small variable segments constitute a major type of diversity of bacterial genomes at the species level小变量部分构成一个主要类型的细菌基因组的多样性物种水平.pdfVIP

Touzain et al. Genome Biology 2010, 11:R45 /2010/11/4/R45 RESEARCH Open Access Small variable segments constitute a major type of diversity of bacterial genomes at the species level 1 2 3 4 1 1* Fabrice Touzain , Erick Denamur , Claudine Médigue , Valérie Barbe , Meriem El Karoui , Marie-Agnès Petit Abstract Background: Analysis of large scale diversity in bacterial genomes has mainly focused on elements such as pathogenicity islands, or more generally, genomic islands. These comprise numerous genes and confer important phenotypes, which are present or absent depending on strains. We report that despite this widely accepted notion, most diversity at the species level is composed of much smaller DNA segments, 20 to 500 bp in size, which we call microdiversity. Results: We performed a systematic analysis of the variable segments detected by multiple whole genome alignments at the DNA level on three species for which the greatest number of genomes have been sequenced: Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes. Among the numerous sites of variability, 62 to 73% were loci of microdiversity, many of which were located within genes. They contribute to phenotypic variations, as 3 to 6% of all genes harbor microdiversity, and 1 to 9% of total genes are located downstream from a microdiversity locus. Microdiversity loci are particularly abundant in genes encoding membrane proteins. In-depth analysis of the E. coli alignments shows that most of the diversity does not correspond to known mobile or repeated elements, and it is likely that they were generated by illegitimate recombination. An intriguing class of microdiversity includes small blocks of highly diverged sequences,