ArticleBMC evolutionary biology2020
Evolutionary directions of single nucleotide substitutions and structural mutations in the chloroplast genomes of the family Calycanthaceae.
Article in BMC evolutionary biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 64 citations in OpenAlex.
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- Understanding the Evolutionary Adaptations and the Associated Functional Dynamics of DiatomCurrent genomics · 2025Article
- Exploring the phylogenetic framework and trait evolution of Impatiens through chloroplast genome analysis.BMC plant biology · 2024Article
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- The pan-plastome ofFrontiers in plant science · 2024Article
- Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae).BMC plant biology · 2023Article
- Genome diploidization associates with cladogenesis, trait disparity, and plastid gene evolution.Plant physiology · 2022Article
- Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation.International journal of environmental research and public health · 2022Article
- Plastome phylogenomics and biogeography of the subfam. Polygonoideae (Polygonaceae).Frontiers in plant science · 2022Article
- Chloroplast Genome Evolution and Species Identification ofBioMed research international · 2022Article
- Haplotype Analysis of Chloroplast Genomes for Jujube Breeding.Frontiers in plant science · 2022Article
- Phylogenomics and Genetic Diversity ofFrontiers in plant science · 2022Article
- Comparative chloroplast genome analysis of Impatiens species (Balsaminaceae) in the karst area of China: insights into genome evolution and phylogenomic implications.BMC genomics · 2021Article
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- Chloroplast phylogenomic insights into the evolution of Distylium (Hamamelidaceae).BMC genomics · 2021Article
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundChloroplast 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.
resultsThere 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
conclusionsOur direct counts of chloroplast genome evolution events provide raw data for correctly modeling the evolution of sequence data for phylogenetic inferences.
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