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
Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics
TL;DR: The evolution of comparative genomics, its impact in understanding pathogen evolution and physiology and the opportunities and challenges presented by next-generation sequencing as applied to pathogen genome comparisons are reviewed.
Genome plasticity and systems evolution in Streptomyces
TL;DR: The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes.
Mugsy: fast multiple alignment of closely related whole genomes
TL;DR: Mugsy does not require a reference sequence, can align mixtures of assembled draft and completed genome data, and is robust in identifying a rich complement of genetic variation including duplications, rearrangements, and large-scale gain and loss of sequence.
High-quality pan-genome of Escherichia coli generated by excluding confounding and highly similar strains reveals an association between unique gene clusters and genomic islands
Tong Yang,Feng Gao +1 more
TL;DR: It is found that the inclusion of highly similar strains also affects the results of unique genes in pan-genome analysis, which leads to a significant underestimation of the number ofunique genes in the pan- genome.
Determining the Genetic Characteristics of Resistance and Virulence of the "Epidermidis Cluster Group" Through Pan-Genome Analysis.
Zhewei Sun,Danying Zhou,Xueya Zhang,Qiaoling Li,Hailong Lin,Wei Lu,Hongmao Liu,Junwan Lu,Xi Lin,Kewei Li,Teng Xu,Qiyu Bao,Hailin Zhang +12 more
TL;DR: Findings suggested that the plasmid and chromosome encoded bla operons of ECG species underwent different evolution paths, as well as they differed in the abundance of virulence genes associated with adherence, invasion, secretion system and immune evasion.
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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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