New approaches in the systematics of rickettsiae.

Abstract

The development of a formal order analysis (FOA) allowed constructing a classification of 49 genomes of Rickettsiaceae family representatives. Recently FOA has been extended with new tools—‘Map of genes,’ ‘Matrix of similarity’ and ‘Locality-sensitive hashing’—for a more in-depth study of the structure of rickettsial genomes. The new classification confirmed and supplemented the previously constructed one by determining the position of Rickettsia africae str. ESF-5, R. heilongjiangensis 054, R. monacensis str. IrR/Munich, R. montanensis str. OSU 85-930, R. raoultii str. Khabarovsk, R. rhipicephali str. 3-7-female6-CWPP and Rickettsiales bacterium str. Ac37b. The ‘Map of genes’ demonstrated the complete genomes and their components in a graphical form. The ‘Matrix of similarity’ was applied for an in-depth classification to a subtaxonomic category of the strain within the species R. rickettsii (11 strains) and R. prowazekii (ten strains). The ‘Matrix of similarity’ determines the degree of homology of complete genomes by pairwise comparison of their components and identification of those being identical and similar in the arrangement of nucleotides. A new genomosystematics approach is proposed for the study of complete genomes and their components through the development and application of FOA tools. Its applications include the development of principles for the classification of microorganisms, based on the analysis of complete genomes and their annotations. This approach may help in the taxonomic classification and characterization of some Candidatus Rickettsia spp. that are found in large numbers in arthropods worldwide.