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Pristionchus pacificus Genomics and Proteomics

The National Human Genome Research Institute (NHGRI) with co-sponsoring of the Max-Planck Society has sequenced the P.pacificus genome. The sequencing project has been carried out by the Genome Sequencing Center (GSC), Washington University, St. Louis:http://www.nhgri.nih.gov/12511858


Press releases regarding the Genome Project 2008:
http://www.mpg.de/488479/pressemitteilung20040913?filter_order=L
http://www.mpg.de/554789/pressemitteilung20080916


Gene predictions are integrated into WormBase (ws194).

We have also setup a dedicated website: http://pristionchus.org  

Our current efforts involve Large Scales Next Generation sequencing of P.pacificus natural isolates: Evolutionary field station on Reunion island

Selected References:

Rödelsperger, C. & Sommer, R. J. (2011): Computational archeology of the Pristionchus pacificus genome reveals evidence of horizontal gene transfer from insects. BMC Evol. Biol., 11: 239.

Featured in:
Danchin, E.G.J. (2011): What Nematode genomes tell us about the importance of horizontal gene transfers in the evolutionary history of animals. Mobile Genetic Elements, 1: 4.

Mayer, W. E., Schuster, L., Bartelmes, G., Dieterich, C. & Sommer R. J. (2011): Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation, high gene turnover and positive selection. BMC Evolutionary Biology, 11: 13.

Featured in:
Scholl, E.H. & McK Bird, D. (2011): Computational and phylogenetic validation of nematode horizontal gene transfer. BMC Biology, 9:9.

Borchert, N., Dieterich, C., Krug, K., Schütz, W., Jung, S., Nordheim, A., Sommer R. J. & Macek, B. (2010): Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models, Genome Research, 20, 837-846.


Dieterich et al. (2008): The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nature Genetics  40, 1193-1198.

Featured in:
Srinivasan, J. & Sternberg, P.W. (2008): Pristionchus pacificus: an appropriate fondness for beetles. Nature Genetics, 40, 1146-1147.


Scientists involved:

Dr. Christian Rödelsperger, Bioinformatic Curator
Dr. Gabriel Markov, Bioinformatics
Amit Sinha, Ph.D. Student
Gabi Bartelmes, Technician
Dr. Werner Mayer, Staff Scientist



The basis for all current genome projects has been the formation of a genome map of Pristionchus pacificus between 2001and 2004:

A genome map of Pristionchus pacificus

In 2001, we have launched a genomic initiative including the generation of a genetic linkage map and a physical map. We have reached several milestones during the last few years:

  1.  2 BAC libraries of together 20.000 clones, completely end-sequenced (Srinivasan et al., 2002)

  2. 1 Fosmid library, with 50.000 sequence-reads.

  3. An EST sequencing project with approx. 40.000 reads.

  4.  A genetic linkage map of around 600 molecular markers (Srinivasan et al.,2002).

  5.  A genetic map of morphological mutants for mapping (Kenning et al., 2004).

  6. An AFLP-fingerprinted physical map of 10.000 BAC clones (Srinivasan et al., 2003).


In response to these results, NIH announced a P. pacificus

sequencing project in August 2004. This project was carried out at the GSC at Washington University in St. Louis and was finished by mid-2006 (http://genome.wustl.edu/). More than 2.500.000 (appr. 10 x coverage) reads of whole genome shotgun (WGS) sequencing are available. The WGS project was complemented by fosmid end-sequencing.

The Max-Planck Society co-sponsored this genome-sequencing initiative by funding throught the „Strategic Innovation Fund of the President“. In this project, we obtained:

- 1 x coverage of a polymorphic strain (P. pacificus var. Washington) and

- 1 x coverage of the related species P. entomophagus and P. maupasi.

These projects provide single nucleotide polymorphisms (SNP) for mapping of mutants and sequence information about potential conserved regulatory elements. All the genomic information on P. pacificus has been made available in a Database “http://www.pristionchus.org” (Dieterich et al., 2007).

The draft sequence of the Pristionchus pacificus genome was published in the October issue of Nature Genetics (2008). Gene predictions are also integrated into wormbase (WS194).


Selected References:

Dieterich C, Clifton SW, Schuster LN, Chinwalla A, Delehaunty K, Dinkelacker I, Fulton L, Fulton R, Godfrey J, Minx P, Mitreva M, Roeseler W, Tian H, Witte H, Yang SP, Wilson RK, Sommer RJ. (2008): The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nature Genetics  40, 1193-1198.

C. Dieterich & R. J. Sommer (2008): A Caenorhabditis motif compendium for studying transcriptional gene regulation.BMC Genomics, 9, 30

Dieterich, D., Roeseler, W., Sobetzko, P., and Sommer R. J. (2007): Pristionchus.org: A genome-centric database of the nematode satellite species Pristionchus pacificus. Nucl. Acid Res. D498-D502.

Kenning, C., Kipping, I. & Sommer, R. J. (2004): Mutations with altered gross-morphology in the nematode Pristionchus pacificus. Genesis, 40, 176-183.

Lee, K.-Z. & Sommer, R. J. (2003): Operon structure and trans-splicing in the nematode Pristionchus pacificus. Mol. Biol. and Evol., 20, 2097-2103.

Srinivasan, J., Sinz, W., Jesse, T., et al. (2003): An integrated physical and genetic map of the nematodePristionchus pacificus. MGG, 269, 715-722.

Lee, K.-Z., Eizinger, A., Nandakumar, R., Schuster, S. C. & Sommer, R. J. (2003): Limited microsynteny between the genomes of Pristionchus pacificus and Caenorhabditis elegans. Nucl. Acid. Res., 10, 2553-2560.

Srinivasan, J., Sinz, W., Lanz, C., et al. (2002): A BAC-based genetic linkage map of the nematode Pristionchus pacificus. Genetics, 162, 129-134.


The Pristionchus pacificus proteome

With the completion of the P. pacificus genome project, we have started a collaboration with the Proteome Center Tübingen (PCT) and initiated a P. pacificus Proteome project. The PCT is part of the Interfaculty Institute for Cell Biology, Tübingen University, and is headed by Prof. Dr. B. Maçek.

The P. pacificus Proteome project has several major aims, such as
1.) the generation of a comprehensive catalogue of the P. pacificus proteome,
2.) the comparison of the P. pacificus secreted proteins of growing larvae versus dauer larvae, and also of different other nematodes, including parasitic and free-living nematodes,
3.) the analysis of P. pacificus ability to detoxify emphasizing in differential expression of glutathione-s-transferases.

Selected References:

Borchert, N., Dieterich, C., Krug, K., Schütz, W., Jung, S., Nordheim, A., Sommer, R.J. & Macek, B. (2010): Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models. Genome Res., 20, 837-846.


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last modified 2012-01-05