The Zebrafish Information Network: major gene page and home page updates

Abstract The Zebrafish Information Network (ZFIN) (https://zfin.org/) is the database for the model organism, zebrafish (Danio rerio). ZFIN expertly curates, organizes, and provides a wide array of zebrafish genetic and genomic data, including genes, alleles, transgenic lines, gene expression, gene function, mutant phenotypes, orthology, human disease models, gene and mutant nomenclature, and reagents. New features at ZFIN include major updates to the home page and the gene page, the two most used pages at ZFIN. Data including disease models, phenotypes, expression, mutants and gene function continue to be contributed to The Alliance of Genome Resources for integration with similar data from other model organisms.

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Precise genome engineering inDrosophilausing prime editing

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2021996118 ◽

2020 ◽

Vol 118 (1) ◽

pp. e2021996118

Author(s):

Justin A. Bosch ◽

Gabriel Birchak ◽

Norbert Perrimon

Keyword(s):

Gene Function ◽

Mammalian Cells ◽

Genome Engineering ◽

Cultured Cells ◽

Germ Line ◽

Point Mutations ◽

Model Organism ◽

Model Organisms ◽

Marker Genes ◽

Germ Line Transmission

Precise genome editing is a valuable tool to study gene function in model organisms. Prime editing, a precise editing system developed in mammalian cells, does not require double-strand breaks or donor DNA and has low off-target effects. Here, we applied prime editing for the model organismDrosophila melanogasterand developed conditions for optimal editing. By expressing prime editing components in cultured cells or somatic cells of transgenic flies, we precisely introduce premature stop codons in three classical visible marker genes,ebony,white, andforked. Furthermore, by restricting editing to germ cells, we demonstrate efficient germ-line transmission of a precise edit inebonyto 36% of progeny. Our results suggest that prime editing is a useful system inDrosophilato study gene function, such as engineering precise point mutations, deletions, or epitope tags.

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Precise genome engineering in Drosophila using prime editing

10.1101/2020.08.05.232348 ◽

2020 ◽

Cited By ~ 3

Author(s):

Justin A. Bosch ◽

Gabriel Birchak ◽

Norbert Perrimon

Keyword(s):

Gene Function ◽

Mammalian Cells ◽

Genome Engineering ◽

Cultured Cells ◽

Germ Line ◽

Point Mutations ◽

Model Organism ◽

Model Organisms ◽

Marker Genes ◽

Germ Line Transmission

AbstractPrecise genome editing is a valuable tool to study gene function in model organisms. Prime editing, a precise editing system developed in mammalian cells, does not require double strand breaks or donor DNA and has low off-target effects. Here, we applied prime editing for the model organism Drosophila melanogaster and developed conditions for optimal editing. By expressing prime editing components in cultured cells or somatic cells of transgenic flies, we precisely installed premature stop codons in three classical visible marker genes, ebony, white, and forked. Furthermore, by restricting editing to germ cells, we demonstrate efficient germ line transmission of a precise edit in ebony to ~50% of progeny. Our results suggest that prime editing is a useful system in Drosophila to study gene function, such as engineering precise point mutations, deletions, or epitope tags.

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The fruit fly at the interface of diagnosis and pathogenic mechanisms of rare and common human diseases

Human Molecular Genetics ◽

10.1093/hmg/ddz135 ◽

2019 ◽

Vol 28 (R2) ◽

pp. R207-R214 ◽

Cited By ~ 14

Author(s):

Hugo J Bellen ◽

Michael F Wangler ◽

Shinya Yamamoto

Keyword(s):

Rare Disease ◽

Gene Function ◽

Rare Variants ◽

Genetic Model ◽

Model Organism ◽

Model Organisms ◽

Pathogenic Mechanisms ◽

Disease Mechanisms ◽

The Impact ◽

Undiagnosed Diseases

Abstract Drosophila melanogaster is a unique, powerful genetic model organism for studying a broad range of biological questions. Human studies that probe the genetic causes of rare and undiagnosed diseases using massive-parallel sequencing often require complementary gene function studies to determine if and how rare variants affect gene function. These studies also provide inroads to disease mechanisms and therapeutic targets. In this review we discuss strategies for functional studies of rare human variants in Drosophila. We focus on our experience in establishing a Drosophila core of the Model Organisms Screening Center for the Undiagnosed Diseases Network (UDN) and concurrent fly studies with other large genomic rare disease research efforts such as the Centers for Mendelian Genomics. We outline four major strategies that use the latest technology in fly genetics to understand the impact of human variants on gene function. We also mention general concepts in probing disease mechanisms, therapeutics and using rare disease to understand common diseases. Drosophila is and will continue to be a fundamental genetic model to identify new disease-causing variants, pathogenic mechanisms and drugs that will impact medicine.

