ral ssBioMed CentBMC Evolutionary Biology Open AcceResearch article Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis

Background: The mutational-hazard hypothesis argues that the noncoding-DNA content of a genome is a consequence of the mutation rate (μ) and the effective number of genes per locus in the population (Ng). The hypothesis predicts that genomes with a high Ngμ will be more compact than those with a small Ngμ. Approximations of Ngμ can be gained by measuring the nucleotide diversity at silent sites (πsilent). We addressed the mutation-hazard hypothesis apropos plastid-genome evolution by measuring πsilent of the Chlamydomonas reinhardtii plastid DNA (ptDNA), the most noncoding-DNA-dense plastid genome observed to date. The data presented here in conjunction with previously published values of πsilent for the C. reinhardtii mitochondrial and nuclear genomes, which are respectively compact and bloated, allow for a complete analysis of nucleotide diversity and genome compactness in all three genetic compartments of this model organism. Results: In C. reinhardtii, the mean estimate of πsilent forthe ptDNA (14.5 × 10-3) is less than that of the nuclear DNA (32 × 10-3) and greater than that of the mitochondrial DNA (8.5 × 10-3). On average, C. reinhardtii has ~4 times more silent-site ptDNA diversity than the mean value reported for land plants, which have more compact plastid genomes. The silent-site nucleotide diversity o