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Comparative Study
. 2006 Oct;188(19):6977-85.
doi: 10.1128/JB.00506-06.

Chromosome Rearrangement and Diversification of Francisella Tularensis Revealed by the Type B (OSU18) Genome Sequence

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Free PMC article
Comparative Study

Chromosome Rearrangement and Diversification of Francisella Tularensis Revealed by the Type B (OSU18) Genome Sequence

Joseph F Petrosino et al. J Bacteriol. .
Free PMC article

Abstract

The gamma-proteobacterium Francisella tularensis is one of the most infectious human pathogens, and the highly virulent organism F. tularensis subsp. tularensis (type A) and less virulent organism F. tularensis subsp. holarctica (type B) are most commonly associated with significant disease in humans and animals. Here we report the complete genome sequence and annotation for a low-passage type B strain (OSU18) isolated from a dead beaver found near Red Rock, Okla., in 1978. A comparison of the F. tularensis subsp. holarctica sequence with that of F. tularensis subsp. tularensis strain Schu4 (P. Larsson et al., Nat. Genet. 37:153-159, 2005) highlighted genetic differences that may underlie different pathogenicity phenotypes and the evolutionary relationship between type A and type B strains. Despite extensive DNA sequence identity, the most significant difference between type A and type B isolates is the striking amount of genomic rearrangement that exists between the strains. All but two rearrangements can be attributed to homologous recombination occurring between two prominent insertion elements, ISFtu1 and ISFtu2. Numerous pseudogenes have been found in the genomes and are likely contributors to the difference in virulence between the strains. In contrast, no rearrangements have been observed between the OSU18 genome and the genome of the type B live vaccine strain (LVS), and only 448 polymorphisms have been found within non-transposase-coding sequences whose homologs are intact in OSU18. Nonconservative differences between the two strains likely include the LVS attenuating mutation(s).

Figures

FIG. 1.
FIG. 1.
Nucleotide alignment for OSU18, LVS, and Schu4. Each pair of genomes was aligned using BLASTN, and high-scoring segment pairs (E ≤ 1e−10) were plotted. Note the many short aligned sequences throughout both genomes. These are the multiple alignments between highly conserved IS elements. All but two syntenic blocks in panel B start and end at these IS elements. (A) OSU18 versus LVS; (B) OSU18 versus Schu4.
FIG. 2.
FIG. 2.
Gene rearrangements between the OSU18 (outer circle) and Schu4 (inner circle) genomes. Homologous recombination at ISFtu1 and ISFtu2 sequences results in rearrangement of 49 syntenic blocks of sequence between OSU18 and Schu4. Two additional pairs of rearrangements originate at rRNA genes. Red triangles, ISFtu1 genes; blue triangles, ISFtu2 genes; pink lines, rearrangement events where an ISFtu1 or ISFtu2 sequence is still present in only the Schu4 genome; blue lines, rearrangement events where an ISFtu1 or ISFtu2 sequence is still present in only the OSU18 genome; green lines, rearrangement events where an ISFtu1or ISFtu2 sequence is still present in both genomes; black lines, rearrangement events involving rRNA genes.
FIG. 3.
FIG. 3.
Optical map comparisons of Francisella strains. EcoRI restriction maps for the type A Schu4 and ATCC 6223 and type B OSU18 chromosomes were constructed by OpGen (Madison, WI). Green indicates areas where the restriction maps are homologous for the paired genomes. Red in the ATCC 6223 genome indicates areas where the restriction maps have homologies in all three genomes. Red in the OSU18 and Schu4 genomes indicates regions in these genomes that are homologous to more than one region in ATCC 6223. The comparison of OSU18 to ATCC 6223 shows a level of rearrangement similar to that found when OSU18 was compared to Schu4 (Fig. 1 and 2). The comparison of Schu4 to ATCC 6223 demonstrates that rearrangement between chromosomes is prevalent within the type A subspecies, whereas the two finished type B genomes examined thus far (LVS and OSU18) suggest that rearrangements in this subspecies may be much less prevalent.

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