Jen Daub et al. (2001) International C. elegans Meeting "Mapping the genome(s) of the human nematode parasite Brugia malayi"

Mike Quail, Mark Blaxter, Jenna Ware, Jeremy Foster, Jen Daub, Ibrahim Kamal, Barton Slatko, The Filarial Genome Project, Bart Barrell, Neil Hall, Mehul Ganatra, David Guiliano

[International C. elegans Meeting, 2001]

The human-infective filarial nematode parasite Brugia malayi contains three genomes : the mitochondrial genome, the genome of the rickettsia-like Wolbachia endosymbiont and the nuclear genome. We have sequenced the mitochondrial genome of Brugia malayi and compared it to the other sequenced nematode mitochondria. The genome is, as expected, very similar to that of Onchocerca volvulus , and is remarkably different from C. elegans in gene order and sequence. Phylogenetic anlysis of nematode mitochondrial DNAs conflict with phylogenies derived from nuclear genes. Most filarial species harbour an bacterium that is believed to be in mutualistic symbiosis with the nematode. The bacteria are closely related to the Wolbachia endosymbionts of arthropods. The genome of the Wolbachia endosymbiont is being mapped and sequenced by a consortium headed by Barton Slatko at New England Biolabs. The nuclear genome of B. malayi is estimated to be 100 Mbp with an expected gene number comparable to C. elegans . To date, the Filarial Genome Project has produced 22,441 ESTs from 11 different cDNA libraries from various stages of the life cycle. These are estimated to represent ~8000 different genes. As a prelude to whole genome sequencing we are now in the process of constructing a physical map for the nuclear genome. A BAC library is being end sequenced, and BAC-derived end-probes hybridised to the gridded library to create contigs in a sampling-without replacement strategy. A number of EST clones have also been hybridised. In the course of this mapping program we have defined the distribution of sattelite repeats in the library, and have identified at least two families of retrotransposon-like elements.

Tzertzinis G et al. (1998) East Coast Worm Meeting "Nuclear receptors from the filarial parasite Brugia malayi"

Maina CV, Tzertzinis G

[East Coast Worm Meeting, 1998]

Brugia malayi, the causative agent of human filariasis, is a parasite transmitted by the bites of infected mosquitoes. More than 100 million people are affected worldwide. Pharmacological evidence suggests ecdysteroids may play a role in parasitic nematode development and homologues of USP and EcR, the components of insect ecdysteroid receptor, have been cloned from the filarial parasite Dirofilaria immitis, the dog heartworm. We have undertaken the isolation of the components of ecdysteroid signal transduction from the parasites Brugia malayi and Onchocerca volvulus in an effort to understand the dependence of their development on ecdysone. Taking advantage of the tools generated for the Filarial Genome Project we are screening collections of cDNAs and genomic cosmids stamped on nylon filter grids, using the D. immitis nuclear receptors as probes and we are surveying the collection of sequenced ESTs for the presence of nuclear receptor homologues. So far we have cloned two B. malayi genes: one homologue to EcR and one homologous to the C. elegans nhr-41 and Drosophila HR78 -an ecdysone inducible nuclear receptor. At least three additional homologues of known nuclear hormone receptors have been reported in the filarial EST database. Filarial hormone receptors may prove promising new targets for therapeutic intervention.

Blaxter ML et al. (1997) International C. elegans Meeting "THE BRUGIA MALAYI GENOME PROJECT"

Blaxter ML, Scott AL, Slatko B, Williams SA, Jayaraman K, Baron L, Jones SJ, Ramzy R, Daub J, Waterfall M

[International C. elegans Meeting, 1997]

Brugia malayi is a filarial nematode, a causative agent of human lymphatic filariasis and elephantiasis. The Brugia genome project aims to aid research on these parasites, particularly research towards new drug targets and vaccines, by a program of gene discovery and gene mapping. cDNA libraries from all lifecycle stages of the parasite have been constructed and EST sequencing performed. Over 7000 sequences have been submitted to dbEST. These correspond to about 4000 genes, or one quarter of the expected number in the parasite. The EST sequences inlude many which are of immediate interest to filarial researchers as well as homologues of a large number of predicted genes from C. elegans. An ACeDB-based database, FilDB, has been developed to handle this data. The Brugia dataset is of value to the C. elegans community for many reasons including: (1) it contains close homologues of C. elegans genes which can confirm otherwise unsupported genefinder genes (2) the stage specific expression patterns of the Brugia genes are known (C. elegans EST sequencing has been from mixed stage libraries in the main).

Paulini, Michael et al. (2019) International Worm Meeting "Supporting nematode research outside of Caenorhabditis."

