Comparison of 61 Sequenced Escherichia Coli Genomes
TLDR
The diversity within the species E. coli, and the overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group of Enterobacteriaceae.Abstract:
Escherichia coli is an important component of the biosphere and is an ideal model for studies of processes involved in bacterial genome evolution. Sixty-one publically available E. coli and Shigella spp. sequenced genomes are compared, using basic methods to produce phylogenetic and proteomics trees, and to identify the pan- and core genomes of this set of sequenced strains. A hierarchical clustering of variable genes allowed clear separation of the strains into clusters, including known pathotypes; clinically relevant serotypes can also be resolved in this way. In contrast, when in silico MLST was performed, many of the various strains appear jumbled and less well resolved. The predicted pan-genome comprises 15,741 gene families, and only 993 (6%) of the families are represented in every genome, comprising the core genome. The variable or ‘accessory’ genes thus make up more than 90% of the pan-genome and about 80% of a typical genome; some of these variable genes tend to be co-localized on genomic islands. The diversity within the species E. coli, and the overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group of Enterobacteriaceae.read more
Citations
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Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli
Katrine Grimstrup Joensen,Flemming Scheutz,Ole Lund,Henrik Hasman,Rolf Sommer Kaas,Eva Møller Nielsen,Frank Møller Aarestrup +6 more
TL;DR: A real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli found whole-genome sequencing typing is a superior alternative to conventional typing strategies and may also be applied to typing and Surveillance of other pathogens.
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Horizontal gene transfer: building the web of life.
TL;DR: How HGT has shaped the web of life is described using examples of HGT among prokaryotes, between proKaryotes and eukaryote, and even between multicellular eukaries, to discuss replacement and additive HGT.
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Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
H. Bjørn Nielsen,Mathieu Almeida,Agnieszka S. Juncker,Simon Rasmussen,Junhua Li,Shinichi Sunagawa,Damian R. Plichta,Laurent Gautier,Anders Gorm Pedersen,Eric Pelletier,Ida Bonde,Trine Nielsen,Chaysavanh Manichanh,Manimozhiyan Arumugam,Jean-Michel Batto,Marcelo B Quintanilha dos Santos,Nikolaj Blom,Natalia Borruel,Kristoffer Sølvsten Burgdorf,Fouad Boumezbeur,Francesc Casellas,Joël Doré,Piotr Dworzynski,Francisco Guarner,Torben Hansen,Falk Hildebrand,Rolf Sommer Kaas,Sean Kennedy,Karsten Kristiansen,Jens Roat Kultima,Pierre Leonard,Florence Levenez,Ole Lund,Bouziane Moumen,Denis Le Paslier,Nicolas Pons,Oluf Pedersen,Edi Prifti,Junjie Qin,Jeroen Raes,Søren J. Sørensen,Julien Tap,Sebastian Tims,David W. Ussery,Takuji Yamada,Pierre Renault,Thomas Sicheritz-Pontén,Peer Bork,Jun Wang,Søren Brunak,S. Dusko Ehrlich +50 more
TL;DR: This work presents a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly of microbial genomes without the need for reference sequences.
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Biochemistry and Evolution of Anaerobic Energy Metabolism in Eukaryotes
Miklós Müller,Marek Mentel,Jaap J. van Hellemond,Katrin Henze,Christian Woehle,Sven B. Gould,Re-Young Yu,Mark van der Giezen,Aloysius G.M. Tielens,William Martin +9 more
TL;DR: The gene distribution across lineages reflects the presence of anaerobic energy metabolism in the eukaryote common ancestor and differential loss during the specialization of some lineages to oxic niches, just as oxphos capabilities have been differentially lost in specialization to anoxic niches and the parasitic life-style.
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Insights from 20 years of bacterial genome sequencing
Miriam Land,Loren Hauser,Se-Ran Jun,Intawat Nookaew,Michael R. Leuze,Tae-Hyuk Ahn,Tatiana Karpinets,Ole Lund,Guruprased H. Kora,Trudy M. Wassenaar,Suresh Poudel,David W. Ussery +11 more
TL;DR: A series of questions are explored to highlight some insights that comparative genomics has produced and how it could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.
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Hervé Tettelin,Vega Masignani,Michael J. Cieslewicz,Claudio Donati,Duccio Medini,Naomi L. Ward,Samuel V. Angiuoli,Jonathan Crabtree,Amanda L. Jones,A. Scott Durkin,Robert T. DeBoy,Tanja M. Davidsen,Marirosa Mora,Maria Scarselli,Immaculada Margarit Y Ros,Jeremy Peterson,Christopher R. Hauser,Jaideep P. Sundaram,William C. Nelson,Ramana Madupu,Lauren M. Brinkac,Robert J. Dodson,M. J. Rosovitz,Steven A. Sullivan,Sean C. Daugherty,Daniel H. Haft,Jeremy D. Selengut,Michelle L. Gwinn,Liwei Zhou,Nikhat Zafar,Hoda Khouri,Diana Radune,George Dimitrov,Kisha Watkins,Kevin J. B. O'Connor,Shannon Smith,Teresa Utterback,Owen White,Craig E. Rubens,Guido Grandi,Lawrence C. Madoff,Dennis L. Kasper,John L. Telford,Michael R. Wessels,Rino Rappuoli,Claire M. Fraser +45 more
TL;DR: The genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans, was generated and Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactic pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.
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