title: Mosaic structure of Mycobacterium bovis BCG genomes as a representation of phage sequences' mobility.
abstract: The control of genome stability is relevant for the worldwide BCG vaccine preventing the acute forms of childhood tuberculosis. BCG sub-strains whole genome comparative analysis and revealing the triggers of sub-strains transition were the purpose of our investigation.
  
  
  
  Whole genome sequencing of three BCG Russia seed lots (1963, 1982, 2006 years) confirmed the stability of vaccine sub-strain genome. Comparative analysis of three Mycobacteruim bovis and nine M. bovis BCG genomes shown that differences between "early" and "late" sub-strains BCG genomes were associated with specific prophage profiles. Several prophages common to all BCG genomes included ORFs which were homologues to Caudovirales. Surprisingly very different prophage profiles characterized BCG Tice and BCG Montreal genomes. These prophages contained ORFs which were homologues to Herpesviruses. Phylogeny of strains cohort based on genome maps restriction analysis and whole genomes sequence data were in agreement with prophage profiles. Pair-wise alignment of unique BCG Tice and BCG Montreal prophage sequences and BCG Russia 368 genome demonstrated only similarity of fragmetary sequences that suggested the contribution of prophages in genome mosaic structure formation.
  
  
  
  Control of the extended sequences is important for genome with mosaic structure. Prophage search tools are effective instruments in this analysis.
authors.affiliation: N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia. olv550@gmail.com.
authors.forename: Olga L
authors.initials: OL
authors.lastname: Voronina
authors.affiliation: N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia.
authors.forename: Marina S
authors.initials: MS
authors.lastname: Kunda
authors.affiliation: N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia.
authors.forename: Ekaterina I
authors.initials: EI
authors.lastname: Aksenova
authors.affiliation: N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia.
authors.forename: Andrey N
authors.initials: AN
authors.lastname: Semenov
authors.affiliation: N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ryzhova
authors.affiliation: N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia.
authors.forename: Vladimir G
authors.initials: VG
authors.lastname: Lunin
authors.affiliation: N.F. Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health, Moscow, Russia.
authors.forename: Alexandr L
authors.initials: AL
authors.lastname: Gintsburg
mesh_terms: D000595:Amino Acid Sequence; D001500:BCG Vaccine / Q000235:genetics / Q000276:immunology; D001435:Bacteriophages / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D023061:Gene Order; D015321:Gene Rearrangement; D016680:Genome, Bacterial; D016679:Genome, Viral; D042822:Genomic Instability; D023281:Genomics / Q000379:methods; D058977:Molecular Sequence Annotation; D009163:Mycobacterium bovis / Q000145:classification / Q000235:genetics* / Q000276:immunology / Q000821:virology; D010802:Phylogeny
chemical_list: D001500:BCG Vaccine; D004251:DNA Transposable Elements; D004269:DNA, Bacterial
keywords: BCG; Daughter sub-strain; Genome rearrangement; Mycobacterium bovis; Phage