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Scientific papers: supplementary material

Comparative genomic indexing reveals the phylogenomics of Escherichia coli pathogens.

Muna F. Anjum, Sacha Lucchini, Arthur Thompson, Jay C.D. Hinton and Martin J. Woodward.

Infection and Immunity
(2003)  71 (8) 4674 - 4683

Background

DNA microarrays offer a new way to assess the presence and absence of genes at the genomic level. We have hybridised 26 field isolates of E. coli from 7 different serotypes representing EHEC and EPEC pathotypes against an E. coli K12 microarray. The microarray data allowed the grouping of strains into EPEC, EHEC or "others" based on the chromosomal relatedness between strains, unlike the results from toxin production and PCR amplification of a small subset of virulence gene markers. 

The functional categories in the COG database were used to analyse the genes that were present or absent from the E. coli strains tested. This established that essential genes involved with core cellular and functional processes were present in all strains, whilst many dispensible genes were commonly missing.

Appendix

Appendix 1 (1548 kb) The complete dataset of CDS derived by CGI of the strains used in this study (supplementary information). The CDS detected by microarray hybridisation are scored as 1; CDS which were not detected are scored as 0. 

Appendix 2 (282 kb) Table of CDS missing from the K12 chromosomal backbone for all strains used in this study (supplementary information). The CDS which were not detected by microarray hybridisation are listed for each strain.