BASIC PROTOCOL 8: VIEWING THE C. BRIGGSAE GENOME AND ITS SYNTENY WITH C. ELEGANS
At least six species in the Caenorhabditis genus have morphology and genetics close enough to C. elegans that they can be classed as its siblings (Cho et al., 2004; Kiontke et al., 2004). Of these sibling species, three (C. briggsae, C. remanei, and C. sp. CB5161) have been isolated as laboratory strains. C. briggsae and C. remanei have undergone whole-genome shotgun sequencing so that they can be compared to C. elegans (Stein et al., 2003; J. Spieth, pers. comm.). As of mid-September 2005, WormBase includes both the C. briggsae genome and a preliminary assembly of the C. remanei genome. C. briggsae's genome can be viewed either by itself or in syntenic linkages to C. elegans.
A standard computer with a reasonably fast connection to the Internet (cable modem, DSL, or Ethernet recommended)
Web browser such as Internet Explorer (http://www.microsoft.com) or Mozilla (http://www.mozilla.org/firefox)
1. Click on the "C. briggsae Genome" link in the Sequences section of the Web site directory on the main WormBase page (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png). This will give a Genome Browser window, from which one can then pick C. briggsae sequences for viewing in the same way as with C. elegans (http://wormbase.org/db/seq/gbrowse/briggsae;).
At this writing, the whole-genome shotgun sequence exists as 5,341 contigs, organized into 142 supercontigs with names like "cb25.fpc0058"; the predicted genes have names like "CBG02462". Such a view is useful for extracting nucleotide sequences, but is rather nondescript.
Usually the C. briggsae sequences are interesting because of their relationship to C. elegans orthologs. Such orthologies can be viewed directly via the Synteny Viewer.
2. Click on the Synteny Viewer link in the Sequences section of the Web site directory on the main WormBase page (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png). This gives a search window in which one can ask for given C. elegans or C. briggsae sequences by its sequence name. A search for either type of sequence gives a syntenic alignment of it with its predicted ortholog (if any) in the opposite species. For instance, searching for zyg-1 by its sequence name F59E12.2 (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_05.png) in the Synteny Viewer gives an alignment of the zyg-1/bli-2 cluster in both species.
Click on the Shown Alignment link to get the two-species sequence alignment in a new browser window.
3. Alternatively, start with a Genome Browser view of some interesting C. elegans gene, and invoke the "Briggsae alignments" track in the viewer (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_10.png). Then, click directly on the blue "Briggsae alignments" line in the diagram. This will move the viewer from a single-genome view to a syntenic view of the region that was clicked on (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_14png). This approach is particularly useful if the C. elegans genomic region one wants to study is complicated, and getting the correct homology for a specific site is crucial.
4. The Synteny Viewer itself can be zoomed outward or inward to view large or small regions, just as the Genome Browser can. Moreover, one genome can be visually flipped with respect to another so that its homology can be disentangled and made easy to see. With some care, it is possible to get pleasingly clear diagrams of what would otherwise be murky homologies.
5. Analysis of the C. briggsae genome identified ~12,000 predicted genes as putative orthologs of C. elegans genes (Stein et al., 2003). These orthologs, where they exist, are listed as hypertext links on each C. elegans Gene page, with the choice of going directly to the C. briggsae gene or to its syntenic alignment (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_03.png). On some C. elegans Gene pages, there will also be BLASTP hits given against the C. briggsae genome; clicking on these hits takes one to a C. briggsae protein page. In general, most WormBase functions work for C. briggsae in the same way as for C. elegans.