Pristionchus pacificus (Nematode, PS312) Assembly and Gene Annotation

NOTE: The genome sequence and annotation for P. pacificus are updated in Ensembl Metazoa infrequently. For the latest genome and annotation, please visit WormBase ParaSite (for an Ensembl-oriented view), or WormBase. The data here corresponds with WormBase WS279.

About Pristionchus pacificus

Pristionchus pacificus is a small, free-living roundworm, which is found on several continents and is associated with scarab beetles and Colorado potato beetles. It is part of the diplogastrids and it is estimated to have diverged from C. elegans 200-300 million years. It, therefore, shares many experimental advantages with C. elegans and is being used as a model organism for developmental biology and ecological studies, particularly in studies involving the analysis of vulval formation.

• P. pacificus data at WormBase ParaSite.
• P. paciificus data at WormBase.
  
• Pristionchus database hosted at the Max-Plank Institute for Evolutionary Biology.

Photo credit: Robbie Rae, Amit Sinha, and Ralf J. Sommer Creative Commons Attribution 1.0 via Wikimedia Commons (Image source)

Assembly

The P. pacificus genome has been sequenced using single-molecule long-read sequencing by the Sommer group at the Max-Planck Institute for Developmental Biology. The assembly version represented here (P_pacificus-El_Paco) has been current in WormBase since 2018, and also browsable at pristionchus.org. This version has been submitted to the INSDC under the accession number ABKE03000000.

Annotation

The original gene predictions were made by the Sommer group at the Max-Planck Institute for Developmental Biology. Some of the gene models have since been reviewed and revised by WormBase.

References

1. Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus.
   Rödelsperger C, Meyer JM, Prabh N, Lanz C, Bemm F, Sommer RJ. Cell Rep, 2017;21(3):834-844.
2. Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation.
   Werner MS, Sieriebriennikov B, Prabh N, Loschko T, Lanz C, Sommer RJ. enome Res, 2018;28(11):1675-1687.
3. The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism.
   Dieterich C, Clifton SW, Schuster LN, Chinwalla A, Delehaunty K, Dinkelacker I, Fulton L, Fulton R, Godfrey J, Minx P et al. 2008. Nature Genetics. 40:1193-1198.

Other data

Various protein and cDNA sequences have been aligned to the P. pacificus genome and can be viewed on the genome browser:

• Complete protein sets from human (UniProtKB), D. melanogaster (FlyBase), S. cerevisae (SGD), and selected other nematodes (WormBase).
• All other reviewed protein sequences from UniProtKB.
• P. pacificus mRNAs and ESTs.

Links

• P. paciificus data at WormBase.
• P. pacificus data at WormBase ParaSite.