Intrinsic Laws Of K-mer Spectra Of Genome Sequences And Evolution Mechanism Of Genomes

K-mer spectra of DNA sequences contain important information about sequence composition and sequence evolution.Studying intrinsic laws of k-mer spectra of genome sequences is an important way to reveal the composition and evolution laws of genome sequences.Based on the previous research,we analyzed and compared the spectrum characteristics of various motif subsets of 920 genome sequences from primates to prokaryotes.The composition and evolution laws of genome sequences were discussed,and the early evolution laws of species were speculated.The main research contents are as follows:1.The 920 genomes were divided into 14 species groups in 4 kingdoms: animals(Primates,Rodents,Other mammals,Other vertebrates and Invertebrates),plants(Dicotyledons,Monocotyledons,Pteridophyta and Green algae),fungi(Agaricomycotina,Pezizomycotina,and Saccharomycetales),and prokaryotes(Archaea and Eubacteria).According to the XY dinucleotide classification method,we studied the spectrum intrinsic laws of each species genome sequence 16 kinds of XY motif subsets.We found that only CG and TA motifs have independent selection phenomenon,and the other 14 kinds of spectra of XY motif subsets do not satisfy this phenomenon.There are two kinds of evolution selection modes in genome sequences.One is named as the CG independent selection mode,the other is named as the TA independent selection mode.By analyzing the distribution characteristics of CG2/CG1/CG0 and TA2/TA1/TA0 motif subsets spectra,we found that two independent selection laws have three properties: Evolution Independence,Evolution Selectivity and Evolution Conservatism.2.Based on the average frequency and the standard deviation of the CG and TA motif subsets and the total motif spectrum distribution,quantitative characterization parameters of the two independent selection intensities are given: the separability and the conservatism.Results showed that the separability of CG1/CG2 motif spectra and of TA1/TA2 motif spectra correlates significantly and positively with the conservatism of them.We named the distribution property as Evolution Correlation of genome sequences.It is the fourth property of CG and TA independent selection laws.It indicates that CG1 and CG2 motifs subsets as well as TA1 and TA2 motifs subsets abide by the same kind of evolutionary selection pattern.They are opposite to the evolutionary trend of CG0 motifs subsets.We named the distribution property as Evolution Homoplasy of genome sequences.It is the fifth property of CG and TA independent selection laws.3.We analyzed intensity distribution of CG and TA independent selection of various genome sequences.It indicated that intensity of CG independent selection and intensity of TA independent selection in each genome sequence is different,and there is a mutual inhibition relationship between CG and TA independent selections.In animal and plant genomes,intensity of CG independent selection was positively correlated with the level of genome evolution,while intensity of TA independent selection was negatively correlated with the level of genome evolution.In fungus and bacteria genomes,intensity of CG and TA independent selection represent the evolution status of species.Based on our results,we proposed an evolution mechanism of genome sequences and found that genome evolution status is determined by the intensities of CG and TA independent selections and the mutual inhibition relationship between CG and TA independent selections.In vertebrate genome sequences,we also found that TA independent selection phenomenon gradually disappears with the level improvement of genome evolution,that is to say,the mutual inhibition relationship between CG and TA independent selections in vertebrates gradually disappears.4.The relationship between the independent selection mode of the genome sequence and G+C content and the intensity of Cp G suppression was studied.The intensity of TA independent selection correlates positively and of the CG independent selection correlates negatively with the G+C content of genome sequences.The CG independent selection correlates positively with the intensity of Cp G suppression.Through the research and analysis of this result,we found that the independent selection phenomenon can reflect the fundamental law of sequence composition and sequence evolution,while the intensity of Cp G suppression and G+C content are two different comprehensive representation of CG and TA independent selection law and the mutual inhibition law between them.5.By the independent selection laws and the evolution mechanism of genome sequences,we speculated the evolution modes of prokaryotes in mild and two extreme environments in the anaerobic age and the evolving process of prokaryotes from anaerobic to aerobic environment on earth.Therefore,the phenomenon of CG and TA independent selection is the fundamental reason why organisms have evolved in response to aerobic and extreme environments.We compared the evolution modes of animals,plants,fungi,and archaea genomes.Based on the continuity and the similarity of genome evolution modes,we considered that the ancestor of animals and Saccharomycetales originated from the archaea with obvious CG independent selection and TA inhibition,and the ancestor of plants,Agaricomycotinas and Pezizomycotinas originated from the archaea with obvious TA independent selection and CG inhibition.We studied the relationship between independent selection modes and the living habits of species.The fungus and prokaryotes with obvious TA independent selection and strong CG inhibition usually live with or infect plants,while the fungus and prokaryotes with obvious CG independent selection and strong TA inhibition usually live with or infect animals.6.According to the evolution mechanism of the genome sequences,we further confirmed the evolutional particularity of Latimeria chalumnae.Many evidences indicate that the biochemical characteristics of Latimeria chalumnae is more similar to tetrapods than to other fishes.We compared CG independent selection mode and the intensity of Cp G suppression among Latimeria chalumnae,other fishes and tetrapods genome sequences.It indicated that the intensity of CG independent selection and the intensity of Cp G suppression of Latimeria chalumnae is more similar to tetrapods than to other fishes.In addition,we believe that the phenomenon of independent selection is not only reflected in the genome level,but must also be reflected in any segment of DNA sequence.For this reason,we analyzed the amino acid sequence of Latimeria chalumnae methylation gene and demethylated genes,and investigated the particularity of Latimeria chalumnae evolution through similarity comparison.The results all show that the evolutionary distance of the Latimeria chalumnae and tetrapods is very close,but farther from other fishes.We have confirmed the conjecture that Latimeria chalumnae and tetrapods have a common ancestor from the genome level and gene level.