Fri, 04 Jul 2008 23:37:32 BST CiteULike: Xavier's Wei http://www.citeulike.org/user/Xavier/author/Wei CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/Xavier/article/2485534 <i>PLoS ONE, Vol. 2, No. 9. (2007)</i><br /><br />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. Complete Genomic Characterization of a Pathogenic A.II Strain of Francisella tularensis Subspecies tularensis. SM Beckstrom-Sternberg RK Auerbach S Godbole JV Pearson JS Beckstrom-Sternberg Z Deng C Munk K Kubota Y Zhou D Bruce J Noronha RH Scheuermann A Wang X Wei J Wang J Hao DM Wagner TS Brettin N Brown P Gilna PS Keim doi:10.1371/journal.pone.0000947 PLoS ONE, Vol. 2, No. 9. (2007) 2008-03-07T16:29:56-00:00 2007 PLoS ONE 1932-6203 2 9 frank http://www.citeulike.org/user/Xavier/article/2465164 <i>Infect Immun, Vol. 71, No. 5. (May 2003), pp. 2775-2786.</i><br /><br />We determined the complete genome sequence of Shigella flexneri serotype 2a strain 2457T (4,599,354 bp). Shigella species cause >1 million deaths per year from dysentery and diarrhea and have a lifestyle that is markedly different from those of closely related bacteria, including Escherichia coli. The genome exhibits the backbone and island mosaic structure of E. coli pathogens, albeit with much less horizontally transferred DNA and lacking 357 genes present in E. coli. The strain is distinctive in its large complement of insertion sequences, with several genomic rearrangements mediated by insertion sequences, 12 cryptic prophages, 372 pseudogenes, and 195 S. flexneri-specific genes. The 2457T genome was also compared with that of a recently sequenced S. flexneri 2a strain, 301. Our data are consistent with Shigella being phylogenetically indistinguishable from E. coli. The S. flexneri-specific regions contain many genes that could encode proteins with roles in virulence. Analysis of these will reveal the genetic basis for aspects of this pathogenic organism's distinctive lifestyle that have yet to be explained. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. J Wei MB Goldberg V Burland MM Venkatesan W Deng G Fournier GF Mayhew G Plunkett DJ Rose A Darling B Mau NT Perna SM Payne LJ Runyen-Janecky S Zhou DC Schwartz FR Blattner Infect Immun, Vol. 71, No. 5. (May 2003), pp. 2775-2786. 2008-03-04T15:43:11-00:00 2003 Infect Immun 0019-9567 71 5 2775 2786 shigella