Comprehensive Analysis Of Nucleotide Bias Correlation Among Bacterial Genomes Based On Z-curve Method

Due to different replication mechanisms between the leading and lagging strands,nucleotide composition asymmetries widely exist in bacterial genomes.It is generally considered that the leading strand is enriched in Guanine(G)and Thymine(T),and the lagging strand shows richness in Adenine(A)and Cytosine(C).However,few bacteria like Bacillus subtilis have been discovered composing more A than T in the leading strand.In order to investigate the regulation and reason of these differences,we prior analyzed the nucleotide asymmetry from the aspect of AT and GC bias correlations.In this study,we proposed a window-free method,the Z-curve Correlation Coefficient(ZCC)index,based on the Z-curve method,and analyzed more than 2000 bacterial genomes.We find that the majority of them reveal negative correlations between AT and GC biases,while most genomes in Firmicutes and Tenericutes hold positive ZCC indexes.Based on the positive/negative division rule according to the Z-curve method,we have also reached a series of conclusions such as the distribution of DNA polymerases,purine asymmetry,stand-biased gene distributions,GC content and so on.This method introduces a new perspective analyzing nucleotide bias along a whole genome,like aerobism,and can be applied to analyze the correlation between RY(Purine and Pyrimidine)and MK(Amino and Keto)bias and so on,which might help finding out more relevant genomic features and make contribution to phylogenetics studies.