Evolution Analysis Of Microbial Genomes Based Onoligonucleotide Transition Probability Matrix

The aim of evolution analysis is to find the whole evolutionary history and phylogeneticrelationship of organisms. DNA, a main hereditary substance, would alter in evolutionaryprocess and bereflected mainly in the change of contents, sequences and structure of nucleotide.The whole-genome contains all the hereditary information so that it could be utilized forevolution analysis.Firstly, we calculated the tri-nucleotide transition probability matrix of the whole genomesof88archaea,100bacterium and40fungi;secondly, analyzed the correlation anddivergenceamong them via Pearson correlationcoefficient, joint histogram diversity and densitycorrelation function;then inferred their phylogenetic relationship.Results show that the tri-nucleotide color matrixes of microbial genomeswerespecies-specificity. There was high similarityin the color matrixes of intragenicorganisms,but this similarity would disappear when the organisms branch for more than family. Inaddition, results of linear correlation analysis of tri-nucleotide transition probability matrixesand their disorder vectors suggest that the linear correlationcoefficientwas only suitable forclose related organisms, but not for distant related organisms which classification level higherthan class.And the novel method based on image registration, which utilizes joint histogramdiversity to compare the differences of organisms, has higher discrimination. For the organismsthat taxonomic categories covered from kingdom to species, it could measure their evolutiondistance. This method must be broadened and developed so that it can be applied to speciesidentification and phylogeny inferring. Otherwise, the results of density correlation analysisshow that the density correlation atlas iscorrelated with evolutionarydegree. The higherevolutionary degree of organisms is, the closer the density correlation atlasapproximates to acurve. On the contrary, it will be more divergent. The interesting results may provide alternatedway to investigate the origin and evolution of organism. With the developing of bio-techniqueand the completing of genomic sequencing, we could research the triplet majority profiles ofmicrobe much further.