Background ========== While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. Results ======= The most accurate gene-finders were 'combiner' algorithms, which made use of transcript- and protein-alignments and multi-genome alignments, as well as gene predictions from other gene-finders. Gene-finders that used alignments of ESTs, mRNAs and proteins came in second. There was a tie for third place between gene-finders that used multi-genome alignments and ab initio gene-finders. The median gene level sensitivity of combiners was 78% and their specificity was 42%, which is nearly the same accuracy reported for combiners in the human genome. C. elegans genes with exons of unusual hexamer content, as well as those with unusually many exons, short exons, long introns, a weak translation start signal, weak splice sites, or poorly conserved orthologs posed the greatest difficulty for gene-finders. Conclusions =========== This experiment establishes a baseline of gene prediction accuracy in Caenorhabditis genomes, and has guided the choice of gene-finders for the annotation of newly sequenced genomes of Caenorhabditis and other nematode species. We have created new gene sets for C. briggsae, C. remanei, C. brenneri, C. japonica, and Brugia malayi using some of the best-performing gene-finders.

North Carolina State University scientists and colleagues have completed the genome sequence and genetic map of one of the world's most common and destructive plant parasites – Meloidogyne hapla, a microscopic, soil-dwelling worm known more commonly as the northern root-knot nematode. The research could help lead to a new generation of eco-friendly tools to manage the ubiquitous parasitic worm, which, along with other species of root-knot nematode, causes an estimated $50 billion in crop and plant damage yearly, says Dr. Charles Opperman, professor of plant pathology at NC State, co-director of the Center for the Biology of Nematode Parasitism and the corresponding author on a scientific paper describing the research. The resulting sequence data has been deposited in public databases, so other researchers interested in the root-knot nematode – how it develops, establishes a host-parasite interaction or evades host defenses, for example – are now able to use the map of the parasite's genes as a tool to discover more specific information about the parasite. The northern root-knot nematode is the smallest multicellular animal genome completely sequenced, says Dr. David McK. Bird, professor of plant pathology at NC State, co-director of the Center for the Biology of Nematode Parasitism and a co-author of the paper.