Testing for Selection on Synonymous Sites in Plant Mitochondrial DNA: The Role of Codon Bias and RNA Editing

• Published in: Journal of molecular evolution Vol. 70; no. 5; pp. 479 - 491
• Main Authors: Sloan, Daniel B, Taylor, Douglas R
• Format: Journal Article
• Language: English
• Published: New York New York : Springer-Verlag 01.05.2010; Springer-Verlag; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Base Composition; Biomedical and Life Sciences; Cell Biology; Codon; Codon usage bias; Conserved Sequence; DNA Fingerprinting; DNA, Mitochondrial; DNA, Mitochondrial - genetics; Evolution, Molecular; Evolutionary Biology; Flowers & plants; genetics; Genome, Mitochondrial; Genome, Plant; Genomics; Life Sciences; Microbiology; Mitochondrial DNA; Mitochondrial genome; Mutation; Mutation bias; Plant Genetics and Genomics; Plant Sciences; Plants; Plants - genetics; Reproducibility of Results; Ribonucleic acid; RNA; RNA Editing; Selection, Genetic; Substitution rate; Synonymous sites; RNA editing; mtDNA; Mutation bias; Mitochondrial genome; Codon usage bias; Substitution rate; Synonymous sites
• ISSN: 0022-2844; 1432-1432; 1432-1432
• DOI: 10.1007/s00239-010-9346-y

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.