Comparison of 61 sequenced Escherichia coli genomes.

Microbial Ecology
Oksana LukjancenkoDavid W Ussery

Abstract

Escherichia coli is an important component of the biosphere and is an ideal model for studies of processes involved in bacterial genome evolution. Sixty-one publically available E. coli and Shigella spp. sequenced genomes are compared, using basic methods to produce phylogenetic and proteomics trees, and to identify the pan- and core genomes of this set of sequenced strains. A hierarchical clustering of variable genes allowed clear separation of the strains into clusters, including known pathotypes; clinically relevant serotypes can also be resolved in this way. In contrast, when in silico MLST was performed, many of the various strains appear jumbled and less well resolved. The predicted pan-genome comprises 15,741 gene families, and only 993 (6%) of the families are represented in every genome, comprising the core genome. The variable or 'accessory' genes thus make up more than 90% of the pan-genome and about 80% of a typical genome; some of these variable genes tend to be co-localized on genomic islands. The diversity within the species E. coli, and the overlap in gene content between this and related species, suggests a continuum rather than sharp species borders in this group of Enterobacteriaceae.

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Jun 7, 2011·Microbial Ecology·Annika JacobsenCarsten Friis
Oct 28, 2011·Microbial Ecology·Oksana LukjancenkoTrudy M Wassenaar
Feb 26, 2013·Applied Microbiology and Biotechnology·Jörn PetersenSilke Pradella
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Methods Mentioned

BETA
electrophoresis

Software Mentioned

MLST
NJPlot
BLAST
ClustalX
RNAmmer
EasyGene
BLASTP

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