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
Pangenomic Analysis of Dickeya dianthicola Strains Related to the Outbreak of Blackleg and Soft Rot of Potato in USA
Tongling Ge,He Jiang,Ek Han Tan,Steven B. Johnson,Robert P. Larkin,Amy O. Charkowski,Gary A. Secor,Jianjun Hao +7 more
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Integration of Comparative Genomics with Genome-Scale Metabolic Modeling to Investigate Strain-Specific Phenotypical Differences.
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Computational Methods in Microbial Population Genomics
Xavier Didelot
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TL;DR: The current state of the art in terms of computation methods used in microbial population genomics is reviewed, which includes software for assembly and alignment of core genomic regions, which is usually a pre-requirement for analysing the ancestry of the genomes, via phylogenetic on non-phylogenetic methods.
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Understanding the commonalities and differences in genomic organizations across closely related bacteria from an energy perspective
Qin Ma,Qin Ma,Xin Chen,Xin Chen,Chao Liu,Chao Liu,Xizeng Mao,Xizeng Mao,Hanyuan Zhang,Hanyuan Zhang,Fei Ji,Fei Ji,ChunGuo Wu,ChunGuo Wu,Ying Xu,Ying Xu,Ying Xu +16 more
TL;DR: A quantitative model is developed that captures the frequencies of the transcription activation of pathways relative to those of the other encoded pathways in an organism as well as the variation in the activation frequencies across the related genomes that play a key role in the observed commonalities and differences in the genomic organizations of genes (and operons) encoding specific pathways across different genomes.
No evidence for a bovine mastitis Escherichia coli pathotype
TL;DR: The definition of the MPEC pathotype is put into question and it is suggested to designate corresponding isolates as MAEC, the first characterization of a phylogenetically diverse strain panel including several MAEC and commensal isolates.
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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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