WormBase ParaSite HomeVersion: WBPS19 (WS291)-  Archive: WBPS18

Parapristionchus giblindavisi

BioProject PRJEB53331 | Data Source Max Planck Institute for Developmental Biology | Taxonomy ID 1187980

About Parapristionchus giblindavisi

The species Parapristionchus giblindavisi is a free-living nematode, of interest as a comparator to a model organism Pristionchus pacificus.

Genome Assembly & Annotation


The genome was assembled using PacBio raw reads filtered for circular consensus sequencing (CCS) with >Q20 using PacBio ccs. The reads were merged using pbmerge before being assembled with Falcon-unzip2. The assembly was polished using pbmm2.


According to Röseler et al. 2022, evidence-based gene annotations were generated based on protein homology and transcriptome data using the PPCAC software (version 1.0; Athanasouli et al. 2020; Rödelsperger 2021). Specifically, the community-curated gene annotations of P. pacificus (El Paco gene annotations, version 3; Athanasouli et al. 2020) and a mixed-stage transcriptome assembly of P. giblindavisi (Rödelsperger et al. 2018) were transferred to the new P. giblindavisi genome assembly by alignment with the software exonerate (version 2.2.0). For each 100-bp window, one representative gene model was chosen by selecting the gene model with the longest open reading frame (minimum protein length 60 amino acids, at least 3 exons). All other alternative gene models within a 100-bp window were discarded.

Key Publications



Assembly Statistics

AssemblyParapristionchus_giblindavisi_II_pacbio, GCA_943737045.1
Database VersionWBPS19
Genome Size251,641,265
Data SourceMax Planck Institute for Developmental Biology
Annotation Version2022-09-WormBase

Gene counts

Coding genes22,488
Gene transcripts22,488

Learn more about this widget in our help section

This widget has been derived from the assembly-stats code developed by the Lepbase project at the University of Edinburgh