Codon usage bias and determining forces in green plant mitochondrial genomes.

The phenomenon of codon usage bias has been observed in a wide range of organisms. As organisms evolve, how their codon usage pattern change is still an intriguing question. In this article, we focused on the green plant mitochondrial genomes to analyze the codon usage patterns in different lineages, and more importantly, to investigate the possible change of determining forces during the plant evolution. Two patterns were observed between the separate lineages of green plants: Chlorophyta and Streptophyta. In Chlorophyta lineages, their codon usages showed substantial variation (from strongly A, T-biased to strongly G, C-biased); while in Streptophyta lineages, especially in the land plants, the overall codon usages are interestingly stable. Further, based on the Nc-GC3s plots and Akashi's scaled χ(2) -tests, we found that lineages within Chlorophyta exhibit much stronger evidence of deviating from neutrality; while lineages within Streptophyta rarely do so. Such differences, together with previous reports based on the chloroplast data, suggests that after plants colonized the land, their codon usages in organellar genomes are more reluctant to be shaped by selection force.