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.
authors: Pathogen Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA.
authors: Stephen M
authors: SM
authors: Beckstrom-Sternberg
authors: Raymond K
authors: RK
authors: Auerbach
authors: Shubhada
authors: S
authors: Godbole
authors: John V
authors: JV
authors: Pearson
authors: James S
authors: JS
authors: Beckstrom-Sternberg
authors: Zuoming
authors: Z
authors: Deng
authors: Christine
authors: C
authors: Munk
authors: Kristy
authors: K
authors: Kubota
authors: Yan
authors: Y
authors: Zhou
authors: David
authors: D
authors: Bruce
authors: Jyothi
authors: J
authors: Noronha
authors: Richard H
authors: RH
authors: Scheuermann
authors: Aihui
authors: A
authors: Wang
authors: Xianying
authors: X
authors: Wei
authors: Jianjun
authors: J
authors: Wang
authors: Jicheng
authors: J
authors: Hao
authors: David M
authors: DM
authors: Wagner
authors: Thomas S
authors: TS
authors: Brettin
authors: Nancy
authors: N
authors: Brown
authors: Paul
authors: P
authors: Gilna
authors: Paul S
authors: PS
authors: Keim
mesh_terms: D004251:DNA Transposable Elements / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004270:DNA, Circular / Q000235:genetics*; D005604:Francisella tularensis / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D023061:Gene Order; D016680:Genome, Bacterial; D006801:Humans; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014774:Virulence / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D004270:DNA, Circular