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. 2009 Sep 16;4(9):e7041.
doi: 10.1371/journal.pone.0007041.

Complete Genome Sequence of Francisella Tularensis Subspecies Holarctica FTNF002-00

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Free PMC article

Complete Genome Sequence of Francisella Tularensis Subspecies Holarctica FTNF002-00

Ravi D Barabote et al. PLoS One. .
Free PMC article

Abstract

Francisella tularensis subspecies holarctica FTNF002-00 strain was originally obtained from the first known clinical case of bacteremic F. tularensis pneumonia in Southern Europe isolated from an immunocompetent individual. The FTNF002-00 complete genome contains the RD(23) deletion and represents a type strain for a clonal population from the first epidemic tularemia outbreak in Spain between 1997-1998. Here, we present the complete sequence analysis of the FTNF002-00 genome. The complete genome sequence of FTNF002-00 revealed several large as well as small genomic differences with respect to two other published complete genome sequences of F. tularensis subsp. holarctica strains, LVS and OSU18. The FTNF002-00 genome shares >99.9% sequence similarity with LVS and OSU18, and is also approximately 5 MB smaller by comparison. The overall organization of the FTNF002-00 genome is remarkably identical to those of LVS and OSU18, except for a single 3.9 kb inversion in FTNF002-00. Twelve regions of difference ranging from 0.1-1.5 kb and forty-two small insertions and deletions were identified in a comparative analysis of FTNF002-00, LVS, and OSU18 genomes. Two small deletions appear to inactivate two genes in FTNF002-00 causing them to become pseudogenes; the intact genes encode a protein of unknown function and a drug:H(+) antiporter. In addition, we identified ninety-nine proteins in FTNF002-00 containing amino acid mutations compared to LVS and OSU18. Several non-conserved amino acid replacements were identified, one of which occurs in the virulence-associated intracellular growth locus subunit D protein. Many of these changes in FTNF002-00 are likely the consequence of direct selection that increases the fitness of this subsp. holarctica clone within its endemic population. Our complete genome sequence analyses lay the foundation for experimental testing of these possibilities.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. A 10 kb hypervariable genomic region carrying three regions of difference between the three F. t. holarctica genomes.
Arrows indicate the direction of gene transcription. Genes and intergenic regions are not to scale. Homologous genes in the three genomes have been assigned the same color. Solid arrows indicate putative functional genes and hatched or grey arrows represent pseudogenes. The horizontal box on the FTNF002-00 chromosomal fragment indicates the 3,868 bp fragment (positioned at 247478–251345) that is inverted with respect to the other two genomes. A vertical box over the three genomes indicates the location of a 962 bp region that is different in OSU18 (see Table 2). The two equal sized horizontal boxes on the OSU18 genomic fragment indicate tandem duplications of a 1933 bp region (see Table 2).
Figure 2
Figure 2. Overview of the shared and unique genomic differences in the three F. t. holarctica genomes.
(A) Total numbers of regions of difference (RDs), (B) number of small insertions and deletions (indels), and (C) number of single nucleotide polymorphisms (SNPs) that are either shared or unique between the three strains. Further details of these differences are included in Tables 2, 3, and 4.
Figure 3
Figure 3. A genome-based model depicting the divergence of the FTNF002 and LVS from the more ancestral OSU18.

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