ArticleJournal of molecular evolution2010
Testing for selection on synonymous sites in plant mitochondrial DNA: the role of codon bias and RNA editing.
Article in Journal of molecular evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Characterization of mitochondrial genomes from three medicinal species of rutaceae and comparative analysis within the family: insights into evolution.BMC genomics · 2026Article
- A record-setting mitogenome in the holoparasitic plant Balanophora yakushimensis accompanied by exceptional loss of organellar DNA repair and recombination genes.BMC biology · 2025Article
- Heteroplasmy Is Rare in Plant Mitochondria Compared with Plastids despite Similar Mutation Rates.Molecular biology and evolution · 2024Article
- Characterization of the Complete Mitochondrial Genome of Wintersweet (Life (Basel, Switzerland) · 2024Article
- Complete chloroplast genomes of 13 species of sect. Tuberculata Chang (Camellia L.): genomic features, comparative analysis, and phylogenetic relationships.BMC genomics · 2024Article
- Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina.BMC genomic data · 2024Article
- Assembly and comparative analysis of the complete mitochondrial genome of Isopyrum anemonoides (Ranunculaceae).PloS one · 2023Article
- The Mitogenome ofBiology · 2022Article
- Article
- Comprehensive analysis of complete chloroplast genome and phylogenetic aspects of ten Ficus species.BMC plant biology · 2022Article
- Deciphering the mitochondrial genome ofFrontiers in plant science · 2022Article
- Detecting de novo mitochondrial mutations in angiosperms with highly divergent evolutionary rates.Genetics · 2021Article
- Plant Mitochondria are a Riddle Wrapped in a Mystery Inside an Enigma.Journal of molecular evolution · 2021Article
- Insights into Comparative Genomics, Codon Usage Bias, and Phylogenetic Relationship of Species from Biebersteiniaceae and Nitrariaceae Based on Complete Chloroplast Genomes.Plants (Basel, Switzerland) · 2020Article
- Article
- The Tempo and Mode of Angiosperm Mitochondrial Genome Divergence Inferred from Intraspecific Variation inG3 (Bethesda, Md.) · 2020Article
- Mitochondrial DNA Repair in anPlants (Basel, Switzerland) · 2020Article
- Map-Based Functional Analysis of theInternational journal of molecular sciences · 2019Article
- Comprehensive Analysis ofPlants (Basel, Switzerland) · 2019Article
- High Level of Conservation of Mitochondrial RNA Editing Sites Among FourG3 (Bethesda, Md.) · 2019Article
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2 authors.
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Abstract
Since plant mitochondrial genomes exhibit some of the slowest known synonymous substitution rates, it is generally believed that they experience exceptionally low mutation rates. However, the use of synonymous substitution rates to infer mutation rates depends on the implicit assumption that synonymous sites are evolving neutrally (or nearly so). To assess the validity of this assumption in plant mitochondrial genomes, we examined coding sequence for footprints of selection acting at synonymous sites. We found that synonymous sites exhibit an AT rich and pyrimidine skewed nucleotide composition compared to both non-synonymous sites and non-coding regions. We also found some evidence for selection associated with both biased codon usage and conservation of regulatory sequences involved in mRNA processing, although some of these findings are subject to alternative non-adaptive interpretations. Regardless, the inferred strength of selection appears too weak to account for the variation in substitution rates between the mitochondrial genomes of plants and other multicellular eukaryotes. Therefore, these results are consistent with the interpretation that plant mitochondrial genomes experience a substantially lower mutation rate rather than increased functional constraints acting on synonymous sites. Nevertheless, there are important nucleotide composition patterns (particularly the differences between synonymous sites and non-coding DNA) that remain largely unexplained.
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