Analysis Of The Relationship Between Genomic GC Content And Patterns Of Base Usage, Codon Usage And Amino Acid Usage In Prokaryotes

With the wide application of high-throughput sequencing technology, a large number of prokaryotic genomes have been published. This makes it very convenient to mine rules or new patterns from the sequences using comparative analysis methods. Among them, the effect of the genomic GC content on nucleotide or amino acid composition receives special attentions. Previous work has demonstrated that the content of G and C bases in the double-stranded DNA are within specific ranges for different species. Especially, some of the work showed that GC content in eukaryotic genomes ranges from about 30% to 50%, and in bacterial genomes ranges from about 25% to 75%.GC contents of 2670 prokaryotic genomes were analyzed in this paper and they belong to diverse phylogenetic lineages. They are in a large range of GC content from 13% to 75%. Then the relationship between genomic GC content and patterns of base usage, codon usage and amino usage in prokaryotes were analyzed, which mainly including the following work:Firstly, we analyzed the distance of base frequencies at three codon positions, codon frequencies and amino acid composition across genomes with respect to the differences of GC content in these bacteria species. We observed the relationship between these distances and genomic GC content through heat maps. We calculated the linear relationship between these distances and genomic GC content difference.Secondly, even though the existence of linear impact of genomic GC content on amino acid usage has been revealed in previous work, we confirmed the conclusion with the whole prokaryotes data. We hypothesized that the genomic GC content has more influence on base usage, codon usage and amino acid usage than phylogenetic lineage. To prove that, we analyzed the data through phylum divided group and GC content divided group respectively. In order to verify whether genomic GC content effects on the transcription process or effects on the bases directly, we drew the linear relationship between genomic GC content and several tRNA usage frequencies.At final stage, we developed a small genomic data preprocessing tool for the data extraction in the later work.