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

文献类型：期刊论文

作者Dong, Wenpan2; Xu, Chao; Wen, Jun1; Zhou, Shiliang3
刊名BMC EVOLUTIONARY BIOLOGY
出版日期2020
卷号20期号:1
关键词Chloroplast genome Calycanthaceae Structural mutations Substitution rate Indels
ISSN号1471-2148
DOI10.1186/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
WOS记录号WOS:000559791100003
出版者BMC
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
源URL[http://ir.ibcas.ac.cn/handle/2S10CLM1/21629]  
专题植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文
作者单位1.Beijing Forestry Univ, Coll Ecol & Nat Conservat, Lab Systemat Evolut & Biogeog Woody Plants, Beijing 100083, Peoples R China
2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
3.Smithsonian Inst, Dept Bot, Natl Museum Nat Hist, Washington, DC 20013 USA
4.Univ Chinese Acad Sci, Beijing 100049, 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).

入库方式： OAI收割

来源：植物研究所

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