Divergence is a leader in the application of comparative and functional genomics to the control of parasitic nematodes. The last decade has seen revolutionary progress in both the generation of sequence information and methods for rapid gene knock-down including RNAi. Divergence was an early adopter in applying these advances to gene target validation for nematicides, anthelmintics, and to the generation of plants resistant to parasitic nematodes. This strategy directs research away from molecules that could have host organism toxicity, focusing instead on targets that are biochemically distinct and vital for the life cycle of the infecting organism. Genomic approaches are also applicable to the discovery of targets for diagnostics.

Genomics:
The exponential growth in available DNA sequence has radically changed what is known about the underlying molecular make-up of life. Publicly available DNA sequence has grown from less than 50 million nucleotides in 1990 to over 200 billion in 2008. Hundreds of genomes, from humans to crops to worms are now complete or in draft form. Washington University's Genome Center (GC) in St. Louis is one of the world's leading genome centers, playing key roles in the sequencing of dozens of genomes including human, mouse, corn, and the nematode C. elegans. In 1998, Divergence Founder and Washington University adjunct faculty member James McCarter initiated the world's largest effort in parasitic nematode sequencing at the GC. This project has now generated and made public over 500,000 expressed sequence tags (ESTs) from 32 nematode species, mostly parasites of plants, animals, and humans. Multiple draft genomes are underway. Focusing on down-stream applications, Divergence has applied bioinformatic mining approaches to select promising targets from this basic genomic information. Divergence and its collaborators have also directly generated genome sequences from key parasites of interest such as soybean cyst nematode. Divergence in-house expertise also includes a cross-species gene discovery approach that can rapidly clone gene orthologs from parasites of interest.

RNA interference:
In organisms from worms to humans to plants, double stranded RNA (dsRNA) can silence genes by degrading the corresponding messenger RNA, a process called RNA interference (RNAi). In 1998, Andrew Fire and Craig Mello, a member of the Divergence Scientific Advisory Board, first discovered the crucial role of dsRNA in gene silencing using the nematode C. elegans. Thousands of publications since then have described the details of this vital and previously unrecognized endogenous cellular pathway for gene regulation. RNAi has been used to systematically reveal the function of all ~20,000 genes in C. elegans. Double stranded small interfering RNAs (siRNAs) are now routinely used to test the roles of human genes in the laboratory and siRNAs are in clinical trials for disease including age-related macular degeneration and hepatitis B. In 2006, Drs. Mello and Fire were awarded the Nobel Prize in Physiology or Medicine for their discovery of RNAi. Divergence was an early adopter of RNAi technology with work beginning in 1999. In 2001, the Company completed its own large scale RNAi phenotype screen of target genes in C. elegans, generating most of this information over 18 months prior to its public availability. RNAi is also being used in plants, both to silence plant genes and to silence the genes of invading pests such as nematodes and insects. Divergence is a leader in the application of RNAi to the control of multiple parasitic nematodes including lesion nematode, work which may lead to the commercialization of nematode resistant plants.

Examples of Divergence Publications in Nematode Genomics:

Yin, Y., J. Martin, S. Abubucker, A. L. Scott, J. P. McCarter, R. K. Wilson, D. P. Jasmer, and M. Mitreva. 2008. "Intestinal Transcriptomes of Nematodes: Comparison of the Parasites Ascaris suum and Haemonchus contortus and the Free-living Caenorhabditis elegans," PLOS Neglected Tropical Diseases, 2:e269.
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Elling, A. A., M. Mitreva, J. Recknor, X. Gai, J. Martin, T. R. Maier, J. P. McDermott, T. Hewezi, D. M. Bird, E. L. Davis, R. S. Hussey, D. S. Nettleton, J. P. McCarter, T. J. Baum. 2007. "Divergent Evolution of Arrested Development in the Dauer Stage of Caenorhabditis elegans and the Infective Stage of Heterodera glycines," Genome Biology, 8:R211.
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Ghedin, E., et al. (65 co-authors). 2007. Draft Genome of the Filarial Nematode Parasite Brugia malayi, Science, 317:1756-1760.
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Mitreva, M., M. C. Wendl, J. Martin, T. Wylie, Y. Yin, A. Larson, J. Parkinson, R. H. Waterston, and J. P. McCarter. 2006. "Codon Usage Patterns in the Phylum Nematoda: Analysis Based on Over 25 Million Codons in Thirty-two Species," Genome Biology, 7:R75.
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Parkinson, J., M. Mitreva, C. Whitton, M. Thomson, J. Daub, J. Martin, N. Hall, B. Barrell, R. H. Waterston, J. P. McCarter and M. Blaxter. 2004. A Transcriptomic Analysis of the Phylum Nematoda, Nature Genetics, 36:1259-1267.
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Examples of Divergence Publications on RNA interference:

McCarter, J. P. 2008. "Molecular Approaches Toward Resistance to Plant-Parasitic Nematodes," Chapter in Cell Biology of Plant Nematode Parasitism, Berg, R. H. and C. G. Taylor eds., Series: Plant Cell Monographs, Vol. 15, Springer Press.
book available online

Lustigman S., Ford L., Crawford MJ. 2008. "RNA Interference: From Functional Genomics to Validation of Drug Targets in Helminths," Chapter in RNA Interference Research Progress, Lyland, R.T. and Browning I.B. eds. pp. 135-162. Nova Science Publishers, Hauppauge, N.Y.
book available online (Nova) | book available online (Amazon)

Brendza, K. M., W. Haakenson, R. E. Cahoon, L. E. Hicks, L. E., L. H. Palavalli, B. J. Chiapelli, M. McLaird, J. P. McCarter, D. J. Williams, M. C. Hresko, J. M. Jez. 2007. "Phosphoethanolamine N-Methyltransferase (PMT-1) Catalyzes the First Reaction of a New Pathway for Phosphocholine Biosynthesis in Caenorhabditis elegans", Biochemistry Journal, 404:439-448.
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Palavalli, L. H., K. M. Brendza, W. Haakenson, R. E. Cahoon, M. McLaird, J. P. McCarter, D. J. Williams, M. C. Hresko, J. M. Jez. 2006 "Defining the Role of Phosphomethylethanolamine N-Methyltransferase from Caenorhabditis elegans in Phosphocholine Biosynthesis by Biochemical and Kinetic Analysis", Biochemistry, 45:6056-6065
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Behm, C. A., M. M. Bendig, J. P. McCarter, A. E. Sluder. 2005. “RNA Interference-based Discovery and Validation of New Drug Targets in Filarial Nematodes”, Trends in Parasitology, 21:97-100.
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McCarter, J. P. 2004. "Genomic Filtering, an Approach to Discovering Novel Antiparasitics", Trends in Parasitology, 20:462-468.
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