Codon Pairs Usage And Genome Evolution For 9 Mode Species

The paper is composed of two chapters:In the first chapter, Codon pair usage in Escherichia coli and Saccharomyces cerevisiae genomes are studied. According to comparison of codon pair usage frequency between the real and statistically predicted frequency of occurrence, it can be observed a significant difference and the distribution is random; besides, according to an especially defined criterion (Δ_REG) by Boycheva, the relations between codon pair usage and gene expression level are studied for E.coli and S.cerevisiae. The results show that the relations between codon pair usage and gene expression level are similar for two species, the highly expressed gene tend to favor codon pairs with positive Δ₍REG values, whereas the codon pairs with negative Δ_{REG values are typical for the poorly expressed gene. From the similarity of the curves in two species, it can be inferred that the mechanisms with respect to the codon pairs usage are similar to each other for E.coli (prokaryote) and S. cerevisiae (eukaryote) .In the second chapter, the distribution of relative modes' number of codon pair in protein coding sequences and intergenic triplet pairs is analyzed respectively in Archaeoglobus. fulgidus, Sulfolobus. solfataricus, Pyrococcus.furiosus, Bacillus.halodurans, Bacillus, subtili, Escherichia. coli, Saccharomyces. cerevisiae, Caenorhabditis. elegans and Arabidopsis. thaliana genomes. Proposed this kind of distribution is r(a,/3) distribution, and its parameters a and fi values of T{a,fi} is relative to genomes evolution both for protein coding sequences and intergenic sequences' triplet pairs .In the third chapter, firstly, comparative analyses of distribution of the observed and statistically predicted codon pair frequency of occurrence, found that the most of the codon pairs' usage are bias, and the preference is different from different species, its distribution is random basically; When the same sense codon is combined with different stop codon, sense - stop codon pair usage depends on the type of stop codon. Secondly, we analysed the base combination and relative synonymous codon usage of preferential codon pairs and rare codon pairs. The results show that codon pair is correlated to relative synonymous codon usage and correlation of double bases.