein-coding, 30 tRNA, and four rRNA genes, and range from 151,808 to 159,998 bp in length. Loss and pseudogenization of multiple genes (i.e., rps2, infA, and rpl22) appear to have occurred multiple times during the evolution of Alloideae. Additionally, eight mutation hotspots, including rps15-ycf1, rps16-trnQ-UUG, petG-trnW-CCA, psbA upstream, rpl32-trnL-UAG, ycf1, rpl22, matK, and ndhF, were identified in the studied Allium species. Additionally, we present the first phylogenomic analysis among the four tribes of Allioideae based on 74 cpDNA coding regions of 21 species of Allioideae, five species of Amaryllidoideae, one species of Agapanthoideae, and five species representing selected members of Asparagales. Our molecular phylogenomic results strongly support the monophyly of Allioideae, which is sister to Amaryllioideae. Within Allioideae, Tulbaghieae was sister to Gilliesieae-Leucocoryneae whereas Allieae was sister to the clade of Tulbaghieae- Gilliesieae-Leucocoryneae. Molecular dating analyses revealed the crown age of Allioideae in the Eocene (40.1 mya) followed by differentiation of Allieae in the early Miocene (21.3 mya). The split of Gilliesieae from Leucocoryneae was estimated at 16.5 mya. Biogeographic reconstruction suggests an African origin for Allioideae and subsequent spread to Eurasia during the middle Eocene. Cool and arid conditions during the late Eocene led to isolation between African and Eurasian species. African Allioideae may have diverged to South American taxa in the late Oligocene. Rather than vicariance, long-distance dispersal is the most likely explanation for intercontinental distribution of African and South American Allioideae species.
类型	Article
语种	英语
开放获取类型	Green Published, gold
收录类别	SCI-E
WOS记录号	WOS:000617535800017
WOS关键词	DNA ; SOFTWARE
WOS类目	Multidisciplinary Sciences
WOS研究方向	Science & Technology - Other Topics
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/369013
作者单位	[Namgung, Ju; Hoang Dang Khoa Do; Kim, Changkyun; Kim, Joo-Hwan] Gachon Univ, Dept Life Sci, Seongnam 13120, South Korea; [Hoang Dang Khoa Do] Nguyen Tat Thanh Univ, Nguyen Tat Thanh Hitech Inst, Ho Chi Minh City, Vietnam; [Choi, Hyeok Jae] Changwon Natl Univ, Dept Biol & Chem, Changwon Si 51140, Gyeongsangnamdo, South Korea
推荐引用方式 GB/T 7714	Namgung, Ju,Hoang Dang Khoa Do,Kim, Changkyun,et al. Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae)[J],2021,11(1).
APA	Namgung, Ju,Hoang Dang Khoa Do,Kim, Changkyun,Choi, Hyeok Jae,&Kim, Joo-Hwan.(2021).Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae).SCIENTIFIC REPORTS,11(1).
MLA	Namgung, Ju,et al."Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae)".SCIENTIFIC REPORTS 11.1(2021).