Parapristionchus giblindavisi

Genome Assembly & Annotation

Assembly

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.

Annotation

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.

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

• Röseler W, Collenberg M, Yoshida K, Lanz C, Sommer RJ, Rödelsperger C. The improved genome of the nematode Parapristionchus giblindavisi provides insights into lineage-specific gene family evolution. G3 (Bethesda), 2022;12(10):jkac215
• Athanasouli M, Witte H, Weiler C, Loschko T, Eberhardt G, Sommer RJ, Rödelsperger C. Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus. BMC Genomics, 2020;21(1):708
• Rödelsperger C. The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes. BMC Genomics, 2021;22(1):216
• Athanasouli M, Witte H, Weiler C, Loschko T, Eberhardt G, Sommer RJ, Rödelsperger C. Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus. BMC Genomics, 2020;21(1):708
• Rödelsperger C, Röseler W, Prabh N, Yoshida K, Weiler C, Herrmann M, Sommer RJ. Phylotranscriptomics of Pristionchus Nematodes Reveals Parallel Gene Loss in Six Hermaphroditic Lineages. Curr Biol, 2018;28(19):3123-3127.e5
• Prabh N, Roeseler W, Witte H, Eberhardt G, Sommer RJ, Rödelsperger C. Deep taxon sampling reveals the evolutionary dynamics of novel gene families in <i>Pristionchus</i> nematodes. Genome Res, 2018;28(11):1664-1674

Resources

Pristionchus.org

Navigation

Genome Browser (JBrowse)

Genome Browser (Ensembl)

Example gene page

Example gene tree

Gene Expression