title: Are Synonymous Substitutions in Flowering Plant Mitochondria Neutral?
abstract: Angiosperm mitochondrial genes appear to have very low mutation rates, while non-gene regions expand, diverge, and rearrange quickly. One possible explanation for this disparity is that synonymous substitutions in plant mitochondrial genes are not truly neutral and selection keeps their occurrence low. If this were true, the explanation for the disparity in mutation rates in genes and non-genes needs to consider selection as well as mechanisms of DNA repair. Rps14 is co-transcribed with cob and rpl5 in most plant mitochondrial genomes, but in some genomes, rps14 has been duplicated to the nucleus leaving a pseudogene in the mitochondria. This provides an opportunity to compare neutral substitution rates in pseudogenes with synonymous substitution rates in the orthologs. Genes and pseudogenes of rps14 have been aligned among different species and the mutation rates have been calculated. Neutral substitution rates in pseudogenes and synonymous substitution rates in genes are significantly different, providing evidence that synonymous substitutions in plant mitochondrial genes are not completely neutral. The non-neutrality is not sufficient to completely explain the exceptionally low mutation rates in land plant mitochondrial genomes, but selective forces appear to play a small role.
authors.affiliation: School of Biological Sciences, E249 Beadle Center, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA.
authors.forename: Emily L
authors.initials: EL
authors.lastname: Wynn
authors.affiliation: School of Biological Sciences, E249 Beadle Center, University of Nebraska-Lincoln, Lincoln, NE, 68588-0666, USA. achristensen2@unl.edu.
authors.forename: Alan C
authors.initials: AC
authors.lastname: Christensen
mesh_terms: D000595:Amino Acid Sequence; D002467:Cell Nucleus / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics*; D019143:Evolution, Molecular; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant; D059645:Mutation Rate; D010802:Phylogeny; D010944:Plants / Q000235:genetics*; D011544:Pseudogenes; D000069456:Silent Mutation
chemical_list: D004272:DNA, Mitochondrial
keywords: Mutation rate; Neutral mutation; Plant mitochondria; Pseudogene; Synonymous substitutions