ArticleScientific reports2019
Crowdsourcing and the feasibility of manual gene annotation: A pilot study in the nematode Pristionchus pacificus.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 35 citations in OpenAlex.
- 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
- ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements.Mobile DNA · 2025Article
- Novel and improved Caenorhabditis briggsae gene models generated by community curation.BMC genomics · 2023Article
- Novel and improvedbioRxiv : the preprint server for biology · 2023Article
- Influence of environmental temperature on mouth-form plasticity in Pristionchus pacificus acts through daf-11-dependent cGMP signaling.Journal of experimental zoology. Part B, Molecular and developmental 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
- Analysis of repeat elements in the Pristionchus pacificus genome reveals an ancient invasion by horizontally transferred transposons.BMC genomics · 2022Article
- Standardized evidence-based approach for assessment of oncogenic and clinical significance of NTRK fusions.Cancer genetics · 2022Article
- Horizontally Acquired Cellulases Assist the Expansion of Dietary Range in Pristionchus Nematodes.Molecular biology and evolution · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes.Genome research · 2021Article
- The community-curated Pristionchus pacificus genome facilitates automated gene annotation improvement in related nematodes.BMC genomics · 2021Article
- Spatial Transcriptomics of Nematodes Identifies Sperm Cells as a Source of Genomic Novelty and Rapid Evolution.Molecular biology and evolution · 2021Article
- Uncovering the Role of Metabolism in Oomycete-Host Interactions Using Genome-Scale Metabolic Models.Frontiers in microbiology · 2021Review
- Rhabditophanes diutinus a parthenogenetic clade IV nematode with dauer larvae.PLoS pathogens · 2020Article
- Improving Transgenesis Efficiency and CRISPR-Associated Tools Through Codon Optimization and Native Intron Addition inGenetics · 2020Article
- Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus.BMC genomics · 2020Article
- Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell.PLoS genetics · 2020Article
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nematodes such as Caenorhabditis elegans are powerful systems to study basically all aspects of biology. Their species richness together with tremendous genetic knowledge from C. elegans facilitate the evolutionary study of biological functions using reverse genetics. However, the ability to identify orthologs of candidate genes in other species can be hampered by erroneous gene annotations. To improve gene annotation in the nematode model organism Pristionchus pacificus, we performed a genome-wide screen for C. elegans genes with potentially incorrectly annotated P. pacificus orthologs. We initiated a community-based project to manually inspect more than two thousand candidate loci and to propose new gene models based on recently generated Iso-seq and RNA-seq data. In most cases, misannotation of C. elegans orthologs was due to artificially fused gene predictions and completely missing gene models. The community-based curation raised the gene count from 25,517 to 28,036 and increased the single copy ortholog completeness level from 86% to 97%. This pilot study demonstrates how even small-scale crowdsourcing can drastically improve gene annotations. In future, similar approaches can be used for other species, gene sets, and even larger communities thus making manual annotation of large parts of the genome feasible.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.