Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli
Rodney A. Welch,Valerie Burland,Guy Plunkett,Peter Redford,Paula L. Roesch,David A. Rasko,Eric L. Buckles,S. R. Liou,S. R. Liou,Adam T. Boutin,Adam T. Boutin,Jeremiah D. Hackett,Jeremiah D. Hackett,D. Stroud,George F. Mayhew,Debra J. Rose,Shiguo Zhou,David C. Schwartz,Nicole T. Perna,Harry L. T. Mobley,Michael S. Donnenberg,Frederick R. Blattner +21 more
TLDR
The complete genome sequence of uropathogenic Escherichia coli, strain CFT073 is presented and Comparisons indicate that extraintestinal pathogenic E. coli arose independently from multiple clonal lineages.Abstract:
We present the complete genome sequence of uropathogenic Escherichia coli, strain CFT073. A three-way genome comparison of the CFT073, enterohemorrhagic E. coli EDL933, and laboratory strain MG1655 reveals that, amazingly, only 39.2% of their combined (nonredundant) set of proteins actually are common to all three strains. The pathogen genomes are as different from each other as each pathogen is from the benign strain. The difference in disease potential between O157:H7 and CFT073 is reflected in the absence of genes for type III secretion system or phage- and plasmid-encoded toxins found in some classes of diarrheagenic E. coli. The CFT073 genome is particularly rich in genes that encode potential fimbrial adhesins, autotransporters, iron-sequestration systems, and phase-switch recombinases. Striking differences exist between the large pathogenicity islands of CFT073 and two other well-studied uropathogenic E. coli strains, J96 and 536. Comparisons indicate that extraintestinal pathogenic E. coli arose independently from multiple clonal lineages. The different E. coli pathotypes have maintained a remarkable synteny of common, vertically evolved genes, whereas many islands interrupting this common backbone have been acquired by different horizontal transfer events in each strain.read more
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Pathogenic Escherichia coli
TL;DR: Few microorganisms are as versatile as Escherichia coli; it can also be a highly versatile, and frequently deadly, pathogen.
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Mauve: multiple alignment of conserved genomic sequence with rearrangements.
TL;DR: This work presents methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer and evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.
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progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
TL;DR: A new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss is described, demonstrating high accuracy in situations where genomes have undergone biologically feasible amounts of genome rearrangement, segmental loss and loss.
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BLAST Ring Image Generator (BRIG) : simple prokaryote genome comparisons
TL;DR: BRIG is a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface and will perform all required file parsing and BLAST comparisons automatically.
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The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
Douglas B. Rusch,Aaron L. Halpern,Granger G. Sutton,Karla B. Heidelberg,Karla B. Heidelberg,Shannon J. Williamson,Shibu Yooseph,Dongying Wu,Dongying Wu,Jonathan A. Eisen,Jonathan A. Eisen,Jeff Hoffman,Karin A. Remington,Karen Beeson,Bao Duc Tran,Hamilton O. Smith,Holly Baden-Tillson,Clare Stewart,Joyce Thorpe,Jason Freeman,Cynthia Andrews-Pfannkoch,Joseph E. Venter,Kelvin Li,Saul A. Kravitz,John F. Heidelberg,John F. Heidelberg,T. Utterback,Yu-Hui Rogers,Luisa I. Falcón,Valeria Souza,Germán Bonilla-Rosso,Luis E. Eguiarte,David M. Karl,Shubha Sathyendranath,Trevor Platt,Eldredge Bermingham,Victor A. Gallardo,Giselle Tamayo-Castillo,Michael Ferrari,Robert L. Strausberg,Kenneth H. Nealson,Kenneth H. Nealson,Robert Friedman,Marvin Frazier,J. Craig Venter +44 more
TL;DR: A metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition, which yielded an extensive dataset consisting of 7.7 million sequencing reads.
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