Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution

doi:10.1016/j.ympev.2015.12.006

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	Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution
	Sun, Yanxia 1; Moore, Michael J.2; Zhang, Shoujun 1; Soltis, Pamela S.3; Soltis, Douglas E.3; Zhao, Tingting 1; Meng, Aiping 1; Li, Xiaodong 1; Li, Jianqiang 1; Wang, Hengchang 1
刊名	MOLECULAR PHYLOGENETICS AND EVOLUTION
	2016-03-01
卷号	96 页码:93-101
关键词	Early-diverging eudicots Plastome Pseudogene IR boundaries Plastome-scale phylogenetic analyses
ISSN号	1055-7903
DOI	10.1016/j.ympev.2015.12.006
英文摘要	The grade of early-diverging eudicots includes five major lineages: Ranunculales, Trochodendrales, Buxales, Proteales and Sabiaceae. To examine the evolution of plastome structure in early-diverging eudicots, we determined the complete plastome sequences of eight previously unsequenced early-diverging eudicot taxa, Pachysandra terminalis (Buxaceae), Meliosma aff. cuneifolia (Sabiaceae), Sabia yunnanensis (Sabiaceae), Epimedium sagittatum (Berberidaceae), Euptelea pleiosperma (Eupteleaceae), Akebia trifoliata (Lardizabalaceae), Stephania japonica (Menispermaceae) and Papaver somniferum (Papaveraceae), and compared them to previously published plastomes of the early-diverging eudicots Buxus, Tetracentron, Trochodendron, Nelumbo, Platanus, Nandina, Megaleranthis, Ranunculus, Mahonia and Macadamia. All of the newly sequenced plastomes share the same 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes, except for that of Epimedium, in which infA is pseudogenized and cipP is highly divergent and possibly a pseudogene. The boundaries of the plastid Inverted Repeat (IR) were found to vary significantly across early-diverging eudicots; IRs ranged from 24.3 to 36.4 kb in length and contained from 18 to 33 genes. Based on gene content, the IR was classified into six types, with shifts among types characterized by high levels of homoplasy. Reconstruction of ancestral IR gene content suggested that 18 genes were likely present in the IR region of the ancestor of eudicots. Maximum likelihood phylogenetic analysis of a 79-gene, 97-taxon data set that included all available early-diverging eudicots and representative sampling of remaining angiosperm diversity largely agreed with previous estimates of early-diverging eudicot relationships, but resolved Trochodendrales rather than Buxales as sister to Gunneridae, albeit with relatively weak bootstrap support, conflicting with what has been found for these three clades in most previous analyses. In addition, Proteales was resolved as sister to Sabiaceae with the highest support (bootstrap >90%) yet observed in plastome-scale phylogenetic analyses. (C) 2015 Elsevier Inc. All rights reserved.
资助项目	Natural Science Foundation of Hubei Province[2015CFB681] ; National Natural Science Foundation of China[31070191] ; National Natural Science Foundation of China[31370223] ; National Natural Science Foundation of China[31370242] ; US National Science Foundation[DEB EF-0431266]
WOS研究方向	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
语种	英语
出版者	ACADEMIC PRESS INC ELSEVIER SCIENCE
WOS记录号	WOS:000371193200009
内容类型	期刊论文
源URL	[http://202.127.146.157/handle/2RYDP1HH/111]
专题	中国科学院武汉植物园
通讯作者	Li, Jianqiang; Wang, Hengchang
作者单位	1.Chinese Acad Sci, Key Lab Plant Germplasm Enhancement & Specialty A, Wuhan Bot Garden, Wuhan, Hubei, Peoples R China 2.Oberlin Coll, Dept Biol, Oberlin, OH 44074 USA 3.Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA
推荐引用方式 GB/T 7714	Sun, Yanxia,Moore, Michael J.,Zhang, Shoujun,et al. Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2016,96:93-101.
APA	Sun, Yanxia.,Moore, Michael J..,Zhang, Shoujun.,Soltis, Pamela S..,Soltis, Douglas E..,...&Wang, Hengchang.(2016).Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution.MOLECULAR PHYLOGENETICS AND EVOLUTION,96,93-101.
MLA	Sun, Yanxia,et al."Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution".MOLECULAR PHYLOGENETICS AND EVOLUTION 96(2016):93-101.