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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 create an inventory of all ROD in the genome of the 2011 O104:H4 outbreak strain in a collaborative fashion in the style of Wikipedia. Please feel free to contribute to this page and its subpages in order to get a complete and throughout analysis and annotation of all ROD.
| id | size / nt | integration site | type | name | payload | note |
|---|---|---|---|---|---|---|
| RD0001 | 60869 | wrbA | prophage | phiStx2 | stxA2, stxB2 | |
| RD0002 | 86630 | ycdU and tRNAserX | O island | Tellurite resistance- and adherence-conferring island | iha, mchBCF, terCDE, yeeVW | adhesine, microcin |
| RD0003 | 48449 | yecE | prophage | |||
| RD0004 | 48778 | tRNAselC and setC | composite 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 example of elevated gene dosage?
- tRNA genes are hot-spots for integration of mobile elements in O104:H4 (which is long known)
- 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.
- 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?
- Prophages are recognized by their integrase/exicionase genes or by genes coding typical phage structural proteins. Are there further prophages in the chromosome?