Tutorial: Using Genome Map to Find the RD2 Deletion
Motivation
Potential pathogenicity elements in mycobacterial genomes can be identified by analyzing gene gain or loss through comparative genomics. An example of such a deletion is the loss of the RD2 region (Rv1978 - Rv1988) encoding the protein antigen MPB64 from some strains of M. bovis BCG (Mahairas et al., J. Bacteriology 1996).
Start
To visualize that the RD2 region is indeed present in M. tb. H37Rv, and deleted from M. bovis BCG, go to the TBDB top menu bar and select Genomic Data > Comparative Analysis. Then, click on "Circular Genome Viewer" in the menu on the left.
Edit Tracks
Then, click on "Edit Tracks" to select a couple of alignments with M. bovis strains for display.
First, deactivate the tracks showing the Epitope Density and the H37Rv Reference to make room for the alignments:
Add Tracks
Then select the M. Bovis BCG and M. Bovis AF2122 genome alignments and click "Apply".
Select Area
At the 6 o'clock position of the two innermost circles you see a gap in the alignments with the M. bovis genomes. You can drag and select with the mouse the region of the H37Rv genome that is deleted in BCG. It shows up in red.
Switch Tools
Right-click on this selected region and choose
"View slice in genome map".
Add Genomes
This will open up a new window with the selected region of M. tb. H37Rv displayed in the Genome Map.
Click on "Select Genomes" to select the other strains, M. bovis BCG and M. bovis AF2122/97.
Select Area
Then, click and drag across the center of the genome map in H37Rv. This will highlight the homologous regions in the M. Bovis map and draw connections between those segments.
Note the two wide areas converging at one point near the center of the M. bovis AF2122/97 genome.
Zoom in
As you zoom in closer on the point of convergence in the M. bovis genome, you may need to recenter the display using the left and right arrows in the navigation widget (or the left and right arrow keys on your keyboard). Once you have reached the zoom level where individual features become visible, you can click the gray marker at the left end of a track to expand tracks with overlapping features.
View annotation
As you move your mouse over the individual genes you will see the callouts for annotations.
Note that an additional genomic region of Mtb H37Rv, corresponding to the the Mce3
(mammalian cell entry 3, Santangelo et al. Microbiology 148 (2002), 2997-3006) locus, is missing in both M. bovis AF2122 and M. bovis BCG. Mce loci have been implicated in virulence of Mtb (Gioffrey et al., Microbes and Infection 7(3) (2005) 325-334). This example highlights the Genome Map's ability to visualize relevant genomic deletions in mycobacteria.
