Based on feedback from the nematode community, WormBase will do a themed release for WS241, which will focus on the curation of protein unfolding response processes.
This will include new publications, ontologies, interactions, gene models and more.
During the course of the curation effort, 412 genes of C.elegans / C.remanei / C.briggsae / C.japonica / C.brenneri and B.malayi have been investigated.
We would like to congratulate the Berriman and Gasser labs to their articles on the Australian and European Haemonchus contortus genome assemblies published in the most recent edition of Genome Biology
Both assemblies will be available at WormBase as part of the upcoming WS239 release.
It has become necessary for us to modify the structure of the “releases” branch FTP site. The reason for this is that we are now required to represent potentially multiple alternative reference genomes sequences for a single nematode species (e.g. Ascaris suum).
In many cases, these references will originate from different strains, but that may not always be the case. We have therefore chosen to differentiate between alternative reference genomes for a single species by including the NCBI BioProject accession (http://www.ncbi.nlm.nih.gov/bioproject) in the directory path and files names. Alternative genome sequencing efforts for the same species will each be assigned their own unique NCBI BioProject accession.
With the International Worm Meeting 2013 coming up soon, I would like to remind you that the submission for the WS238 release of WormBase will be at the end of April. If you have a large or complex dataset, please tell us well ahead of time, to allow for processing of the data.
While WS238 will most likely not be live during the meetings, it will be, soon after.
Congratulations to the Broad institute, as their Loa loa genome (shown on WormBase) has been successfully published in Nature Genetics.
Nat Genet. 2013 Mar 24. doi: 10.1038/ng.2585.
Desjardins CA, Cerqueira GC, Goldberg JM, Hotopp JC, Haas BJ, Zucker J, Ribeiro JM, Saif S, Levin JZ, Fan L, Zeng Q,Russ C, Wortman JR, Fink DL, Birren BW, Nutman TB.
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, L. loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4-Mb genome of L. loa and that of the related filarial parasite Wuchereria bancrofti and predict 14,907 L. loa genes on the basis of microfilarial RNA sequencing. By comparing these genomes to that of another filarial parasite, Brugia malayi, and to those of several other nematodes, we demonstrate synteny among filariae but not with nonparasitic nematodes. The L. loa genome encodes many immunologically relevant genes, as well as protein kinases targeted by drugs currently approved for use in humans. Despite lacking Wolbachia, L. loa shows no new metabolic synthesis or transport capabilities compared to other filariae. These results suggest that the role of Wolbachia in filarial biology is more subtle than previously thought and reveal marked differences between parasitic and nonparasitic nematodes.