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Abstract

The phylum Nematoda occupies a huge range of ecological niches, from free-living microbivores to human parasites. We analyzed the genomic biology of the phylum using 265,494 expressed-sequence tag sequences, corresponding to 93,645 putative genes, from 30 species, including 28 parasites. From 35% to 70% of each species' genes had significant similarity to proteins from the model nematode Caenorhabditis elegans. More than half of the putative genes were unique to the phylum, and 23% were unique to the species from which they were derived. We have not yet come close to exhausting the genomic diversity of the phylum. We identified more than 2,600 different known protein domains, some of which had differential abundances between major taxonomic groups of nematodes. We also defined 4,228 nematode-specific protein families from nematode-restricted genes: this class of genes probably underpins species- and higher-level taxonomic disparity. Nematode-specific families are particularly interesting as drug and vaccine targets.

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Acknowledgements

We thank all our nematology and parasitology colleagues for supplying materials (see Supplementary Methods online) and for their enthusiasm for this project and A. Anthony, J. Wasmuth and A. Hedley for trace2dbest, PartiGene and prot4EST software. The UK arm of the project was funded by the Wellcome Trust, and the US arm by the National Institutes of Health (National Institute of Allergy and Infectious Diseases). J.P.M. was supported by a Helen Hay Whitney/Merck fellowship. Sequencing at The Wellcome Trust Sanger Institute was carried out by C. Churcher, T. Chillingworth, P. Cummings, Z. Hance, K. Jagels, S. Moule and S. Whitehead. Most of the computational analyses were done using facilities at the Center for Computational Biology, Hospital for Sick Children, Toronto.

Author information

Author notes

    • Neil Hall
    •  & Robert H Waterston

    Present addresses: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA (N.H.); Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA (R.H.W.).

Affiliations

  1. Hospital for Sick Children, 555 University Avenue; Departments of Biochemistry and Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario M5G 1X8, Canada.

    • John Parkinson
  2. School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK.

    • John Parkinson
    • , Claire Whitton
    • , Marian Thomson
    • , Jennifer Daub
    • , Ralf Schmid
    •  & Mark L Blaxter
  3. Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA.

    • Makedonka Mitreva
    • , John Martin
    • , Robert H Waterston
    •  & James P McCarter
  4. Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK.

    • Neil Hall
    •  & Bart Barrell
  5. Divergence, St Louis, Missouri 63141, USA.

    • James P McCarter

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Competing interests

J.P.M. is an employee of and equity holder in Divergence, Inc.

Corresponding author

Correspondence to John Parkinson.

Supplementary information

PDF files

  1. 1.

    Supplementary Fig. 1

    Novel nematode-specific domains showing high sequence conservation.

  2. 2.

    Supplementary Table 1

    Polypeptide and domain predictions for nematode species.

  3. 3.

    Supplementary Table 2

    Most abundant InterPro domains in the nematode partial genomes.

  4. 4.

    Supplementary Table 3

    Representation of partial genomes in KEGG metabolic pathways.

  5. 5.

    Supplementary Methods

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DOI

https://doi.org/10.1038/ng1472

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