ArticleBMC genomics2020
Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Evaluating beta-tubulin variants as predictors of benzimidazole resistance across Caenorhabditis nematodes.PLoS pathogens · 2026Article
- Bacterial diet influences mutation rate in Pristionchus pacificus.G3 (Bethesda, Md.) · 2026Article
- Hookworm genes encoding intestinal excreted-secreted proteins are transcriptionally upregulated in response to the host's immune system.PLoS neglected tropical diseases · 2026Article
- Characterization of Heat Shock Protein Expression and Its Application to Temporal Gene Expression in the Nematode Pristionchus pacificus.Development, growth & differentiation · 2026Article
- Lessons learned from manual curation of thousands of gene models in the nematode Pristionchus pacificus.PloS one · 2026Article
- Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival.Genome research · 2025Article
- Comparative connectomics of two distantly related nematode species reveals patterns of nervous system evolution.Science (New York, N.Y.) · 2025Article
- Transposable Elements Drive Regulatory and Functional Innovation of F-box Genes.Molecular biology and evolution · 2025Article
- EBAX-1/ZSWIM8 destabilizes miRNAs, resulting in transgenerational inheritance of a predatory trait.Science advances · 2025Article
- High Nutritional Conditions Influence Feeding Plasticity in Pristionchus pacificus and Render Worms Non-Predatory.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2025Article
- Genome Announcement: Further Improved Genome Assembly ofJournal of nematology · 2025Article
- cGMP-dependent pathway and a GPCR kinase are required for photoresponse in the nematode Pristionchus pacificus.PLoS genetics · 2024Article
- Genome Assembly of the Nematode Rhabditoides Inermis From a Complex Microbial Community.Genome biology and evolution · 2024Article
- Neurogenesis in Caenorhabditis elegans.Genetics · 2024Review
- Article
- Nematode genome announcement: A chromosome-scale genome assembly for theJournal of nematology · 2024Article
- Co-option of an Astacin Metalloprotease Is Associated with an Evolutionarily Novel Feeding Morphology in a Predatory Nematode.Molecular biology and evolution · 2023Article
- Novel and improved Caenorhabditis briggsae gene models generated by community curation.BMC genomics · 2023Article
- Thousands of Pristionchus pacificus orphan genes were integrated into developmental networks that respond to diverse environmental microbiota.PLoS genetics · 2023Article
- Novel and improvedbioRxiv : the preprint server for biology · 2023Article
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7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics.
resultsHere, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-to-one orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths, screens for atypical domain combinations and species-specific orphan genes resulted in 4311 candidate genes that were subject to community-based curation. Corrections for 2946 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%.
conclusionsOur work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes.
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