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The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

Nature Genetics volume 40, pages 1193–1198 (2008)Cite this article

Abstract

Here we present a draft genome sequence of the nematode Pristionchus pacificus, a species that is associated with beetles and is used as a model system in evolutionary biology. With 169 Mb and 23,500 predicted protein-coding genes, the P. pacificus genome is larger than those of Caenorhabditis elegans and the human parasite Brugia malayi. Compared to C. elegans, the P. pacificus genome has more genes encoding cytochrome P450 enzymes, glucosyltransferases, sulfotransferases and ABC transporters, many of which were experimentally validated. The P. pacificus genome contains genes encoding cellulase and diapausin, and cellulase activity is found in P. pacificus secretions, indicating that cellulases can be found in nematodes beyond plant parasites. The relatively higher number of detoxification and degradation enzymes in P. pacificus is consistent with its necromenic lifestyle and might represent a preadaptation for parasitism. Thus, comparative genomics analysis of three ecologically distinct nematodes offers a unique opportunity to investigate the association between genome structure and lifestyle.

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Figure 1: Phylogeny and comparison of genomic features in nematodes.
Figure 2: Orthology assignment in nematodes and comparison to non-nematode species.
Figure 3: Examples of P. pacificus–specific expansions.
Figure 4: Schematic representation of the metabolism of xenobiotics.
Figure 5: Cellulase activity in P. pacificus.

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Acknowledgements

We thank P.W. Sternberg, J. Srinivasan and members of the Sommer lab for discussion and helpful comments on the manuscript. This work was funded by National Human Genome Research Institute grant U54HG003079 and the Max-Planck Society.

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Authors and Affiliations

  1. Max-Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen, 72076, Germany

    Christoph Dieterich, Lisa N Schuster, Iris Dinkelacker, Waltraud Roeseler, Huiyu Tian, Hanh Witte & Ralf J Sommer

  2. Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Boulevard, St. Louis, 63108, Missouri, USA

    Sandra W Clifton, Asif Chinwalla, Kimberly Delehaunty, Lucinda Fulton, Robert Fulton, Jennifer Godfrey, Pat Minx, Makedonka Mitreva, Shiaw-Pyng Yang & Richard K Wilson

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Contributions

C.D. carried out most of the bioinformatics analysis; the Genome Sequencing Center team at Washington University (S.W.C., A.C., K.D., L.F., R.F., J.G., P.M., M.M., S.-P.Y., R.K.W.) conducted the genome sequencing project; L.N.S. and H.T. did the experimental gene confirmation; I.D., W.R. and H.W. experimentally linked the genetic linkage map to the P. pacificus genome; and C.D., S.W.C., R.K.W. and R.J.S. designed these studies and contributed to the writing of this paper.

Corresponding authors

Correspondence to Richard K Wilson or Ralf J Sommer.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 708 kb)

Supplementary Table 1

Repeat family annotation. (XLS 2669 kb)

Supplementary Table 2

Gene modeller performance. (XLS 155 kb)

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Dieterich, C., Clifton, S., Schuster, L. et al. The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nat Genet 40, 1193–1198 (2008). https://doi.org/10.1038/ng.227

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