Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae

doi:10.1186/s12862-020-01661-0

CORC > 植物研究所 > 中国科学院植物研究所 > 系统与进化植物学国家重点实验室

	Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae
	Dong, Wenpan 4; Xu, Chao ; Wen, Jun 1; Zhou, Shiliang 2
刊名	BMC EVOLUTIONARY BIOLOGY
	2020
卷号	20 期号:1
关键词	Chloroplast genome Calycanthaceae Structural mutations Substitution rate Indels
ISSN号	1471-2148
DOI	10.1186/s12862-020-01661-0
文献子类	Article
英文摘要	Background Chloroplast genome sequence data is very useful in studying/addressing the phylogeny of plants at various taxonomic ranks. However, there are no empirical observations on the patterns, directions, and mutation rates, which are the key topics in chloroplast genome evolution. In this study, we used Calycanthaceae as a model to investigate the evolutionary patterns, directions and rates of both nucleotide substitutions and structural mutations at different taxonomic ranks. Results There were 2861 polymorphic nucleotide sites on the five chloroplast genomes, and 98% of polymorphic sites were biallelic. There was a single-nucleotide substitution bias in chloroplast genomes. A -> T or T -> A (2.84%) and G -> C or C -> G (3.65%) were found to occur significantly less frequently than the other four transversion mutation types. Synonymous mutations kept balanced pace with nonsynonymous mutations, whereas biased directions appeared between transition and transversion mutations and among transversion mutations. Of the structural mutations, indels and repeats had obvious directions, but microsatellites and inversions were non-directional. Structural mutations increased the single nucleotide mutations rates. The mutation rates per site per year were estimated to be 0.14-0.34 x 10(- 9)for nucleotide substitution at different taxonomic ranks, 0.64 x 10(- 11)for indels and 1.0 x 10(- 11)for repeats. Conclusions Our direct counts of chloroplast genome evolution events provide raw data for correctly modeling the evolution of sequence data for phylogenetic inferences.
学科主题	Evolutionary Biology ; Genetics & Heredity
出版地	LONDON
WOS关键词	MOLECULAR EVOLUTION ; INTERGENIC REGIONS ; SMALL INVERSIONS ; RATES ; PHYLOGENY ; SEQUENCES ; PATTERNS ; MAIZE ; DNA ; GENE
WOS研究方向	Evolutionary Biology ; Genetics & Heredity
语种	英语
出版者	BMC
WOS记录号	WOS:000559791100003
资助机构	Special Fund for Strategic Pilot Technology of Chinese Academy of Sciences [XDA23080204] ; Strategic Biological Resources Network Service of Chinese Academy of Sciences
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/21629]
专题	系统与进化植物学国家重点实验室
作者单位	1.Beijing Forestry Univ, Coll Ecol & Nat Conservat, Lab Systemat Evolut & Biogeog Woody Plants, Beijing 100083, Peoples R China 2.Smithsonian Inst, Dept Bot, Natl Museum Nat Hist, Washington, DC 20013 USA 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Dong, Wenpan,Xu, Chao,Wen, Jun,et al. Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae[J]. BMC EVOLUTIONARY BIOLOGY,2020,20(1).
APA	Dong, Wenpan,Xu, Chao,Wen, Jun,&Zhou, Shiliang.(2020).Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae.BMC EVOLUTIONARY BIOLOGY,20(1).
MLA	Dong, Wenpan,et al."Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae".BMC EVOLUTIONARY BIOLOGY 20.1(2020).