This is really just to test out the polling system of the forum but it is still a valid topic for discussion.
The level of C.briggsae annotation is dependant on available resources as well as how valuable the effort would be. In an ideal world we’d have an army of annotators to do a full job on any worm that was sequenced but in reality we don’t. Please bear this in mind when voting.
Hopefully this may spark some discussion of the subject elsewhere on the forum.
Ant
It is a shame really that the second worm species to be sequenced did not have any large-scale EST sequencing project as this would maybe make it a lot easier to improve many gene predictions. As I understand (though I may not be remembering this correctly), either C. remanei or C. japonica will have some large-scale EST sequencing. If it was C. remanei then I would say it is better to put more effort into curating this genome. As it is much closer to C. briggsae than C. elegans, you could use transcript evidence to get a good set of gene predictions and then (at some future point) use C. remanei to annotate C. briggsae.
Having said that, I have found numerous examples (which I have previously emailed to WormBase) or C. briggsae genes with minor errors in their gene structure (missing exons, additional spurious exons) which are easily corrected by comparing to the C. elegans ortholog. In many cases, the twinscan predictions seem to produce more believable C. briggsae predictions than the current hybrid set. So maybe there is a middle ground of taking the confirmed gene set in elegans, comparing to C. briggsae and fixing just those that seem to have more obvious problems (especially the C. briggsae genes with impossibly short introns).
However, my favoured scenario would be to always try to curate genes in tandem across those species with sequenced genomes. I.e. carry on curating C. elegans, but any time you make a change to a C. elegans gene check the ortholog in C. briggsae, C. remanei etc and fix those genes at the same time. This would save time compared to curating the orthlogs at different time points in the future. Of course, you can only do this if you think you know what the true ortholog is.
Keith
Would there be interest in generating briggsae ESTs? In Edinburgh we have pipelines for doing this, and if anyone has a cDNA library we could rapidly sample and generate a small but significant amount of data.
mark
Hi Keith,
I agree it is unfortunate there is currently no large-scale EST data set for briggsae. Maybe someone will undertake one. I see that Mark has offered to do some using his pipeline. I guess the issue now is what libraries to use. There are currently 2531 mRNA sequences for briggsae in GenBank so there are libraries out there.
A modest number of ESTs are being sequenced for remanei, japonica and PB2801 as part of their genome projects. Only remanei ESTs have been completed. There were around 20K reads that fell into ~9800 clusters, which probably represents ~9300 genes.
You’re right about curating across species, but unfortunately it currently doesn’t fit well with WormBase’s work flow. Initially I really think curating orthologs across multiple species could probably be done more efficiently with a genome-wide approach once we have sequence and gene sets for all the Caenorhabditis genomes in the pipeline. After this then maybe any time an elegans gene is changed the orthologs can also be examined.
John
I think WashU sequenced a few C.briggsae ESTs. Maybe they have a good source for cDNA libraries.
Michael
I have been playing around with orthologs of roughly 50 elegans genes in both C. briggsae and C. remanei, and I am currently digging in sp.4 and japonica trace archives. I would have a lot of annotations and comments to add to wormbase (and I know a couple of other people who could contribute on several other loci); would it be possible to annotate these genomes in a collaborative, user-friendly way, like a wiki? Or maybe use the wormbase wiki, even if it’s not really tailored for the annotation of genome sequences?
We would greatly appreciate your contributions. I think the best way currently is to wait until sp.4 and japonica have gene sets and genome browsers up at WormBase. Then see how you annotations compare and send us any updates by email, or you can send them now and we’ll look at them when the gene sets are built. There is a WormBase Wiki site (http://www.wormbase.org/wiki) that you could also post your annotations (in the other nematodes section http://www.wormbase.org/wiki/index.php/Other_nematodes).
John