Complete genomic characterization of a pathogenic A.II strain of francisella tularensis subspecies tularensis

Stephen M Beckstrom-Sternberg, Raymond K. Auerbach, Shubhada Godbole, John V. Pearson, James S. Beckstrom-Sternberg, Zuoming Deng, Christine Munk, Kristy Kubota, Yan Zhou, David Bruce, Jyothi Noronha, Richard H. Scheuermann, Aihui Wang, Xianying Wei, Jianjun Wang, Jicheng Hao, David M Wagner, Thomas S. Brettin, Nancy Brown, Paul Gilna & 1 others Paul S Keim

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

Francisella tularensis is the causative agent of tularemia, which is a highly lethal disease from nature and potentially from a biological weapon. This species contains four recognized subspecies including the North American endemic F. tularensis subsp. tularensis (type A), whose genetic diversity is correlated with its geographic distribution including a major population subdivision referred to as A.I and A.II. The biological significance of the A.I-A.II genetic differentiation is unknown, though there are suggestive ecological and epidemiological correlations. In order to understand the differentiation at the genomic level, we have determined the complete sequence of an A.II strain (WY96-3418) and compared it to the genome of Schu S4 from the A.I population. We find that this A.II genome is 1,898,476 bp in size with 1,820 genes, 1,303 of which code for proteins. While extensive genomic variation exists between "WY96" and Schu S4, there is only one whole gene difference. This one gene difference is a hypothetical protein of unknown function. In contrast, there are numerous SNPs (3,367), small indels (1,015), IS element differences (7) and large chromosomal rearrangements (31), including both inversions and translocations. The rearrangement borders are frequently associated with IS elements, which would facilitate intragenomic recombination events. The pathogenicity island duplicated regions (DR1 and DR2) are essentially identical in WY96 but vary relative to Schu S4 at 60 nucleotide positions. Other potential virulence-associated genes (231) varied at 559 nucleotide positions, including 357 non-synonymous changes. Molecular clock estimates for the divergence time between A.I and A.II genomes for different chromosomal regions ranged from 866 to 2131 years before present. This paper is the first complete genomic characterization of a member of the A.II clade of Francisella tularensis subsp. tularensis.

Original languageEnglish (US)
Article numbere947
JournalPLoS One
Volume2
Issue number9
DOIs
StatePublished - Sep 26 2007

Fingerprint

Francisella tularensis
Francisella tularensis subsp. tularensis
Genes
genomics
DNA Transposable Elements
Genome
genome
genes
Nucleotides
nucleotides
Biological Warfare Agents
tularemia
pathogenicity islands
Tularemia
Genomic Islands
genetic variation
founder effect
lethal genes
Genetic Recombination
Population

ASJC Scopus subject areas

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

Cite this

Complete genomic characterization of a pathogenic A.II strain of francisella tularensis subspecies tularensis. / Beckstrom-Sternberg, Stephen M; Auerbach, Raymond K.; Godbole, Shubhada; Pearson, John V.; Beckstrom-Sternberg, James S.; Deng, Zuoming; Munk, Christine; Kubota, Kristy; Zhou, Yan; Bruce, David; Noronha, Jyothi; Scheuermann, Richard H.; Wang, Aihui; Wei, Xianying; Wang, Jianjun; Hao, Jicheng; Wagner, David M; Brettin, Thomas S.; Brown, Nancy; Gilna, Paul; Keim, Paul S.

In: PLoS One, Vol. 2, No. 9, e947, 26.09.2007.

