Pristionchus exspectatus

Genome Assembly & Annotation

Assembly

This assembly was generated from an inbred line of the type strain of P. exspectatus, RS5522B.

According to Yoshida K, et al. (2023), raw long sequencing PacBio reads were assembled using the Canu assembler. The assembly was processed by HaploMerger2 to build the haploid genome. The resulting assembly was scaffolded using Hi-C scaffolding.

Annotation

According to Yoshida K, et al. (2023), gene annotation was generated by the Perl Package for Customized Annotation Computing annotation pipeline (version 1.0): A transcriptome assembly of P. exspectatus and the community-curated P. pacificus gene annotation (version El Paco gene annotation 3) were aligned against the P. exspectatus de novo assembly with the help of the exonerate alignment tool (version 2.2.0), and the longest open reading frames per 100 bp windows were chosen as representative gene models.

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

• Yoshida K, Rödelsperger C, Röseler W, Riebesell M, Sun S, Kikuchi T, Sommer RJ. Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. Nat Ecol Evol, 2023;7(3):424-439
• Rödelsperger C. The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes. BMC Genomics, 2021;22(1):216

Navigation

View karyotype

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression