Regions of difference

Regions of difference

The term "Regions of difference" (ROD) referres to loci within a bacterial genome which are found only in some members of a species. These loci are typically prophages, transposons, plasmids integrated into the chromosome, and remnants of all these mobil elements. If their evolutionary origin cannot be deduced, they are just called genomic island. Chromosomal encoded virulence factors and antibiotic resistence determinats are most often haboured in ROD. In an excellent publication ChaudhuriRR-SebaihiaM-2010 have used the concept of ROD to analyze the full genome of the prototypical enteroaggregative Escherichia coli strain 042.

This page is intended to be the start point for an analysis and annotation of ROD in the 2011 O104:H4 outbreak strain. Please contribute to this page and its subpages.

id	size / nt	integration site	type	name	payload	note
RD0001	60869	wrbA	prophage	phiStx2	stxA2, stxB2
RD0002	86630	ycdU and tRNAserX	island		iha, mchBCF, terCDE, yeeVW	adhesine, microcin
RD0003	48449	yecE	prophage ?
RD0004	48778	tRNAselC and setC	island		merDA, tetRA, flu, yeeVW

Preliminary findings:

• it is amazing to see how all the promiment virulence and resistence factors cluster together at only a few sites.
• the yeeVW gene cluster is found on the chromosome at 3 locations. Is this an artefact of assembling or an exmaple of elevated gene dosage?
• tRNA genes are hot-spots for integration of mobile elements in O104:H4 (which is long known)

Technical notes

• create a separate wiki page for every ROD you have found. The page name should be the next free identifier as found on this page. Using numerical identifiers will make it more easy to change the nice name of a ROD later on without breaking hyperlinks.
• the identifier are RD0001, RD0002 ... and they are intended to be distinguishable from the identiers used by ChaudhuriRR-SebaihiaM-2010 (ROD01, ROD02 ...)
• identifier must be unique but they do not have any meaning, especially not about the location on the chromosome or ordering.
• link new pages into the master table on this page. The master table is maintained in vanilla HTML markup.
• if you create a new ROD page, you may first copy the raw content of an existing page to the new page and then modify it accordingly.
• it is suggested to avoid terms like 'pathogenicity island' or 'resistence island'. These term just relate to the payload carried by an island or a bacteriophage, but there is no principle difference between them.
• the exact location of a ROD is not listed in the master table but only on its subpage. The locations may change as we see new assemblies and there should be only one place were they are stored.
• a WIKI is not a really good way to store structured data. However, the advantage of a WIKI is that many people can contribute with a minimal learning effort. The single ROD pages a intended to contain mostly free text and hyperlinks which point to primary research papers, genbank entries and other stuff describing the structure of that island and its payload genes.

Wish list

• Can we generate annotated feature lists for the ROD automatically, can we generate maps? Maps could be stored in the GIT repository and then linked into WIKI pages with the tag.
• The outbreak strain carries at least three SPATE genes (pic, sepA, sigA). In which ROD are they located?