Evolutionary rates in nuclear and mitochondrial genes of Chlamydomonas

The unicellular green alga Chlamydomonas reinhardtii has been used as an experimental model organism to investigate many biological phenomena. Although the nuclear, mitochondrial, and chloroplast genetic compartments of this taxon are well characterized, little is known about the relative evolutionary rates in these genomes. This study examines relative rates of nucleotide substitution in the nuclear and mitochondrial genomes, based on comparison between C. reinhardtii and Chlamydomonas incerta DNA sequences. The work involved sequencing 7569 ESTs from a cDNA library of C. incerta , which was constructed as part of the Protist EST Program, as well as sequencing the C. incerta mitochondrial genome. It also exploited the large supply of expression/genomic sequence data and the mitochondrial gene sequences available for C. reinhardtii. Relative rates of synonymous and nonsynonymous substitution across nuclear genes were found to vary widely and showed a strong negative correlation with the level of gene expression as estimated by the codon adaptation index. Taken together with comparative analysis of substitution rates in introns of lowly and highly expressed genes the results support natural selection as a larger contributor than mutation to the observed correlation between evolutionary rates and gene expression level in Chlamydomonas. The overall synonymous substitution rates as well as nonsynonymous substitution rates do not differ significantly between the mitochondrial and nuclear compartments and it seems that the mutation rate is rather similar in the two genomes. However, the mitochondrial rRNA-coding regions are much more rapidly evolving than their nuclear counterparts. This difference might be explained by more relaxed purifying selection acting on the mitochondrial translational apparatus compared to the cytosolic one as a result of the small number of proteins translated in Chlamydomonas mitochondria. The non-standard mitochondrial gene, rtl, which resembles a reverse transcriptase-like sequence, appears to be functional in both C. reinhardtii and C. incerta although under relaxed functional constraints.