Repeat structure in \emph{Salmonella} genomes

L. A. Miroshnichenko ; N. A. Arefieva ; Yu. P. Dzhioev ; V. D. Gusev ; A. Yu. Borisenko ; S. V. Erdyneev ; Yu. S. Bukin

Matematičeskaâ biologiâ i bioinformatika, Tome 18 (2023) no. 2, pp. 602-620.

Résumé

Salmonella is a genus of gram-negative, facultative and non-spore-forming anaerobic bacteria. The genus includes two species: S. bongori and S. enterica. All Salmonella, which are pathogenic to humans and animals, belong to the species S. enterica. It includes seven subspecies, which includes more than 2500 serotypes. According to global statistics, they cause about 2.8 billion cases of diarrheal diseases annually, and the mortality rate reaches more than 300000 cases. S. enterica spp strains that have acquired multidrug resistance to antibiotics have become especially dangerous. Against the backdrop of this global problem, a detailed study of the complete genomes of various representatives of the genus Salmonella becomes relevant. Repeats play an important role in the regulation of basic genetic processes during the life cycle and evolution. The work examines various manifestations of repetition in the genomes of S. enterica. Taking into account common fragments of different genomes serves as the basis for the formation of a matrix of pairwise relative complexity, which is used in constructing a phylogenetic tree. Long repeats within individual genomes typically correspond to large individual duplications. The main attention is paid to local structural regularities, most of which are represented by tandem repeats. Of significant interest are multivalued repeats, such as tandem repeats forming a palindrome, repeats with regular substitutions or complex monomer structure.

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