Large direct repeats flank genomic rearrangements between a new clinical isolate of Francisella tularensis subsp. tularensis A1 and schu S4

Ufuk Nalbantoglu, Khalid Sayood, Michael P. Dempsey, Peter Charles Iwen, Stephen C. Francesconi, Ravi D. Barabote, Gary Xie, Thomas S. Brettin, Steven Heye Hinrichs, Paul D Fey

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Francisella tularensis subspecies tularensis consists of two separate populations A1 and A2. This report describes the complete genome sequence of NE061598, an F. tularensis subspecies tularensis A1 isolated in 1998 from a human with clinical disease in Nebraska, United States of America. The genome sequence was compared to Schu S4, an F. tularensis subspecies tularensis A1a strain originally isolated in Ohio in 1941. It was determined that there were 25 nucleotide polymorphisms (22 SNPs and 3 indels) between Schu S4 and NE061598; two of these polymorphisms were in potential virulence loci. Pulsed-field gel electrophoresis analysis demonstrated that NE061598 was an A1a genotype. Other differences included repeat sequences (n = 11 separate loci), four of which were contained in coding sequences, and an inversion and rearrangement probably mediated by insertion sequences and the previously identified direct repeats I, II, and III. Five new variable-number tandem repeats were identified; three of these five were unique in NE061598 compared to Schu S4. Importantly, there was no gene loss or gain identified between NE061598 and Schu S4. Interpretation of these data suggests there is significant sequence conservation and chromosomal synteny within the A1 population. Further studies are needed to determine the biological properties driving the selective pressure that maintains the chromosomal structure of this monomorphic pathogen.

Original languageEnglish (US)
Article numbere9007
JournalPloS one
Volume5
Issue number2
DOIs
StatePublished - Feb 3 2010

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Francisella tularensis subsp. tularensis
Francisella tularensis
Nucleic Acid Repetitive Sequences
Genes
Polymorphism
genomics
genetic polymorphism
Genome
Sequence Inversion
Synteny
Minisatellite Repeats
loci
genome
minisatellite repeats
Insertional Mutagenesis
Pulsed Field Gel Electrophoresis
Pathogens
pulsed-field gel electrophoresis
Electrophoresis
varespladib methyl

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Large direct repeats flank genomic rearrangements between a new clinical isolate of Francisella tularensis subsp. tularensis A1 and schu S4. / Nalbantoglu, Ufuk; Sayood, Khalid; Dempsey, Michael P.; Iwen, Peter Charles; Francesconi, Stephen C.; Barabote, Ravi D.; Xie, Gary; Brettin, Thomas S.; Hinrichs, Steven Heye; Fey, Paul D.

In: PloS one, Vol. 5, No. 2, e9007, 03.02.2010.

Research output: Contribution to journalArticle

Nalbantoglu, Ufuk ; Sayood, Khalid ; Dempsey, Michael P. ; Iwen, Peter Charles ; Francesconi, Stephen C. ; Barabote, Ravi D. ; Xie, Gary ; Brettin, Thomas S. ; Hinrichs, Steven Heye ; Fey, Paul D. / Large direct repeats flank genomic rearrangements between a new clinical isolate of Francisella tularensis subsp. tularensis A1 and schu S4. In: PloS one. 2010 ; Vol. 5, No. 2.
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