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
Multilocus sequence typing analysis of Streptococcus mutans strains with the cnm gene encoding collagen-binding adhesin.
Jinthana Lapirattanakul,Kazuhiko Nakano,Ryota Nomura,Pattarawadee Leelataweewud,Narumon Chalermsarp,Arthit Klaophimai,Ratchapin Laovanitch Srisatjaluk,Shigeyuki Hamada,Takashi Ooshima +8 more
TL;DR: The collagen-binding properties of S. mutans strains with the cnm gene were significantly greater than those of strains without the gene, although four cnm-negative strains classified into two sequence types (STs), ST110 and ST136, showed extremely high collagen- binding rates suggesting the presence of additional genes involved with collagen binding in these STs.
Comparative Genomic Analyses of the Genus Nesterenkonia Unravels the Genomic Adaptation to Polar Extreme Environments
TL;DR: Functional analysis revealed the enrichment of specific genes involved in bacteriorhodopsin synthesis, biofilm formation, and more diverse nutrient substance metabolism genes in the NES-AT clade, suggesting potential adaptation strategies for energy metabolism in polar environments.
Pan-Tetris: an interactive visualisation for Pan-genomes.
TL;DR: Pan-Tetris is introduced, a Java based interactive software tool that provides a clearly structured and suitable way for the visual inspection of gene occurrences in a pan-genome table and is currently the only interactive pan- genome visualisation tool.
Optimized Probe Selection for Pan-genomic DNA Microarrays
Adam M. Phillippy
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TL;DR: This paper presents a new probe selection algorithm (PanArray) that can target multiple whole genomes in a minimal number of probes and guarantees that every subsequence of the genomes is independently targeted by a full complement of probes, increasing the flexibility and accuracy of the associated comparative analysis and genotypes.
From molecular to genomic epidemiology: transforming surveillance and control of infectious diseases
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TL;DR: This thematic issue of Eurosurveillance, published in two parts, provides a series of review and original research articles that gauge progress in molecular epidemiology strategies and tools, and illustrate their applications in public health.
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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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