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A transcriptomic analysis of the phylum Nematoda

Nature Genetics volume 36, pages 1259–1267 (2004)Cite this article

An Author Correction to this article was published on 15 June 2020

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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Figure 1: EST data sets from across the phylum Nematoda.
Figure 2: Gene discovery in nematode EST data sets.
Figure 3: Chromosomal location of C. elegans homologs of other nematode genes.
Figure 4: Comparing partial genomes across the Nematoda.
Figure 5: Evolutionary origins of unique genes and gene families in the phylum Nematoda.
Figure 6: Functional annotation of genes using Gene Ontology terms.

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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

  1. Neil Hall

    Present address: The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland, 20850, USA

  2. Robert H Waterston

    Present address: Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA

Authors and Affiliations

  1. Hospital for Sick Children, 555 University Avenue

    John Parkinson

  2. Departments of Biochemistry and Medical Genetics and Microbiology, University of Toronto, Toronto, M5G 1X8, Ontario, Canada

    John Parkinson

  3. School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JT, UK

    John Parkinson, Claire Whitton, Marian Thomson, Jennifer Daub, Ralf Schmid & Mark L Blaxter

  4. Genome Sequencing Center, Washington University School of Medicine, St Louis, 63108, Missouri, USA

    Makedonka Mitreva, John Martin, Robert H Waterston & James P McCarter

  5. Pathogen Sequencing Unit, Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK

    Neil Hall & Bart Barrell

  6. Divergence, St Louis, 63141, Missouri, USA

    James P McCarter

  7. The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland, 20850, USA

    Robert H Waterston

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Correspondence to John Parkinson.

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Competing interests

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

Supplementary information

Supplementary Fig. 1

Novel nematode-specific domains showing high sequence conservation. (PDF 33 kb)

Supplementary Table 1

Polypeptide and domain predictions for nematode species. (PDF 9 kb)

Supplementary Table 2

Most abundant InterPro domains in the nematode partial genomes. (PDF 9 kb)

Supplementary Table 3

Representation of partial genomes in KEGG metabolic pathways. (PDF 9 kb)

Supplementary Methods (PDF 25 kb)

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Parkinson, J., Mitreva, M., Whitton, C. et al. A transcriptomic analysis of the phylum Nematoda. Nat Genet 36, 1259–1267 (2004). https://doi.org/10.1038/ng1472

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