Research output: Contribution to journalArticle

Beckstrom-Sternberg, SM, Auerbach, RK, Godbole, S, Pearson, JV, Beckstrom-Sternberg, JS, Deng, Z, Munk, C, Kubota, K, Zhou, Y, Bruce, D, Noronha, J, Scheuermann, RH, Wang, A, Wei, X, Wang, J, Hao, J, Wagner, DM, Brettin, TS, Brown, N, Gilna, P & Keim, PS 2007, 'Complete genomic characterization of a pathogenic A.II strain of francisella tularensis subspecies tularensis', PLoS One, vol. 2, no. 9, e947. https://doi.org/10.1371/journal.pone.0000947
Beckstrom-Sternberg, Stephen M ; Auerbach, Raymond K. ; Godbole, Shubhada ; Pearson, John V. ; Beckstrom-Sternberg, James S. ; Deng, Zuoming ; Munk, Christine ; Kubota, Kristy ; Zhou, Yan ; Bruce, David ; Noronha, Jyothi ; Scheuermann, Richard H. ; Wang, Aihui ; Wei, Xianying ; Wang, Jianjun ; Hao, Jicheng ; Wagner, David M ; Brettin, Thomas S. ; Brown, Nancy ; Gilna, Paul ; Keim, Paul S. / Complete genomic characterization of a pathogenic A.II strain of francisella tularensis subspecies tularensis. In: PLoS One. 2007 ; Vol. 2, No. 9.
@article{19d996474ab8490c8df51ac12dd8a0ba,
title = "Complete genomic characterization of a pathogenic A.II strain of francisella tularensis subspecies tularensis",
abstract = "Francisella tularensis is the causative agent of tularemia, which is a highly lethal disease from nature and potentially from a biological weapon. This species contains four recognized subspecies including the North American endemic F. tularensis subsp. tularensis (type A), whose genetic diversity is correlated with its geographic distribution including a major population subdivision referred to as A.I and A.II. The biological significance of the A.I-A.II genetic differentiation is unknown, though there are suggestive ecological and epidemiological correlations. In order to understand the differentiation at the genomic level, we have determined the complete sequence of an A.II strain (WY96-3418) and compared it to the genome of Schu S4 from the A.I population. We find that this A.II genome is 1,898,476 bp in size with 1,820 genes, 1,303 of which code for proteins. While extensive genomic variation exists between {"}WY96{"} and Schu S4, there is only one whole gene difference. This one gene difference is a hypothetical protein of unknown function. In contrast, there are numerous SNPs (3,367), small indels (1,015), IS element differences (7) and large chromosomal rearrangements (31), including both inversions and translocations. The rearrangement borders are frequently associated with IS elements, which would facilitate intragenomic recombination events. The pathogenicity island duplicated regions (DR1 and DR2) are essentially identical in WY96 but vary relative to Schu S4 at 60 nucleotide positions. Other potential virulence-associated genes (231) varied at 559 nucleotide positions, including 357 non-synonymous changes. Molecular clock estimates for the divergence time between A.I and A.II genomes for different chromosomal regions ranged from 866 to 2131 years before present. This paper is the first complete genomic characterization of a member of the A.II clade of Francisella tularensis subsp. tularensis.",
author = "Beckstrom-Sternberg, {Stephen M} and Auerbach, {Raymond K.} and Shubhada Godbole and Pearson, {John V.} and Beckstrom-Sternberg, {James S.} and Zuoming Deng and Christine Munk and Kristy Kubota and Yan Zhou and David Bruce and Jyothi Noronha and Scheuermann, {Richard H.} and Aihui Wang and Xianying Wei and Jianjun Wang and Jicheng Hao and Wagner, {David M} and Brettin, {Thomas S.} and Nancy Brown and Paul Gilna and Keim, {Paul S}",
year = "2007",
month = "9",
day = "26",
doi = "10.1371/journal.pone.0000947",
language = "English (US)",
volume = "2",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "9",

}

TY - JOUR

T1 - Complete genomic characterization of a pathogenic A.II strain of francisella tularensis subspecies tularensis

AU - Beckstrom-Sternberg, Stephen M

AU - Auerbach, Raymond K.

AU - Godbole, Shubhada

AU - Pearson, John V.

AU - Beckstrom-Sternberg, James S.

