Genomics of Loa loa, a Wolbachia-free filarial parasite of humans

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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.

Genomics of Loa loa, a Wolbachia-free filarial parasite of humans.

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.

Abstract

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.

Featured Paper: The origin and function of anti-fungal peptides in C. elegans

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The origin and function of anti-fungal peptides in C. elegans: open questions
by Nathalie Pujol, Paul A. Davis* and Jonathan J. Ewbank

This paper describes a gene-class of short proteins expressed during fungal challenge and covers most nematodes included in WormBase.

Front Immunol. 2012;3:237. doi: 10.3389/fimmu.2012.00237. Epub 2012 Aug 1.

*Disclaimer: Paul Davis is a WormBase curator at the EBI

Legacy allele information in WormBase

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As of WS236, published and unpublished allele phenotypes from the books,  C. elegans I and II, will be available through gene and allele pages displayed in the phenotype widget. This focused effort added 4,819 phenotype annotations to 1,431 genes. Until now, these data had been hidden in legacy information from C. elegans I and II,  and were available in WormBase as a block of text under the concise description in the overview widget of the gene page.  As these descriptions constitute valuable gene function information, we are pleased to have these data available for query and computational analysis.

New gene expression data

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Interested in seeing the expression profile of your favorite gene during development? When you are on the gene page of interest, select the expression widget to open it, and click on the object whose description begins with ‘Developmental gene expression time-course’.  On the graph page, clicking on the graphs will result in larger images.  We have recently incorporated graphs for over 19,000 genes from the study published in Developmental Cell (Levin et al., 2012).  Check out tbx-34 as an example.