Codon Usage Bias And Determining Forces In Green Plant Mitochondrial Genomes

The phenomenon of unequal usage of synonymous codons is called codon usage bias. Mutation and translation-drived selection are two major forces that contribute to codon bias level. How those forces, along with other possible factors, shape the codon usage pattern during evolution is an interesting topic. During the land plant evolution, mitochondrial genome becomes increasingly dynamic with changes such as GC content variation, genome structure rearrangements, and gene gains, losses or transfers. Exploring how the codon usage pattern changed during plant mitochondrial evolution will help us to better understand evolutionary dynamics of mitochondrial genome.In this study, I used some well-developed tools in codon bias field to investigate the evolution of codon usage patterns in plant mitochondria. Starting with comparing the codon bias pattern among different phylogenetic groups, I detected the influence of mutation pressure, selection, context-dependent mutation on the codon usages. How different amino acid families contribute to the overall gene bias level was also analyzed in detail. To characterize the selection force, I examined the tRNA gene compositions in plant mitochondrial genomes, as well as their impacts on codon usage bias.The obtained results showed that the overall codon bias level decreases along the phylogenetic direction, correlated with the reducing selective influences on codon usages of mitochondrial genes. Detectable context-dependent mutation exists both on 2nd/3rd and 1st/3rd codon positions. Different amino acids and codons contribute unequally to mitochondrial genes' overall codon bias level, in which Phe, Ile, Thr, Val and Leu2 give most contribution. Selection was found to play an important role in Chlorophyta group, but not in Streptophyta group.This study systematically analyzed the codon usage pattern in 36 plant mitochondria genomes and illustrated important factors responsible for shaping codon. usages during the green plant evolution. Given the importance of codon usage in genetic region, a better understanding of mitochondrial codon bias evolution will contribute to endosymbiotic organelle research.