Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes.

ABSTRACT:

Background

Escherichia coli exists in commensal and pathogenic forms. By measuring the variation of individual genes across more than a hundred sequenced genomes, gene variation can be studied in detail, including the number of mutations found for any given gene. This knowledge will be useful for creating better phylogenies, for determination of molecular clocks and for improved typing techniques.

Results

We find 3,051 gene clusters/families present in at least 95% of the genomes and 1,702 gene clusters present in 100% of the genomes. The former 'soft core' of about 3,000 gene families is perhaps more biologically relevant, especially considering that many of these genome sequences are draft quality. The E. coli pan-genome for this set of isolates contains 16,373 gene cluste

SUBMITTER: Kaas RS 

PROVIDER: S-EPMC3575317 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature