Distributions and associations between structural and genomic location traits in microsatellites of pathogenic bacteria

Abstract

Introduction: The presence of microsatellites in bacteria and eukaryotic organisms is higher than expected by chance, and the evolutionary forces and structural features that influence their distribution dynamics and localization in the genome are not fully understood. Neither are the associations between these traits known, which would allow us to elucidate the molecular and evolutionary dynamics of these markers.

Objective: To analyze the distributions and associations between the structural features of microsatellites according to the size of the repeat unit, the region they occupy in the genome in relation to genes, the type of genome (main or plasmid), the pattern composition and the degree of polymorphism.

Methods: 59 bacterial species belonging to 6 phyla, all of biomedical interest, were selected. 2780 and 966 genomic and plasmid sequences were processed, respectively. The detection of polymorphic microsatellites was performed with MIDAS and PSSRExtractor.

Results: 33506 microsatellites were found. Half of them are located in coding regions and their flanks. Their distributions by pattern size and region relative to genes showed significant differences. Pattern sizes influence the polymorphism of their loci and other features such as copy number and flank entropy. The nucleotide composition also showed a relationship with the degree of polymorphism.

Conclusions: Global association analyzes as well as the particularized frequencies and distributions for the 59 pathogenic species constitute a valuable bioinformatics record that allows to guide experimental studies related to the dynamics of microsatellites and their evolutionary forces, for a better understanding of the molecular biology of pathogenesis.