What are nematodes and why do they matter?
Nematodes are unsegmented round worms. In terms of individuals, nematodes
account for an estimated four of every five animals in the world. (The other
fifth are mostly beetles.) There are 10,000 known species and the actual
number may be more than 100,000. While most nematodes are free-living,
parasitic nematodes are major challenges to human health and agriculture.
Parasitic nematodes, including whipworm, Ascaris, hookworm, and filarial worms,
currently infect about 3 billion people. Plant parasitic nematodes, such as
root knot nematode, cause an estimated 80 billion dollars in crop damage
annually. The free-living nematode C. elegans has been used extensively since
the late 1960's as a genetic model organism and is among the most completely
characterized of all metazoans. The C. elegans genome was the first
comprehensively sequenced metazoan genome (1998).

What are ESTs and why are they being generated?
Expressed sequence tags (ESTs) are single pass sequences from cDNA clones.
They provide partial sequences corresponding to messenger RNAs and provide a
rapid and cost-effective method for initial characterization of genomes.
However, they tend to be redundant and do not provide information about
non-exonic sequences or genome organization. ESTs can be used to identify
individual genes within parasitic nematodes. Such genes can be targets for
anthelmintics, vaccines, or nematicides. Gene sequences are also critical
reagents for most molecular studies of an organism. Most ESTs being generated
for the GSC's parasitic nematode project are 5' reads. To date (10/01),
sequences have come from non-normalized libraries. Some libraries are
generated by PCR using the nematode transplice leader SL1, thereby ensuring
that the 5' end is sequenced. Other libraries are directionally cloned but
without selection for a splice leader.

How were species selected for sequencing?
125,000 ESTs are being generated as a part of the NIH-NIAID grant "A Genomic
Approach to Parasites from the Phylum Nematoda." Species were selected for 1)
medical or economic importance, 2) use as an accessible system for studies with
an interested scientific community, 3) distribution across the phyla nematoda.
The bulk of these species are human or animal parasites with some sequencing
from plant parasitic nematodes. Species were selected to prevent overlap with
species being sequenced by the Blaxter Lab / Sanger Centre as part of a
Wellcome Trust grant. 80,000 ESTs are being generated as a part of the NSF
grant "Genomic Dissection of a Nematode-Plant Interaction: a Tool to Study
Plant Biology". Most of the ESTs are from Meloidogyne (root knot) species.
Additional smaller collaborations are in progress for other species such as
Pristionchus pacificus and Strongyloides ratti. In total, 20 collaborations
have been established with investigators internationally providing access to
material from collected nematodes. Species lists have been modified somewhat
from original plans depending on material availability and interest.
Individuals interested in establishing collaborations should contact Jim
McCarter at mccarter@genetics.wustl.edu.

For more information on the project, please see:

Wylie, T., J.C. Martin, M. Dante, M. D. Mitreva, S. W. Clifton, A. Chinwalla, R. H. Waterston, R. K. Wilson, and J. P. McCarter. 2004. Nematode.net: A Tool for Navigating Sequences from Parasitic and Free-living Nematodes, 32:D423-D426 Nucleic Acids Research, 2004.