Russel, Matthew, Williams, Gary, Paulini, Michael, Davis, Paul, Rodgers, Faye, Howe, Kevin

[International Worm Meeting, 2019]

WormBase (http://www.wormbase.org) is a central data repository for genetic and genomic data relating to C. elegans and other well studied nematodes. WormBase is also a founding member of the Alliance of Genome Resources (https://www.alliancegenome.org), an effort to align data representation and curation workflows between the major model organism databases (MODs). We will present an update on the curation of nematode genomes outside the Caenorhabditis genus, demonstrate how we use data-mining to add information from current and historical publications, and show examples of the use and benefit to the nematode community. The genome of Trichuris muris has been added by WormBase to act as a representative reference genome for Blaxter clade I group. WormBase have performed first-pass annotation of the genome and manual curation of selected gene structures, with the aim of helping with annotation efforts of closely related Trichuris species. We have also added an updated version of the Pristionchus pacificus genome. This represents the start of a formal collaboration between WormBase and pristionchus.org on the joint maintenance and curation of the reference annotation. Finally, the curation of the Brugia malayi genome is ongoing, and reference annotation provided by WormBase is being used by research groups to analyse the evolution of filarial nematodes and the diseases they cause.

Blaxter, M.L. et al. (2017) International Worm Meeting "Nuclear fossils of Wolbachia reveal the complex history of nematode-Wolbachia evolution."

Laetsch, D.R., Blaxter, M.L., Koutsovoulos, G.

[International Worm Meeting, 2017]

Much of the natural world exists in symbiosis. Wolbachia are common, intracellular, maternally transmitted, parasitic symbionts of terrestrial arthropods, causing a variety of reproductive manipulations to assure their own survival. Arthropod Wolbachia can also be beneficial, protecting their hosts from viral and bacterial infections. Filarial nematodes in the Onchocercidae (including human parasites Brugia malayi, Wuchereria bancrofti and Onchocerca volvulus) also carry Wolbachia symbionts, and these are targets for anti-filarial chemotherapeutic interventions. While it was initially believed that onchocercid Wolbachia had a single origin and diversified with their nematode hosts, it is now becoming clear that the history of association between filarial nematodes and their symbionts is more complex. The symbionts of Onchocercidae derive from four Wolbachia supergroups (C, D F and J). Using 15 whole genome sequences of filarial nematodes and their C and D strain Wolbachia, we explored the evolutionary history of this symbiosis. Nematode phylogeny based on nuclear genes places Setaria labiatopapillosa basal to other sequenced species. Within the other Onchocercidae, four species (Onchocerca flexuosa, Acanthocheilonema viteae, Loa loa and Eleaphora elaphi) must have independently lost their infections. We screened the nematode genome sequences for nuclear Wolbachia transfers (NUWTs) -fragments of Wolbachia genomes integrated into the nuclear genome. S. labiatopapillosa had no NUWTs and is therefore primitively uninfected. NUWTs in O. flexuosa, A. viteae, L. loa and E. elaphi confirm these species as being aposymbiotic. We identified the supergroup membership of the Wolbachias from which the NUWTs originated, and found that aposymbotic species carried NUWTs derived from C type genomes, even if their most closely related symbiotic species carried D Wolbachia. Thus the history of Wolbachia in onchocercid nematodes includes not only cospeciation (as observed in the Onchocerca-Dirofilaria group in association with group C Wolbachia) and loss (in the aposymbiotic species), but also symbiont replacement. The supergroup D lineage of Wolbachia, found in the human parasites W. bancrofti and B. malayi, derives from a replacement event. We suggest that the biology of symbiosis may differ strongly in stably symbiotic species compared to those in which symbiont replacement has occurred.

Ana L Egana et al. (2005) International Worm Meeting "Identification of nuclear receptors from the parasitic filarial nematode Brugia malayi"

Ana L Egana, Chris R Gissendanner, Claude V Maina

[International Worm Meeting, 2005]

Nuclear receptors (NRs) are a superfamily of transcription factors that play a role in the regulation of a number of developmental and physiological processes. Members of the NR superfamily share a DNA binding site that consists of two zinc fingers, a transactivation domain and a ligand-binding domain located at the C-terminus and composed of 12 helices. The activity of some NRs is regulated by the interaction with small molecules, such as hormones, while others have no identified ligand and have been labeled as orphan receptors. The sequencing of the C. elegans genome revealed that the NR superfamily in nematodes has undergone extensive expansion. While most multicellular organisms contain a repertoire of 30-50 NRs, C. elegans contains within its genome 284 nuclear receptors. The sequencing of the genome of the parasitic filarial nematode B. malayi is near completion. A search for members of the NR superfamily in this filarial nematode has resulted in the identification of 30 NRs. Half of B. malayi NRs are homologous to NRs found in other organism, including EcR and RXR/Usp receptors, which have not been identified in C. elegans. Most of the other half corresponds to homologs of some of the Caenorhabditis divergent NRs, while three B. malayi NRs seem to be species specific. We have begun the cloning of these 30 NRs from cDNA generated from stage-specific RNA and cDNA libraries. We have found that as with NRs in other organisms, a number of B. malayi nuclear receptors are expressed in several alternatively spliced isoforms. The temporal expression pattern of a few of these genes will also be presented.

