论文部分内容阅读
Background: DNA replication, particularly that of microbes, includes a set of asymmetric mechanisms, among which is a division into lagging and leading strands.Due to the asymmetric replication mechanism, nucleotide compositions between the two replicating strands of bacteria are usually biased.Since 1998, foreign researchers have found that a total of 10 bacterial genomes have so extremely strong strand-specific composition bias that genes on the two strands have separate codon usages.However, it is still unclear why the strong bias exist only in some special genomes and not in others and which genomes should have so strong bias.Methods: Sequence and annotation files of nearly 1000 bacterial genomes were obtained from NCBI ftp site on June 2006.All of published work from other groups adopted one single method, namely CA of RSCU and this leads to the peripheral analysis.Comparatively, we combined multiple methods to analyze hundreds of bacterial genomes.Among them, the Z curve method is used in this issue for the first time.To analyze gene content associated with the strong bias, we resort to comparative genomics method.That is to say, we will compare the contents of replication associated genes between the two bacterial groups with and without strong biases.Also, statisticanalyses such as t test is employed.Results: Based on the series of works, we found that most of bacterial genomes with strong composition bias are obligate intracellular parasites or symbionts.From the point of gene content, genomes with strong bias tend to lose genes responsible for mutation repair.From the evolutionary point of view, these genomes have much fewer recombinants event and lower translation selections.Furthermore, we found some other common genomic characters of these genomes, for example, they tend to have small genome sizes.Conclusions: Through a five-year sequential studies, we have found the common genomic characters of obligate intracellular bacteria with strong strand composition bias.Also, this work has provided analyzing methods and scientific explanations for researches on the composition asymmetry of bacterial genomes, particularly those obligate intracellular .