WormBase 2024: status and transitioning to Alliance infrastructure

Genetics, Год журнала: 2024, Номер 227(1)

Опубликована: Апрель 4, 2024

Abstract WormBase has been the major repository and knowledgebase of information about genome genetics Caenorhabditis elegans other nematodes experimental interest for over 2 decades. We have 3 goals: to keep current with fast-paced C. research, provide better integration resources, be sustainable. Here, we discuss state as well progress plans moving core infrastructure Alliance Genome Resources (the Alliance). As an member, will continue interact community, develop new features needed, curate key from literature large-scale projects.

Язык: Английский

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Updates to the Alliance of Genome Resources central infrastructure

Genetics, Год журнала: 2024, Номер 227(1)

Опубликована: Март 29, 2024

Abstract The Alliance of Genome Resources (Alliance) is an extensible coalition knowledgebases focused on the genetics and genomics intensively studied model organisms. organized as individual knowledge centers with strong connections to their research communities a centralized software infrastructure, discussed here. Model organisms currently represented in are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, rat, Gene Ontology Consortium. project rapid development phase harmonize knowledge, store it, analyze present it community through web portal, direct downloads, application programming interfaces (APIs). Here, we focus developments over last 2 years. Specifically, added enhanced tools for browsing genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching literature (Textpresso), sequence similarity (SequenceServer). We existing interactive tables table paralogs complement our representation orthology. To support organism communities, implemented species-specific “landing pages” will add disease-specific portals soon; addition, common forum Discourse software. describe progress toward central persistent database curation, modeling that underpins harmonization, state-of-the-art curation system integrated artificial intelligence machine learning (AI/ML).

Язык: Английский

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CaeNDR, the Caenorhabditis Natural Diversity Resource

Nucleic Acids Research, Год журнала: 2023, Номер 52(D1), С. D850 - D858

Опубликована: Окт. 19, 2023

Abstract Studies of model organisms have provided important insights into how natural genetic differences shape trait variation. These discoveries are driven by the growing availability genomes and expansive experimental toolkits afforded to researchers using these species. For example, Caenorhabditis elegans is increasingly being used identify measure effects variants on traits quantitative genetics. Since 2016, C. Natural Diversity Resource (CeNDR) has facilitated many studies providing an archive wild strains, genome-wide sequence variant data for each strain, a association (GWA) mapping portal community. Here, we present updated platform, (CaeNDR), that enables genetics genomics across three species: elegans, briggsae tropicalis. The CaeNDR platform hosts several databases continually addition new whole-genome annotated variants. Additionally, provides interactive tools explore variation enable GWA mappings. All accessible through freely available web located at caendr.org.

Язык: Английский

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Neurogenesis in Caenorhabditis elegans

Genetics, Год журнала: 2024, Номер 228(2)

Опубликована: Авг. 21, 2024

Abstract Animals rely on their nervous systems to process sensory inputs, integrate these with internal signals, and produce behavioral outputs. This is enabled by the highly specialized morphologies functions of neurons. Neuronal cells share multiple structural physiological features, but they also come in a large diversity types or classes that give system its broad range plasticity. diversity, first recognized over century ago, spurred classification efforts based morphology, function, molecular criteria. Caenorhabditis elegans, precisely mapped at anatomical level, an extensive description most neurons, genetic amenability, has been prime model for understanding how neurons develop diversify mechanistic level. Here, we review gene regulatory mechanisms driving neurogenesis diversification neuron subclasses C. elegans. We discuss our current specification neuronal progenitors differentiation terms transcription factors involved ensuing changes expression chromatin landscape. The central theme emerged identity defined modules batteries are under control parallel yet interconnected mechanisms. focus how, achieve terminal identities, information along developmental lineages. Moreover, diversified postembryonically time-, sex-, activity-dependent manner. Finally, development can provide insights into evolution diversity.

Язык: Английский

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Independent mechanisms of benzimidazole resistance across Caenorhabditis nematodes

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Март 15, 2025

Benzimidazoles (BZs), a widely used class of anthelmintic drugs, target beta-tubulin proteins, disrupt microtubule formation, and cause nematode death. In parasitic species, mutations in genes ( e.g. , isotype-1 beta-tubulin) are predicted to inhibit BZ binding associated with resistance. Similarly, the free-living Caenorhabditis elegans an ortholog, ben-1 primary drivers The recurrent association resistance beta-tubulins suggests that is repeatedly caused by genes, example repeated evolution drug across species. To evaluate hypothesis mediated beta-tubulin, we identified alleles wild strains from three species: C. briggsae tropicalis . We hypothesized that, if these species experienced similar selective pressures, they would evolve BZs any tbb-1 tbb-2 ). Using high-throughput development assays, tested found heterogeneous set variants were only two encode premature stop codon (W21stop) missense substitution (Q134H), but neither was might have evolved other or not Our findings reveal lack highlight importance defining mechanisms outside beta-tubulins.

