ArticleBMC genomics2021
The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- Bacterial diet influences mutation rate in Pristionchus pacificus.G3 (Bethesda, Md.) · 2026Article
- Lessons learned from manual curation of thousands of gene models in the nematode Pristionchus pacificus.PloS one · 2026Article
- Parallel Evolution of X Chromosome-Specific Structural Maintenance of Chromosomes Complexes in Two Nematode Lineages.Molecular biology and evolution · 2025Article
- EBAX-1/ZSWIM8 destabilizes miRNAs, resulting in transgenerational inheritance of a predatory trait.Science advances · 2025Article
- Genome Announcement: Further Improved Genome Assembly ofJournal of nematology · 2025Article
- High-level phylogenetic relationships withinIMA fungus · 2025Article
- Rapid chromosome evolution and acquisition of thermosensitive stochastic sex determination in nematode androdioecious hermaphrodites.Nature communications · 2024Article
- Genome Assembly of the Nematode Rhabditoides Inermis From a Complex Microbial Community.Genome biology and evolution · 2024Article
- AssessingiScience · 2024Article
- Article
- Nematode genome announcement: A chromosome-scale genome assembly for theJournal of nematology · 2024Article
- A Mediator subunit imparts robustness to a polyphenism decision.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation.Nature ecology & evolution · 2023Article
- Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis.Genome research · 2023Article
- A New Hope: A Hermaphroditic Nematode Enables Analysis of a Recent Whole Genome Duplication Event.Genome biology and evolution · 2022Article
- The improved genome of the nematode Parapristionchus giblindavisi provides insights into lineage-specific gene family evolution.G3 (Bethesda, Md.) · 2022Article
- Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons.BMC genomics · 2022Article
- MultipleGenome research · 2022Article
- Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics.Genome biology and evolution · 2022Article
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Abstract
backgroundThe nematode Pristionchus pacificus is an established model organism for comparative studies with Caenorhabditis elegans. Over the past years, it developed into an independent animal model organism for elucidating the genetic basis of phenotypic plasticity. Community-based curations were employed recently to improve the quality of gene annotations of P. pacificus and to more easily facilitate reverse genetic studies using candidate genes from C. elegans.
resultsHere, I demonstrate that the reannotation of phylogenomic data from nine related nematode species using the community-curated P. pacificus gene set as homology data substantially improves the quality of gene annotations. Benchmarking of universal single copy orthologs (BUSCO) estimates a median completeness of 84% which corresponds to a 9% increase over previous annotations. Nevertheless, the ability to infer gene models based on homology already drops beyond the genus level reflecting the rapid evolution of nematode lineages. This also indicates that the highly curated C. elegans genome is not optimally suited for annotating non-Caenorhabditis genomes based on homology. Furthermore, comparative genomic analysis of apparently missing BUSCO genes indicates a failure of ortholog detection by the BUSCO pipeline due to the insufficient sample size and phylogenetic breadth of the underlying OrthoDB data set. As a consequence, the quality of multiple divergent nematode genomes might be underestimated.
conclusionsThis study highlights the need for optimizing gene annotation protocols and it demonstrates the benefit of a high quality genome for phylogenomic data of related species.
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