Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region

doi:10.3389/fpls.2021.712064

KIB OpenIR

	Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region
	Wei,Neng ; Perez-Escobar,Oscar A.; Musili,Paul M.; Huang,Wei-Chang ; Yang,Jun-Bo ; Hu,Ai-Qun ; Hu,Guang-Wan ; Grace,Olwen M.; Wang,Qing-Feng
	2021
发表期刊	FRONTIERS IN PLANT SCIENCE
ISSN	1664-462X
卷号	12 页码:712064
摘要	With c. 2,000 species, Euphorbia is one of the largest angiosperm genera, yet a lack of chloroplast genome (plastome) resources impedes a better understanding of its evolution. In this study, we assembled and annotated 28 plastomes from Euphorbiaceae, of which 15 were newly sequenced. Phylogenomic and comparative analyses of 22 plastome sequences from all four recognized subgenera within Euphorbia revealed that plastome length in Euphorbia is labile, presenting a range of variation c. 42 kb. Large-scale expansions of the inverted repeat (IR) region were identified, and at the extreme opposite, the near-complete loss of the IR region (with only 355 bp left) was detected for the first time in Euphorbiaceae. Other structural variations, including gene inversion and duplication, and gene loss/pseudogenization, were also observed. We screened the most promising molecular markers from both intergenic and coding regions for phylogeny-based utilities, and estimated maximum likelihood and Bayesian phylogenies from four datasets including whole plastome sequences. The monophyly of Euphorbia is supported, and its four subgenera are recovered in a successive sister relationship. Our study constitutes the first comprehensive investigation on the plastome structural variation in Euphorbia and it provides resources for phylogenetic research in the genus, facilitating further studies on its taxonomy, evolution, and conservation.
关键词	comparative genomics organellar evolution phylogenetic inference plastome rearrangement spurge family structural variations COMPLETE CHLOROPLAST GENOME RETICULATE EVOLUTION MOLECULAR PHYLOGENY SUBSTITUTION RATES MULTIPLE ALIGNMENT DNA-SEQUENCES CLASSIFICATION REVEAL PLANT RECOMBINATION
DOI	10.3389/fpls.2021.712064
WOS记录号	WOS:000688084800001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73247
专题	中国科学院昆明植物研究所
作者单位	1.Chinese Acad Sci, Key Lab Plant Germplasm Enhancement & Specialty A, Wuhan Bot Garden, Wuhan, Peoples R China 2.Wei, Neng; Perez-Escobar, Oscar A.; Hu, Ai-Qun; Grace, Olwen M.] Royal Bot Gardens, Richmond, Surrey, England 3.Chinese Acad Sci, Ctr Conservat Biol, Core Bot Gardens, Wuhan, Peoples R China 4.Univ Chinese Acad Sci, Beijing, Peoples R China 5.Musili, Paul M.] Natl Museums Kenya, East African Herbarium, Nairobi, Kenya 6.Chinese Acad Sci, Shanghai Chenshan Plant Sci Res Ctr, Chenshan Bot Garden, Shanghai, Peoples R China 7.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming, Yunnan, Peoples R China 8.Chinese Acad Sci, Sino Africa Joint Res Ctr, Wuhan, Peoples R China
推荐引用方式 GB/T 7714	Wei,Neng,Perez-Escobar,Oscar A.,Musili,Paul M.,et al. Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region[J]. FRONTIERS IN PLANT SCIENCE,2021,12:712064.
APA	Wei,Neng.,Perez-Escobar,Oscar A..,Musili,Paul M..,Huang,Wei-Chang.,Yang,Jun-Bo.,...&Wang,Qing-Feng.(2021).Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region.FRONTIERS IN PLANT SCIENCE,12,712064.
MLA	Wei,Neng,et al."Plastome Evolution in the Hyperdiverse Genus Euphorbia (Euphorbiaceae) Using Phylogenomic and Comparative Analyses: Large-Scale Expansion and Contraction of the Inverted Repeat Region".FRONTIERS IN PLANT SCIENCE 12(2021):712064.