AU - Deng, Zuoming

AU - Munk, Christine

AU - Kubota, Kristy

AU - Zhou, Yan

AU - Bruce, David

AU - Noronha, Jyothi

AU - Scheuermann, Richard H.

AU - Wang, Aihui

AU - Wei, Xianying

AU - Wang, Jianjun

AU - Hao, Jicheng

AU - Wagner, David M

AU - Brettin, Thomas S.

AU - Brown, Nancy

AU - Gilna, Paul

AU - Keim, Paul S

PY - 2007/9/26

Y1 - 2007/9/26

N2 - Francisella tularensis is the causative agent of tularemia, which is a highly lethal disease from nature and potentially from a biological weapon. This species contains four recognized subspecies including the North American endemic F. tularensis subsp. tularensis (type A), whose genetic diversity is correlated with its geographic distribution including a major population subdivision referred to as A.I and A.II. The biological significance of the A.I-A.II genetic differentiation is unknown, though there are suggestive ecological and epidemiological correlations. In order to understand the differentiation at the genomic level, we have determined the complete sequence of an A.II strain (WY96-3418) and compared it to the genome of Schu S4 from the A.I population. We find that this A.II genome is 1,898,476 bp in size with 1,820 genes, 1,303 of which code for proteins. While extensive genomic variation exists between "WY96" and Schu S4, there is only one whole gene difference. This one gene difference is a hypothetical protein of unknown function. In contrast, there are numerous SNPs (3,367), small indels (1,015), IS element differences (7) and large chromosomal rearrangements (31), including both inversions and translocations. The rearrangement borders are frequently associated with IS elements, which would facilitate intragenomic recombination events. The pathogenicity island duplicated regions (DR1 and DR2) are essentially identical in WY96 but vary relative to Schu S4 at 60 nucleotide positions. Other potential virulence-associated genes (231) varied at 559 nucleotide positions, including 357 non-synonymous changes. Molecular clock estimates for the divergence time between A.I and A.II genomes for different chromosomal regions ranged from 866 to 2131 years before present. This paper is the first complete genomic characterization of a member of the A.II clade of Francisella tularensis subsp. tularensis.

AB - Francisella tularensis is the causative agent of tularemia, which is a highly lethal disease from nature and potentially from a biological weapon. This species contains four recognized subspecies including the North American endemic F. tularensis subsp. tularensis (type A), whose genetic diversity is correlated with its geographic distribution including a major population subdivision referred to as A.I and A.II. The biological significance of the A.I-A.II genetic differentiation is unknown, though there are suggestive ecological and epidemiological correlations. In order to understand the differentiation at the genomic level, we have determined the complete sequence of an A.II strain (WY96-3418) and compared it to the genome of Schu S4 from the A.I population. We find that this A.II genome is 1,898,476 bp in size with 1,820 genes, 1,303 of which code for proteins. While extensive genomic variation exists between "WY96" and Schu S4, there is only one whole gene difference. This one gene difference is a hypothetical protein of unknown function. In contrast, there are numerous SNPs (3,367), small indels (1,015), IS element differences (7) and large chromosomal rearrangements (31), including both inversions and translocations. The rearrangement borders are frequently associated with IS elements, which would facilitate intragenomic recombination events. The pathogenicity island duplicated regions (DR1 and DR2) are essentially identical in WY96 but vary relative to Schu S4 at 60 nucleotide positions. Other potential virulence-associated genes (231) varied at 559 nucleotide positions, including 357 non-synonymous changes. Molecular clock estimates for the divergence time between A.I and A.II genomes for different chromosomal regions ranged from 866 to 2131 years before present. This paper is the first complete genomic characterization of a member of the A.II clade of Francisella tularensis subsp. tularensis.

UR - http://www.scopus.com/inward/record.url?scp=41549136979&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=41549136979&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0000947

DO - 10.1371/journal.pone.0000947

M3 - Article

VL - 2

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 9

M1 - e947

ER -