John Spieth (2005) International Worm Meeting "An Update on the Caenorhabditis remanei, japonica and PB2801 Genome Sequencing Projects"

John Spieth

[International Worm Meeting, 2005]

In January 2004, NHGRI announced support for draft sequencing of three additional Caenorhabditis genomes; C. remanei, C. japonica and PB2801. The genome sequences, which are being generated at the Washington University (St. Louis) Genome Sequencing Center, and the accompanying analyses are meant to enhance the utility of the existing C. elegans finished, genome sequence. The sequencing plan calls for an approximate nine-fold coverage of each genome through a combination of whole-genome shotgun sequencing of short insert plasmids and fosmid ends, and two rounds of automated, primer-directed, sequence improvement. For each genome 12 randomly-chosen fosmid clones will be finished to help assess assembly accuracy, and approximately 10,000 ESTs will be generated to assist in, and assess the quality of, automated gene prediction. We will present an update on the sequencing, assembly and analysis of the three genomes.

Marcel A et al. (1996) European Worm Meeting "Cytochrome P450s in Caenorhabditis elegans"

Charles G, Eric H, Marcel A, Laurent K, Jean-Baptiste B

[European Worm Meeting, 1996]

We are interested in the cytochrome P450 superfamily of genes in invertebrates. The sequencing project of the genome of C. elegans provided us data concerning cytochrome P450 genes in this organism. First the number of these genes will be large, as more than 25 of them are already identified. The repartition of these genes in the genome is heterogenous as some are isolated whereas others are organized in clusters. Sequences comparisons suggest that gene conversion may have occured for several genes. Such extensive sequence data are not available for other organisms than C. elegans. They should be very important to understand the mechanisms underlying cytochrome P450 sequences evolution.

Wilson, Natalie et al. (2021) International Worm Meeting "Identification of novel ivermectin resistance and hypersensitivity associated genes in a primary C. elegans mutant screen"

Reaves, Barbara, Wilson, Natalie, Wolstenholme, Adrian, Price, Elexis

[International Worm Meeting, 2021]

In 2016, nearly 800 million tablets of ivermectin were distributed to countries for use in elimination programs for human filarial diseases. Despite its widespread use, the mode of action of ivermectin against filarial nematodes is not well understood, and its in vivo potency cannot be replicated in vitro. To better understand how ivermectin affects filarial worms, our lab previously performed a transcriptomics study to identify differently expressed genes (DEG) in Brugia malayi adults and microfilariae after treatment of infected gerbils. Forty-four of these DEG had C. elegans orthologs available as mutant strains through the C. elegans Genetics Center. We have assayed these mutant strains for differential sensitivity to ivermectin by measuring three phenotypes affected by ivermectin: egg production, development, and motility. We have identified several resistant and hypersensitive strains of C. elegans as well as differences between responses to the three assays. Mutations conferring resistance included those in che-12 (e1812), a gene involved in chemotaxis, cilium assembly, and hyperosmotic response; and inx-14 (ag17), which is predicted to have gap junction hemi-channel activity and is expressed in the muscular, nervous, and reproductive systems. The che-12 mutants are additionally resistant to ivermectin's effect on pharyngeal pumping, while inx-14 mutants are not different from control. Overall, twenty-three genes, with eleven strong candidate genes, have been identified as altering ivermectin sensitivity in at least one assay, supporting the validity of the overall approach. These may give insight into how ivermectin acts against filarial parasites as well as potential mechanisms of resistance. These results are currently being used as the basis of an RNAi screen in B. malayi to identify the effect of these candidate genes on ivermectin sensitivity in filarial parasites.

LM Miller (1999) International C. elegans Meeting "A project-based laboratory course using C. elegans"

LM Miller

[International C. elegans Meeting, 1999]

This NSF-sponsored project integrates research and education by developing an intensive new laboratory course in which undergraduate students participate in a supervised research project. This research project is directly related to ongoing research in the laboratory of the principal investigator. The course is called "Project Lab" and is taught for one quarter each year with a class size of 7-16 students. Each year, the course focuses on research activities appropriate for that particular stage of the research project. The addition of this course to our biology curriculum enhances the science education of undergraduate students at Santa Clara University by providing hands-on laboratory experience and exposure to real research problems. It also enhances the research program of the principal investigator by training and motivating students for research. Specifically, students isolate and study mutations in genes that are required for cell fate determination in the process of vulval development in the nematode, C. elegans . The identification and analysis of these genes will set the stage for future experiments in cell fate determination. C. elegans is ideally suited for an undergraduate laboratory course. With appropriate training, undergraduate students can quickly learn to manipulate nematodes for use in genetic and/or molecular experiments. The first two Project Lab classes have made considerable progress on two different projects. For the first project, Project Lab students isolated and characterized over 30 new mutations that represents genes involved in the proper choice of cell fate during C. elegans vulval development. For the second project, several Project Lab students have been involved in a structure/function analysis of a transcription factor required for proper patterning of cell fate in C. elegans vulval development. There is a manuscript in preparation for this project, which will be submitted for publication within the next year. Three Project Lab students will be authors on this paper. I have also successfully used C. elegans in my upper division genetics laboratory course. This is a 10-week course in which students use nematodes to study inheritance patterns and map genes (using STS mapping).