| | |
| El Paco assembly (2017) - data sets |
| Genome assembly - de novo assembly based on PacBio data alone, scaffolded using BACs/Fosmids and genetic linkage map, Rödelsperger et al. Cell Reports. 2017 |
| Gene annotations (V1) annotations based on MAKER2 pipeline, Rödelsperger et al. Cell Reports. 2017 |
| Gene annotations (V2) includes manual curation of C. elegans orthologs, Rödelsperger et al. Scientific Reports. 2019 |
| Gene annotations (V2.1) version 2 with some duplicate entries removed, Rödelsperger et al. Scientific Reports. 2019 |
| Gene annotations (V3) version 3 with additional curations of large gene families and orphan genes, Athanasouli et al. BMC Genomics. 2020 |
| Gene annotations (TAU, SNAP Hybrid1) exonerate mappings of old annotations |
| Gene annotations (Pinocchio PPCAC) exonerate mappings of old annotations |
| Werner et al. Genome Research. 2018 Epigenome profiles from adult worms |
| Werner et al. Genome Research. 2018 ISO-seq assemblies |
| Athanasouli and Rödelsperger. BMC Genomics. 2022 Repeat Annotation |
| Protein domain annotation, generated by the hmmsearch program (version 3.3, -E 0.001 option) against the Pfam-A.hmm database (version 3.1b2) |
| Hybrid2 assembly (2016) - data sets |
| Genome assembly - PacBio improved genome with the help of Barbara Meyer and Erich Schwarz 2014 |
| Gene Predictions - Gene predictions based on AUGUSTUS |
| Hybrid1 assembly (2010) - data sets |
| Genome assembly - improved genome assembly as used in Borchert et al., 2010 |
| Hybrid1 SNAP annotation file - in gff3 format |
| Protein sequences - SNAP gene predictions (Hybrid1) |
| Sinha et al., 2012 - sequences for microarray studies by Sinha et al., generated in 2011 (TAU) |
| Sinha et al., 2014 - sequences for operon project by Sinha et al., generated in 2012 (OP) |
| AUGUSTUS 2013 predictions - complementary gene predictions by the AUGUSTUS gene finder |
| Second generation linkage map - based on of 32 RILs between california and south africa |
| Variants for 104 strains - Variant calls for resequencing data of 104 natural isolates |
| Assembly1 Freeze (2008) - data sets |
|
Genome assembly - initial genome assembly as described in Dieterich et al.,2008 |
| Protein sequences - SNAP gene predictions |
| Pristionchus species and strains |
| PS1843 Version 2 from Roeseler et al., unpublished Chromosome-scale genome assembly and annotations for P. pacificus strain PS1843 , |
| P. mayeri, P. entomophagus, P. fissidentatus assemblies from Yoshida et al. 2024 Chromosome-scale genome assemblies and annotations for P. mayeri, P. entomophagus, P. fissidentatus |
| P. exspectatus Yoshida et al. Chromosome-scale genome assembly and annotations for P. exspectatus |
| Strain genomes - Assemblies and protein-coding gene annotations for seven P. pacificus strains - Prabh and Roedelsperger. Genome Research. 2022 |
| Washington - low coverage washington genome assembly from Dieterich et al. 2008 |
| maupasi - low coverage genome sequences from Dieterich et al. 2008 |
| entomophagus - low coverage genome sequences from Dieterich et al. 2008 |
| exspectatus - high coverage de novo assembly and initial annotations (SNAP2012) |
| exspectatus - update of annotations (AUGUSTUS2013) |
| exspectatus - reference transcriptome (2013) |
| diplogastrid transcriptomes - ten mixed-stage transcriptomes (454 reads and assemblies),
Mayer et al. 2011 |
| Prabh et al. Genome Research. 2018 - phylogenomic data set of ten diplogastrid genomes and annotations |
| updated annotations for Prabh et al. Genome Research. 2018 - PPCAC (version 1) Roedelsperger BMC Genomics. 2021 |
| Roedelsperger et al. 2018 - phylotranscriptomic data set |
| Other genomic data |
| Rhabditoides inermis - genome assembly and annotations (unpublished) |
| Oryctes borbonicus - genome assembly and annotations (v2015-02) |
| Parapristionchus giblindavisi - genome assembly and annotations (version 2, 2022) from Röseler et al. G3. 2022 |
| Allodiplogaster sudhausi - genome assembly and annotations (Wighard et al. Genome biology and Evolution. 2022) |
| Rhabditoides inermis - genome assembly and annotations (Roedelsperger et al. bioarxiv . 2024) |
| Phylogenetic trees |
| Pristionchus phylogeny - Species tree from Herrmann et al. (2024) |
| Pristionchus phylogeny - Species tree from Kanzaki et al. (2021) |
| Pristionchus phylogeny - Species tree from Roedelsperger et al. (2018) |
