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• W316149968 abstract "Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity Christopher B. Walker, 1,2† Sergey Stolyar, 1,2 Dylan Chivian, 2,3 Nicolas Pinel, 1 Jeffrey A. Gabster, 1,2 Paramvir S. Dehal, 2,3 Zhili He, 2,4 Zamin Koo Yang, 2,6 Huei-Che B. Yen, 2,5 Jizhong Zhou, 2,4 Judy D. Wall, 2,5 Terry C. Hazen, 2,3 Adam P. Arkin 2,3 and David A. Stahl 1,2 * Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA. Virtual Institute for Microbial Stress and Survival (vimss.lbl.gov). Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA, USA. Institute for Environmental Genomics, Oklahoma, University, Norman, OK, USA. Biochemistry Division, University of Missouri, Columbia, MO, USA. Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. Summary The genome of Desulfovibrio vulgaris strain DePue, a sulfate-reducing Deltaproteobacterium isolated from heavy metal-impacted lake sediment, was completely sequenced and compared with the type strain D. vulgaris Hildenborough. The two genomes share a high degree of relatedness and synteny, but harbour distinct prophage and signatures of past phage encounters. In addition to a highly variable phage contribution, the genome of strain DePue contains a cluster of open-reading frames not found in strain Hildenborough coding for the production and export of a capsule exopolysaccharide, possibly ofrelevance to heavy metal resistance. Comparative whole-genome microarray analysis on four additional D. vulgaris strains established greater interstrain variation within regions associated with phage insertion and exopolysaccharide biosynthesis. emi_1946 2244..2252 Introduction Bacteriophage and other mobile elements represent a large reservoir of genetic information affecting the structure and evolution of microbial ecosystems. Complete genome sequences for numerous environmentally relevant microbes have highlighted both a relatively conserved core genome and a remarkable contribution of bacteriophage to the pan-genome; the pan- genome composed of the sum of all unique genes distributed in a described species (Tettelin et al., 2005; Coleman et al., 2006; Cuadros-Orellana et al., 2007; Lindell et al., 2007). For example, while comparative genomic analysis of only three Prochlorococcus species revealed the core genome, sequencing of 12 isolates suggested a pangenome at least an order of magnitude larger than any single genome (Lindell et al., 2007). Although anaerobes are as yet less well represented by completed genome sequences, the comparative analyses of closely related Desulfovibrio isolates presented here indicates a similar contribution of viruses and other mobile genetic elements to the pan-genome of this representative anaerobe. Desulfovibrio are sulfate-reducing microorganisms that participate in global sulfur- and carbon-cycling, often forming complex communities with other anaerobes and facilitating the complete decomposition of organic material (for review, see Rabus et al., 2005). The significance of phage to population structure was initially suggested by the isolation and characterization of D. vulgaris strain DePue. This sulfate-reducing microorganism, isolated from a heavy metal-impacted lake sediment, lacks prophages present in strain Hildenborough (Walker et al., 2006). The recently completed genome sequence of strain DePue reported here now provides the basis for a more complete census of phage-associated divergence among different described strains of Desulfovibrio vulgaris and highlights the role of CRISPR (clusters of regularly interspaced palindromic repeats) immunity among closely related strains. Previous studies have demonstrated that strain DePue was sensitive to lytic infection by viruses carried as prophages in strain Hildenborough (Walker et al., Complementary whole-genome microarray comparisons with other D. vulgaris strains now shows that among this study set, strain DePue is unique in lacking any of the six prophage annotated in the Hildenborough genome. Thus," @default.
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• W316149968 date "2010-03-15" @default.
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• W316149968 title "Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity" @default.
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