Journal Article10.1016/J.GDE.2005.09.006
The microbial pan-genome
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TL;DR: A decade after the beginning of the genomic era, the question of how genomics can describe a bacterial species has not been fully addressed and the pan-genome, which is composed of a "core genome" containing genes present in all strains, and a "dispensable genome", might be orders of magnitude larger than any single genome.
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About: This article is published in Current Opinion in Genetics & Development. The article was published on 01 Dec 2005. The article focuses on the topics: Minimal genome & Bacterial genome size.
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Citations
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A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies.
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TL;DR: The latest improvements of the EDGAR platform for comparative genome analyses are described and recent examples of its application for the phylogenomic analysis of different taxa are presented.
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Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus
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Strong seed-bank effects in bacterial evolution.
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TL;DR: It is reasoned that certain bacterial population genetics anomalies could be explained by the prevalence of strong seed-bank effects among bacteria, and the genome of the bacterium Azotobacter vinelandii is analyzed and it is shown that genes that code for functions that are essential for the bacteria biology do not have a relation of ancestry with closely related bacteria, or are ORFan genes.
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References
Diversity of the human intestinal microbial flora.
Paul B. Eckburg,Elisabeth M. Bik,Charles N. Bernstein,Elizabeth Purdom,Les Dethlefsen,Michael Sargent,Steven R. Gill,Karen E. Nelson,David A. Relman,David A. Relman,David A. Relman +10 more
TL;DR: A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms, and significant intersubject variability and differences between stool and mucosa community composition were discovered.
Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter,Karin A. Remington,John F. Heidelberg,Aaron L. Halpern,Doug Rusch,Jonathan A. Eisen,Dongying Wu,Ian T. Paulsen,Karen E. Nelson,William C. Nelson,Derrick E. Fouts,Samuel Levy,Anthony H. Knap,Michael W. Lomas,Kenneth H. Nealson,Owen White,Jeremy Peterson,Jeff Hoffman,Rachel Parsons,Holly Baden-Tillson,Cynthia Pfannkoch,Yu-Hui Rogers,Hamilton O. Smith +22 more
TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome”
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.
2.5K
Mobile elements: drivers of genome evolution.
TL;DR: Mobile elements within genomes have driven genome evolution in diverse ways and are becoming useful tools for learning more about genome evolution and gene function.
1.9K
Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion
TL;DR: The current review presents the available genomics and biological data on prophages from bacterial pathogens in an evolutionary framework to demonstrate that the chromosomes from bacteria and their viruses (bacteriophages) are coevolving.
1.7K