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Link to original content: http://pubmed.ncbi.nlm.nih.gov/25869380/
Mutation rates in plastid genomes: they are lower than you might think - PubMed Skip to main page content
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. 2015 Apr 13;7(5):1227-34.
doi: 10.1093/gbe/evv069.

Mutation rates in plastid genomes: they are lower than you might think

David Roy Smith  1
Affiliations

Mutation rates in plastid genomes: they are lower than you might think

David Roy Smith. Genome Biol Evol. .

Abstract

Within plastid-bearing species, the mutation rate of the plastid genome is often assumed to be greater than that of the mitochondrial genome. This assumption is based on early, pioneering studies of land plant molecular evolution, which uncovered higher rates of synonymous substitution in plastid versus mitochondrial DNAs. However, much of the plastid-containing eukaryotic diversity falls outside of land plants, and the patterns of plastid DNA evolution for embryophytes do not necessarily reflect those of other groups. Recent analyses of plastid and mitochondrial substitution rates in diverse lineages have uncovered very different trends than those recorded for land plants. Here, I explore these new data and argue that for many protists the plastid mutation rate is lower than that of the mitochondrion, including groups with primary or secondary plastids as well as nonphotosynthetic algae. These findings have far-reaching implications for how we view plastid genomes and how their sequences are used for evolutionary analyses, and might ultimately reflect a general tendency toward more efficient DNA repair mechanisms in plastids than in mitochondria.

Keywords: chloroplast genome; mitochondrial DNA; mutation rate; plastid DNA; synonymous substitution.

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Figures

F<sc>ig</sc>. 1.—
Fig. 1.—
Relative rates in plastid-bearing protists. (A) The relative rate of synonymous substitutions in mitochondrial versus plastid genomes (dS ratio) for various plastid-bearing protists. An mtDNA/ptDNA dS ratio of ≥1 is shown with a green circle and <1 with a purple circle. (B) Synonymous substitution rates in plastid, mitochondrial, and nuclear genomes. ptDNA is shown in green, mtDNA in blue, and nucDNA in orange. The Archaeplastida comprises glaucophytes (Glauco), red algae, green algae, and land plants, all of which have primary plastids. The haptophyte (Hapto) Phaeocystis and the dinoflagellate (Dino) Symbiodinium have secondary, red–algal-derived plastids. The methods used to estimate dS and the number and type of loci investigated sometimes differed among the various taxa. The ML approach was used to estimate dS for all taxa without an asterisk in front of their names. Alternative methods were used for those with an asterisk (see Materials and Methods).
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