Genome Sequence of Additional Caenorhabditis species : Enhancing the Utility of C . elegans as a Model Organism

Overview The value of Caenorhabditis elegans as a model organism for biomedical research is unquestioned. The interpretation of its 100.2 Mb complete genome sequence has been enhanced by a high quality, 98% complete draft genome sequence for Caenorhabditis briggsae. However, comparison of any two species is not sufficient to define many sequence features, since features evolve at different rates, are of differing sizes and are detected with varying ease by a variety of tools. To allow better genome alignment, gene interpretation, promoter analysis, identification of non-coding RNAs (ncRNAs) and other functional features, as well as to explore the forces that mold these genomes, we propose sequencing the genomes of three additional Caenorhabditis species: Caenorhabditis remanei, Caenorhabditis n. sp. CB5161 and Caenorhabditis japonica. The first two are about the same evolutionary distance from C. elegans as is C. briggsae, while C. japonica is the closest outgroup to these four. Pilot studies that compare the sequence of known transcriptional enhancers from four species demonstrate that addition of C. remanei and CB5161 add great value when combined with C. briggsae data in the analysis of the C. elegans genome. Marginally conserved sequences between C. elegans and C. briggsae can be given more attention if also conserved in additional Caenorhabditis species or less attention if not conserved. Other functional elements may emerge from statistical noise in a four or five-way comparison and additional orthology will be determined, all of which will enhance and expand the value of C. elegans as a model for understanding human health and disease, and basic biological processes. In addition, these genomes will enable a variety of evolutionary genetic analyses in part because they encode male-female sexual systems while C. briggsae and C. elegans have hermaphrodite-male reproduction.

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