Pristionchus pacificus

Genome Assembly & Annotation

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.

Downloads

• Genomic Sequence (FASTA)
• Hard-masked Genomic Sequence (FASTA)
• Soft-masked Genomic Sequence (FASTA)
• Annotations (GFF3)
• Proteins (FASTA)
• Full-length transcripts (FASTA)
• CDS transcripts (FASTA)

Tools

• Search for sequences in the genome and proteome using BLAST
• Work with lists of data using the WormBase ParaSite BioMart data-mining tool
• Programatically access WormBase ParaSite data using the REST API
• Predict the effects of variants using the Variant Effect Predictor

Key Publications

• Rödelsperger C, Meyer JM, Prabh N, Lanz C, Bemm F, Sommer RJ. Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus. Cell Rep, 2017;21(3):834-844
• Werner MS, Sieriebriennikov B, Prabh N, Loschko T, Lanz C, Sommer RJ. Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation. Genome Res, 2018;28(11):1675-1687

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression