Francisella tularensis subtype A.II genomic plasticity in comparison with subtype A.I

Marilynn A Larson, Ufuk Nalbantoglu, Khalid Sayood, Emily B. Zentz, Amanda M. Bartling, Stephen C. Francesconi, Paul D Fey, Michael P. Dempsey, Steven Heye Hinrichs

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Although Francisella tularensis is considered a monomorphic intracellular pathogen, molecular genotyping and virulence studies have demonstrated important differences within the tularensis subspecies (type A). To evaluate genetic variation within type A strains, sequencing and assembly of a new subtype A.II genome was achieved for comparison to other completed F. tularensis type A genomes. In contrast with the F. tularensis A.I strains (SCHU S4, FSC198, NE061598, and TI0902), substantial genomic variation was observed between the newly sequenced F. tularensis A.II strain (WY-00W4114) and the only other publically available A.II strain (WY96-3418). Genome differences between WY-00W4114 and WY96-3418 included three major chromosomal translocations, 1580 indels, and 286 nucleotide substitutions of which 159 were observed in predicted open reading frames and 127 were located in intergenic regions. The majority of WY-00W4114 nucleotide deletions occurred in intergenic regions, whereas most of the insertions and substitutions occurred in predicted genes. Of the nucleotide substitutions, 48 (30%) were synonymous and 111 (70%) were nonsynonymous. WY-00W4114 and WY96-3418 nucleotide polymorphisms were predominantly G/C to A/T allelic mutations, with WY-00W4114 having more A+T enrichment. In addition, the A.II genomes contained a considerably higher number of intact genes and longer repetitive sequences, including transposon remnants than the A.I genomes. Together these findings support the premise that F. tularensis A.II may have a fitness advantage compared to the A.I subtype due to the higher abundance of functional genes and repeated chromosomal sequences. A better understanding of the selective forces driving F. tularensis genetic diversity and plasticity is needed.

Original languageEnglish (US)
Article numbere0124906
JournalPloS one
Volume10
Issue number4
DOIs
StatePublished - Apr 28 2015

Fingerprint

Francisella tularensis
Plasticity
Genes
genomics
Genome
Nucleotides
nucleotides
genome
Intergenic DNA
intergenic DNA
Substitution reactions
Genetic Translocation
genetic variation
repetitive sequences
genes
Nucleic Acid Repetitive Sequences
transposons
genotyping
Open Reading Frames
Virulence

ASJC Scopus subject areas

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

Cite this

Francisella tularensis subtype A.II genomic plasticity in comparison with subtype A.I. / Larson, Marilynn A; Nalbantoglu, Ufuk; Sayood, Khalid; Zentz, Emily B.; Bartling, Amanda M.; Francesconi, Stephen C.; Fey, Paul D; Dempsey, Michael P.; Hinrichs, Steven Heye.

In: PloS one, Vol. 10, No. 4, e0124906, 28.04.2015.

Research output: Contribution to journalArticle

Larson, Marilynn A ; Nalbantoglu, Ufuk ; Sayood, Khalid ; Zentz, Emily B. ; Bartling, Amanda M. ; Francesconi, Stephen C. ; Fey, Paul D ; Dempsey, Michael P. ; Hinrichs, Steven Heye. / Francisella tularensis subtype A.II genomic plasticity in comparison with subtype A.I. In: PloS one. 2015 ; Vol. 10, No. 4.
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abstract = "Although Francisella tularensis is considered a monomorphic intracellular pathogen, molecular genotyping and virulence studies have demonstrated important differences within the tularensis subspecies (type A). To evaluate genetic variation within type A strains, sequencing and assembly of a new subtype A.II genome was achieved for comparison to other completed F. tularensis type A genomes. In contrast with the F. tularensis A.I strains (SCHU S4, FSC198, NE061598, and TI0902), substantial genomic variation was observed between the newly sequenced F. tularensis A.II strain (WY-00W4114) and the only other publically available A.II strain (WY96-3418). Genome differences between WY-00W4114 and WY96-3418 included three major chromosomal translocations, 1580 indels, and 286 nucleotide substitutions of which 159 were observed in predicted open reading frames and 127 were located in intergenic regions. The majority of WY-00W4114 nucleotide deletions occurred in intergenic regions, whereas most of the insertions and substitutions occurred in predicted genes. Of the nucleotide substitutions, 48 (30{\%}) were synonymous and 111 (70{\%}) were nonsynonymous. WY-00W4114 and WY96-3418 nucleotide polymorphisms were predominantly G/C to A/T allelic mutations, with WY-00W4114 having more A+T enrichment. In addition, the A.II genomes contained a considerably higher number of intact genes and longer repetitive sequences, including transposon remnants than the A.I genomes. Together these findings support the premise that F. tularensis A.II may have a fitness advantage compared to the A.I subtype due to the higher abundance of functional genes and repeated chromosomal sequences. A better understanding of the selective forces driving F. tularensis genetic diversity and plasticity is needed.",
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AU - Bartling, Amanda M.

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