Worm Breeder's Gazette 16(4): 16 (October 1, 2000)
These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.
Genome Sequencing Center, Department of Genetics, Box 8501, Washington University School of Medicine, St. Louis, Missouri 63108, USA, firstname.lastname@example.org
C. elegans is one of 10,000 known nematode species; actual species may number more than 100,000. Parasitic nematodes infect over half the world's human population, resulting in significant morbidity. Nematodes also attack livestock and pets, and cause over 80 billion dollars in crop damage annually. The C. elegans genome offers a wealth of information about nematodes that could lead to new drugs, vaccines, and non-toxic pesticides. Expressed Sequence Tags (ESTs) from parasites offer the most rapid and cost-effective way to directly connect C. elegans knowledge to identifiable genes in these species.
Here we present a progress report on publicly available ESTs from other nematodes. Currently, 64,295 ESTs are available from 19 nematodes other than C. elegans and C. briggsae (Table 1), including 7 human parasites, 5 animal parasites, 5 plant parasites, and 2 free-living bacterivores. The majority of ESTs were generated in 1999-2000. Projects are currently underway at the Genome Sequencing Center that will generate 225,000 ESTs from 14 nematode species by 2003. Additionally, the Sanger Centre and Edinburgh Univ. are generating 80,000 ESTs from 7 species. Generated sequences are immediately submitted to the dbEST division of GenBank and are available at www.ncbi.nlm.nih.gov/dbEST/index.html. By the completion of these efforts, we anticipate the identification of over 80,000 new nematode genes.
As a first step toward analysis, we have collapsed ESTs into clusters using a three-part method of BLAST clustering, alignment with Phred/Phrap, and hand curation in Consed. Using this method, we have generated 1,860 clusters from 5,713 Meloidogyne incognita (root knot nematode) ESTs. In general, each cluster represents a transcript and multiple clusters may derive from one gene by alternative splicing or by coverage of non-overlapping regions of the same gene. For each cluster with multiple members, we have generated a consensus sequence that is longer and of higher quality than each stand-alone EST read. We have used the results of clustering analysis to create the NemaGene gene index which we plan to build into a comprehensive list of nematode genes from species other than C. elegans. NemaGene M. i v1.0 is available at: www.nematode.net. We are currently building clusters for other species that will be available at this site later in 2000. Using NemaGene M. i v1.0, we have found that 72% of identified transcripts have significant database matches in other organisms (BLAST, E < 10 -5), while 28% are novel. Matches to other species were dominated by C. elegans - of transcripts with database matches, 91% of transcripts matched a C. elegans gene and 73% had a C. elegans gene as the best matching sequence.
Parasitic nematode sequencing at the GSC, St. Louis, is supported by NIH, NSF, and the Max Planck Institute, while sequencing at the Sanger Centre, Hinxton, UK, is supported by the Wellcome Trust.
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McCombie et al., 1992 (720)
Washington State, WA 9
Total Non-Caenorhabditis ESTs
1. Korhara et al., National Institute of Genetics, Mishima
2. World Health Organization Filarial Genome Network, Williams et al., Dept. of Biology, Smith College, Northampton, MA USA, Blaxter et al., Institute of Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh, UK
3. Williams et al., Dept. of Biology, Smith College, Northampton, MA USA
4. McCarter et al., Genome Sequencing Center, Washington Univ. School of Medicine, St. Louis, MO USA
5. Marra et al., Genome Sequencing Center, Washington Univ. School of Medicine, St. Louis, MO USA
6. Jones et al., Nematology Dept., Scottish Crop Research Inst., Dundee, UK and Laboratory of Nematology, Wageningen Univ., Wageningen, The Netherlands
7. Maizels et al., Institute of Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh, UK
8. Blaxter et al., Institute of Cell, Animal, and Population Biology, University of Edinburgh, Edinburgh, UK
9. Jasmer et al., Dept. of Veterinary Microbiology and Pathology, Washington State Univ., Pullman, WA USA