Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae
Abstract 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 th...
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| Format: | Article |
| Language: | English |
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BMC
2020-07-01
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| Series: | BMC Evolutionary Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12862-020-01661-0 |
| _version_ | 1819017843439566848 |
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| author | Wenpan Dong Chao Xu Jun Wen Shiliang Zhou |
| author_facet | Wenpan Dong Chao Xu Jun Wen Shiliang Zhou |
| author_sort | Wenpan Dong |
| collection | DOAJ |
| description | Abstract 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 × 10− 9 for nucleotide substitution at different taxonomic ranks, 0.64 × 10− 11 for indels and 1.0 × 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. |
| first_indexed | 2024-12-21T03:09:58Z |
| format | Article |
| id | doaj.art-3d23602ad2a94114abeb55df71201d88 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-21T03:09:58Z |
| publishDate | 2020-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-3d23602ad2a94114abeb55df71201d882022-12-21T19:18:00ZengBMCBMC Evolutionary Biology1471-21482020-07-0120111210.1186/s12862-020-01661-0Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family CalycanthaceaeWenpan Dong0Chao Xu1Jun Wen2Shiliang Zhou3State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of SciencesAbstract 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 × 10− 9 for nucleotide substitution at different taxonomic ranks, 0.64 × 10− 11 for indels and 1.0 × 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.http://link.springer.com/article/10.1186/s12862-020-01661-0Chloroplast genomeCalycanthaceaeStructural mutationsSubstitution rateIndels |
| spellingShingle | Wenpan Dong Chao Xu Jun Wen Shiliang Zhou Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae BMC Evolutionary Biology Chloroplast genome Calycanthaceae Structural mutations Substitution rate Indels |
| title | Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae |
| title_full | Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae |
| title_fullStr | Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae |
| title_full_unstemmed | Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae |
| title_short | Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae |
| title_sort | evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family calycanthaceae |
| topic | Chloroplast genome Calycanthaceae Structural mutations Substitution rate Indels |
| url | http://link.springer.com/article/10.1186/s12862-020-01661-0 |
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