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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A simple guide to de novo transcriptome assembly and annotation

Briefings in Bioinformatics, Год журнала: 2021, Номер 23(2)

Опубликована: Дек. 10, 2021

A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily attainable proxy catalog of protein-coding genes when genome assembly unnecessary, expensive or difficult. In the absence a sequenced to guide reconstruction process, must be assembled de novo using only information available in RNA-seq reads. Subsequently, sequences annotated order identify sequence-intrinsic and evolutionary features them (for example, regions). Although straightforward at first glance, annotation can quickly prove challenging undertakings. addition familiarizing themselves with conceptual technical intricacies tasks hand numerous pre- post-processing steps involved, those interested also grapple overwhelmingly large choice tools. The lack standardized workflows, fast pace development new tools techniques paucity authoritative literature have served exacerbate difficulty task even further. Here, we present comprehensive overview annotation. We discuss procedures including steps, compendium corresponding

Язык: Английский

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Fission stories: using PomBase to understand Schizosaccharomyces pombe biology

Genetics, Год журнала: 2021, Номер 220(4)

Опубликована: Дек. 23, 2021

Abstract PomBase (www.pombase.org), the model organism database (MOD) for fission yeast Schizosaccharomyces pombe, supports research within and beyond S. pombe community by integrating presenting genetic, molecular, cell biological knowledge into intuitive displays comprehensive data collections. With new content, novel query capabilities, biologist-friendly summaries visualization, also drives innovation in MOD community.

Язык: Английский

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NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport

Nature Protocols, Год журнала: 2021, Номер 16(9), С. 4177 - 4200

Опубликована: Авг. 4, 2021

Язык: Английский

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Genome-scale metabolic network reconstruction of model animals as a platform for translational research

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 118(30)

Опубликована: Июль 19, 2021

Genome-scale metabolic models (GEMs) are used extensively for analysis of mechanisms underlying human diseases and malfunctions. However, the lack comprehensive high-quality GEMs model organisms restricts translational utilization omics data accumulating from use various disease models. Here we present a unified platform that covers five major animals, including Mouse1 (Mus musculus), Rat1 (Rattus norvegicus), Zebrafish1 (Danio rerio), Fruitfly1 (Drosophila melanogaster), Worm1 (Caenorhabditis elegans). These represent most coverage network by considering both orthology-based pathways species-specific reactions. All can be interactively queried via accompanying web portal Metabolic Atlas. Specifically, through integrative with RNA-sequencing brain tissues transgenic mice identified coordinated up-regulation lysosomal GM2 ganglioside peptide degradation which appears to signature alteration in Alzheimer's (AD) mouse phenotype amyloid precursor protein overexpression. This shift was further validated proteomics cerebrospinal fluid samples patients. The elevated enzymes thus hold potential as biomarker early diagnosis AD. Taken together, foresee this evolving open-source will serve an important resource facilitate development systems medicines biomedical applications.

Язык: Английский

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FlyAtlas 2 in 2022: enhancements to the Drosophila melanogaster expression atlas

Nucleic Acids Research, Год журнала: 2021, Номер 50(D1), С. D1010 - D1015

Опубликована: Окт. 8, 2021

Abstract FlyAtlas 2 (flyatlas2.org) is a database and web application for studying the expression of genes Drosophila melanogaster in different tissues adults larvae. It based on RNA-Seq data, incorporates both encoding proteins microRNAs. We have now completed population with 13 from male female adults, five sex-specific tissues, eight larval tissues. Larval garland cell nephrocytes also been included. Major enhancements made to application. First, facility has added ‘Profile’ search similar pattern tissue as query gene. This may help establish function which this currently unknown. Second, dedicated midgut, where difference gene regions pH can be explored. A variety further improvements interface are described.

Язык: Английский

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Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes

Current Biology, Год журнала: 2022, Номер 32(12), С. 2632 - 2639.e2

Опубликована: Май 18, 2022

Comparisons of genomes different species are used to identify lineage-specific genes, those genes that appear unique one or clade. Lineage-specific often thought represent genetic novelty underlies adaptations. Identification these depends not only on genome sequences, but also inferred gene annotations. Comparative analyses typically use available have been annotated using methods, increasing the risk orthologous DNA sequences may be erroneously as a in another, appearing lineage specific result. To evaluate impact such "annotation heterogeneity," we identified four clades with sequenced more than publicly annotation, allowing us compare number when differing annotation methods resulting method is uniform across In case studies, heterogeneity increases apparent by up 15-fold, suggesting substantial source potential artifact.

Язык: Английский

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Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2021, Номер unknown

Опубликована: Июль 5, 2021

Abstract The ability to obtain single cell transcriptomes for stable types and dynamic states is ushering in a new era biology. We created the Tabula Drosophilae , atlas of adult fruit fly which includes 580k cells from 15 individually dissected sexed tissues as well entire head body. Over 100 researchers community contributed annotations >250 distinct across all tissues. provide an in-depth analysis type-related gene signatures transcription factor markers, sexual dimorphism, whole animal. Analysis common that are shared between tissues, such blood muscle cells, allowed discovery rare tissue-specific subtypes. This provides valuable resource Drosophila serves comprehensive reference study genetic perturbations disease models at resolution.

Язык: Английский

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An expanded toolkit for Drosophila gene tagging using synthesized homology donor constructs for CRISPR-mediated homologous recombination

eLife, Год журнала: 2022, Номер 11

Опубликована: Июнь 20, 2022

Previously, we described a large collection of

Язык: Английский

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The Drosophila ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters

eLife, Год журнала: 2022, Номер 11

Опубликована: Окт. 4, 2022

RNA interference systems depend on the synthesis of small precursors whose sequences define target spectrum these silencing pathways. The Drosophila Heterochromatin Protein 1 (HP1) variant Rhino permits transcription PIWI-interacting (piRNA) within transposon-rich heterochromatic loci in germline cells. Current models propose that Rhino’s specific chromatin occupancy at piRNA source is determined by histone marks and maternally inherited piRNAs, but also imply existence other, undiscovered specificity cues. Here, we identify a member diverse family zinc finger associated domain (ZAD)-C 2 H proteins, Kipferl, as critical cofactor ovaries. By binding to guanosine-rich DNA motifs interacting with chromodomain, Kipferl recruits stabilizes it chromatin. In kipferl mutant flies, lost from most its instead accumulates pericentromeric Satellite arrays, resulting decreased levels transposon targeting piRNAs impaired fertility. Our findings reveal sequence, addition H3K9me3 mark, determines identity provide insight into how might be caught crossfire genetic conflicts.

Язык: Английский

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