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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 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 restince factors cluster together in only a few islands.
- 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.
- Can we generate annotated feature lists for the ROD automatically?