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.
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.
The good work of the C. elegans Deletion Mutant Consortium is now described in a paper in the current issue of the journal G3. The paper describes the methods used to generate the mutant strains and lists the multigene families for which mutants are available.
We have been working on marking possible genome sequence errors in the C.elegans reference genome using data from the following projects:
– Weber KP et al. (2010) PLoS One “Whole genome sequencing highlights genetic changes associated with laboratory ….” (PMID 21085631)
– Doitsidou M et al. (2010) PLoS One “C. elegans mutant identification with a one-step whole-genome-sequencing and ….” (PMID 21079745)
– McGrath PT et al. (2011) Nature “Parallel evolution of domesticated Caenorhabditis species targets pheromone ….” (PMID 21849976)
This data has been used to mark regions for improvement (also available as GFF3 features), taking the total of these locations in the C. elegans database to 2,428.
We will address some of them in the next WormBase release WS234.
Update: the genome changes were deferred from WS234 to WS235
The newly published Bursaphelenchus xylophilus (Kikuchi et.al) is as of WS229 available at WormBase including it’s gene set. The data are available as GFF3 and FASTA files for download, and has been added to GBrowse and BLAST.
Bursaphelenchus xylophilus is a pine parasite causing considerable economic damage and can give insights into evolution of plant parasites by comparing it, for example, to Meloidogyne.