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
Complete sequence and comparative genomic analysis of eight native Pseudomonas syringae plasmids belonging to the pPT23A family
TL;DR: It is confirmed that plasmid phylogeny is incongruent with P. syringae pathovar or host of isolation and conserved genes among seven sequenced plasmids within the same phylogenetic group were limited toplasmid-specific functions including maintenance and transfer functions.
Efficient oligonucleotide probe selection for pan-genomic tiling arrays
TL;DR: A new probe selection algorithm (PanArray) that can tile multiple whole genomes using a minimal number of probes and uses an unbiased, probe-centric approach that does not rely on annotations, gene clustering, or multi-alignments.
Pan- and core- network analysis of co-expression genes in a model plant.
Fei He,Sergei Maslov +1 more
TL;DR: This work reanalyzed public expression data to construct a large collection of 134 coexpression networks based on expression datasets reported in individual publications to help the plant research community to better explore the information contained within the existing vast collection of gene expression data in Arabidopsis.
The relationship of the whole genome sequence identity to DNA hybridization varies between genera of prokaryotes.
TL;DR: The average nucleotide identity (ANIb), a surrogate for the ΔTm, and the calculated DDH (cDDH) were determined from the complete genomes of representatives of 17 genera of prokaryotes and it is no longer appropiate to consider both measures of relatedness when delineating species.
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BlastFrost: fast querying of 100,000s of bacterial genomes in Bifrost graphs
TL;DR: BlastFrost as mentioned in this paper queries a Bifrost data structure for sequences of interest and extracts local subgraphs, enabling the identification of the presence or absence of individual genes or single nucleotide sequence variants.
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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.
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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.
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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.
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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.
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