Язык: Английский

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Teaching transposon classification as a means to crowd source the curation of repeat annotation – a tardigrade perspective

Mobile DNA, Год журнала: 2024, Номер 15(1)

Опубликована: Май 6, 2024

Abstract Background The advancement of sequencing technologies results in the rapid release hundreds new genome assemblies a year providing unprecedented resources for study evolution. Within this context, significance in-depth analyses repetitive elements, transposable elements (TEs) particular, is increasingly recognized understanding Despite plethora available bioinformatic tools identifying and annotating TEs, phylogenetic distance target species from curated classified database element sequences constrains any automated annotation effort. Moreover, manual curation raw repeat libraries deemed essential due to frequent incompleteness automatically generated consensus sequences. Results Here, we present an example crowd-sourcing effort aimed at curating TE two non-model built around collaborative, peer-reviewed teaching process. Manual classification are time-consuming processes that offer limited short-term academic rewards typically confined few research groups where methods taught through hands-on experience. Crowd-sourcing efforts could therefore significant opportunity bridge gap between learning effectively empowering scientific community with high-quality, reusable libraries. Conclusions collaborative TEs tardigrade species, which there were no available, resulted successful characterization diverse reasonable time frame. Our setting can be used as reference guide similar projects: A hidden treasure awaits discovery within organisms.

Язык: Английский

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A standard workflow for community-driven manual curation ofStrongyloidesgenome annotations

Philosophical Transactions of the Royal Society B Biological Sciences, Год журнала: 2023, Номер 379(1894)

Опубликована: Ноя. 27, 2023

Advances in the functional genomics and bioinformatics toolkits for Strongyloides species have positioned these as genetically tractable model systems gastrointestinal parasitic nematodes. As community interest mechanistic studies of continues to grow, publicly accessible reference genomes associated genome annotations are critical resources researchers. Genome multiple broadly available via WormBase ParaSite online repositories. However, a recent phylogenetic analysis receptor-type guanylate cyclase (rGC) gene family two highlights potential errors large percentage current models. Here, we present three examples annotation updates within rGC family; each example illustrates type error that may occur frequently data genomes. We also extend our 405 previously curated genes confirm found at high rates across families. Finally, introduce standard manual curation workflow assessing quality generating corrections, discuss how it be used facilitate community-driven nematode biodata. This article is part Theo Murphy meeting issue 'Strongyloides: omics worm-free populations'.

Язык: Английский

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Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 22, 2023

Abstract The Alliance of Genome Resources (Alliance) is an extensible coalition knowledgebases focused on the genetics and genomics intensively-studied model organisms. organized as individual knowledge centers with strong connections to their research communities a centralized software infrastructure, discussed here. Model organisms currently represented in are budding yeast, C. elegans , Drosophila zebrafish, frog, laboratory mouse, rat, Gene Ontology Consortium. project rapid development phase harmonize knowledge, store it, analyze present it community through web portal, direct downloads, APIs. Here we focus developments over last two years. Specifically, added enhanced tools for browsing genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching literature (Textpresso), sequence similarity (SequenceServer). We existing interactive tables table paralogs complement our representation orthology. To support organism communities, implemented species-specific “landing pages” will add disease-specific portals soon; addition, common forum Discourse. describe progress towards central persistent database curation, modeling that underpins harmonization, state-of-the art curation system integrated Artificial Intelligence Machine Learning (AI/ML).

Язык: Английский

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Quantitative tests of albendazole resistance in beta-tubulin mutants

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 13, 2024

Abstract Benzimidazole (BZ) anthelmintics are among the most important treatments for parasitic nematode infections in developing world. Widespread BZ resistance veterinary parasites and emerging human raise major concerns continued use of BZs. Knowledge mechanisms is necessary to make informed treatment decisions circumvent resistance. has traditionally been associated with mutations natural variants C. elegans beta-tubulin gene ben-1 orthologs species. However, alone do not explain differences responses across parasite populations. Here, we examine roles five genes ( tbb-1 , mec-7 tbb-4 tbb-6 ) identify role each plays response. We generated strains a loss gene, as well or genetic background that also lacks test redundancy found only individual conferred substantial level resistance, although was confer small benefit presence albendazole (ABZ). The an almost complete rescue animal development 30 µM ABZ, likely explaining why no additive effects caused by second were observed. demonstrate where confers Highlights - Loss provides (ABZ) different does ABZ enhance

Язык: Английский

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The

PubMed, Год журнала: 2024, Номер 2024

Опубликована: Янв. 1, 2024

The

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