Fri, 25 Jul 2008 15:23:25 BST CiteULike: Xavier Darling http://www.citeulike.org/user/Xavier/author/Darling CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/Xavier/article/2640930 <i>Methods in molecular biology (Clifton, N.J.), Vol. 396 (2007), pp. 135-152.</i><br /><br />During the course of evolution, genomes can undergo large-scale mutation events such as rearrangement and lateral transfer. Such mutations can result in significant variations in gene order and gene content among otherwise closely related organisms. The Mauve genome alignment system can successfully identify such rearrangement and lateral transfer events in comparisons of multiple microbial genomes even under high levels of recombination. This chapter outlines the main features of Mauve and provides examples that describe how to use Mauve to conduct a rigorous multiple genome comparison and study evolutionary patterns. Analyzing patterns of microbial evolution using the mauve genome alignment system. AE Darling TJ Treangen X Messeguer NT Perna Methods in molecular biology (Clifton, N.J.), Vol. 396 (2007), pp. 135-152. 2008-04-08T08:45:04-00:00 2007 Methods in molecular biology (Clifton, N.J.) 1064-3745 396 135 152 no-tag 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