ArticleBMC genomics2023
Novel and improved Caenorhabditis briggsae gene models generated by community curation.
Article in BMC genomics, 2023. 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.
- A gap-free, telomere-to-telomere genome assembly for the Caenorhabditis briggsae reference strain AF16.G3 (Bethesda, Md.) · 2026Article
- Population structure and punctuated genomic hyper-diversity in Caenorhabditis briggsae.Molecular biology and evolution · 2026Article
- Evaluating beta-tubulin variants as predictors of benzimidazole resistance across Caenorhabditis nematodes.PLoS pathogens · 2026Article
- A gap-free, telomere-to-telomere genome assembly for thebioRxiv : the preprint server for biology · 2026Article
- The potato cyst nematode Globodera pallida overcomes major potato resistance through selection on standing variation at a single locus.The New phytologist · 2026Article
- Hookworm genes encoding intestinal excreted-secreted proteins are transcriptionally upregulated in response to the host's immune system.PLoS neglected tropical diseases · 2026Article
- High-Throughput Toxicity Screening withEnvironmental science & technology · 2026Review
- Lessons learned from manual curation of thousands of gene models in the nematode Pristionchus pacificus.PloS one · 2026Article
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- ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements.Mobile DNA · 2025Article
- A dataset of expression profile of certain microRNAs in Caenorhabditis elegans.Scientific data · 2025Article
- Neurogenesis in Caenorhabditis elegans.Genetics · 2024Review
- Gene duplication and evolutionary plasticity of lin-12/Notch gene function in Caenorhabditis.Genetics · 2024Article
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- Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.Mobile DNA · 2024Article
- Quantitative tests of albendazole resistance in beta-tubulin mutants.bioRxiv : the preprint server for biology · 2024Article
- A standard workflow for community-driven manual curation ofPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Article
- CaeNDR, the Caenorhabditis Natural Diversity Resource.Nucleic acids research · 2024Article
- ThemicroPublication biology · 2024Article
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11 authors.
Funding
Abstract
backgroundThe nematode Caenorhabditis briggsae has been used as a model in comparative genomics studies with Caenorhabditis elegans because of their striking morphological and behavioral similarities. However, the potential of C. briggsae for comparative studies is limited by the quality of its genome resources. The genome resources for the C. briggsae laboratory strain AF16 have not been developed to the same extent as C. elegans. The recent publication of a new chromosome-level reference genome for QX1410, a C. briggsae wild strain closely related to AF16, has provided the first step to bridge the gap between C. elegans and C. briggsae genome resources. Currently, the QX1410 gene models consist of software-derived gene predictions that contain numerous errors in their structure and coding sequences. In this study, a team of researchers manually inspected over 21,000 gene models and underlying transcriptomic data to repair software-derived errors.
resultsWe designed a detailed workflow to train a team of nine students to manually curate gene models using RNA read alignments. We manually inspected the gene models, proposed corrections to the coding sequences of over 8,000 genes, and modeled thousands of putative isoforms and untranslated regions. We exploited the conservation of protein sequence length between C. briggsae and C. elegans to quantify the improvement in protein-coding gene model quality and showed that manual curation led to substantial improvements in the protein sequence length accuracy of QX1410 genes. Additionally, collinear alignment analysis between the QX1410 and AF16 genomes revealed over 1,800 genes affected by spurious duplications and inversions in the AF16 genome that are now resolved in the QX1410 genome.
conclusionsCommunity-based, manual curation using transcriptome data is an effective approach to improve the quality of software-derived protein-coding genes. The detailed protocols provided in this work can be useful for future large-scale manual curation projects in other species. Our manual curation efforts have brought the QX1410 gene models to a comparable level of quality as the extensively curated AF16 gene models. The improved genome resources for C. briggsae provide reliable tools for the study of Caenorhabditis biology and other related nematodes.
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