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Zebrafish Information Network, the knowledgebase for Danio rerio research

10.1101/2021.09.22.461443 ◽

2021 ◽

Author(s):

Yvonne M Bradford ◽

Ceri E Van Slyke ◽

Amy Singer ◽

Holly Paddock ◽

Anne Eagle ◽

...

Keyword(s):

Danio Rerio ◽

Model Organism ◽

Genomic Data ◽

Research Data ◽

Disease Models ◽

Information Network ◽

Web Interfaces ◽

Founding Member ◽

Gene Expression Phenotype ◽

Central Repository

The Zebrafish Information Network (ZFIN, zfin.org) is the central repository for zebrafish genetic and genomic data. ZFIN expertly curates, integrates, and displays zebrafish data including genes, alleles, human disease models, gene expression, phenotype, gene function, orthology, morpholino, CRISPR, TALEN, and antibodies. ZFIN makes zebrafish research data Findable, Accessible, Interoperable, and Reusable (FAIR) through nomenclature, curatorial and annotation activities, web interfaces, and data downloads. ZFIN is a founding member of the Alliance of Genome Resources, providing zebrafish data for integration into the cross species platform as well as contributing to model organism data harmonization efforts.

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FlyBase: updates to the Drosophila melanogaster knowledge base

Nucleic Acids Research ◽

10.1093/nar/gkaa1026 ◽

2020 ◽

Vol 49 (D1) ◽

pp. D899-D907 ◽

Cited By ~ 1

Author(s):

Aoife Larkin ◽

Steven J Marygold ◽

Giulia Antonazzo ◽

Helen Attrill ◽

Gilberto dos Santos ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Knowledge Base ◽

Fast Track ◽

Model Organism ◽

Disease Models ◽

Online Database ◽

Experimental Tool

Abstract FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays (‘ribbons’) of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.

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In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽

10.3390/ani11082226 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2226

Author(s):

Sazia Kunvar ◽

Sylwia Czarnomska ◽

Cino Pertoldi ◽

Małgorzata Tokarska

Keyword(s):

Reference Genome ◽

De Novo ◽

Bos Taurus ◽

Model Organism ◽

Genotyping By Sequencing ◽

Model Organisms ◽

European Bison ◽

Model Animal ◽

Pcr Duplicates ◽

Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

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Alliance of Genome Resources Portal: unified model organism research platform

Nucleic Acids Research ◽

10.1093/nar/gkz813 ◽

2019 ◽

Vol 48 (D1) ◽

pp. D650-D658 ◽

Cited By ~ 36

Author(s):

◽

Julie Agapite ◽

Laurent-Philippe Albou ◽

Suzi Aleksander ◽

Joanna Argasinska ◽

...

Keyword(s):

Gene Ontology ◽

Model Organism ◽

Model Organisms ◽

Data Types ◽

Primary Model ◽

Genomic Studies ◽

Health And Disease ◽

Extensive Body ◽

Access To Data ◽

Model Organism Databases

Abstract The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human and well-studied model organisms by providing a highly integrated and comprehensive platform that enables researchers to leverage the extensive body of genetic and genomic studies in these organisms. Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data. All data types represented in the Alliance portal (e.g. genomic data and phenotype descriptions) have common data models and workflows for curation. All data are open and freely available via a variety of mechanisms. Long-term plans for the Alliance project include a focus on coverage of additional model organisms including those without dedicated curation communities, and the inclusion of new data types with a particular focus on providing data and tools for the non-model-organism researcher that support enhanced discovery about human health and disease. Here we review current progress and present immediate plans for this new bioinformatics resource.

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Transgenic Epigenetics: Using Transgenic Organisms to Examine Epigenetic Phenomena

Genetics Research International ◽

10.1155/2012/689819 ◽

2012 ◽

Vol 2012 ◽

pp. 1-14 ◽

Cited By ~ 2

Author(s):

Lori A. McEachern

Keyword(s):

Molecular Mechanisms ◽

Model Organism ◽

Evolutionary Conservation ◽

Model Organisms ◽

Valuable Insight ◽

Epigenetic Control ◽

Transgenic Organisms ◽

Epigenetic Analysis ◽

Insight Into ◽

Epigenetic Processes

Non-model organisms are generally more difficult and/or time consuming to work with than model organisms. In addition, epigenetic analysis of model organisms is facilitated by well-established protocols, and commercially-available reagents and kits that may not be available for, or previously tested on, non-model organisms. Given the evolutionary conservation and widespread nature of many epigenetic mechanisms, a powerful method to analyze epigenetic phenomena from non-model organisms would be to use transgenic model organisms containing an epigenetic region of interest from the non-model. Interestingly, while transgenic Drosophila and mice have provided significant insight into the molecular mechanisms and evolutionary conservation of the epigenetic processes that target epigenetic control regions in other model organisms, this method has so far been under-exploited for non-model organism epigenetic analysis. This paper details several experiments that have examined the epigenetic processes of genomic imprinting and paramutation, by transferring an epigenetic control region from one model organism to another. These cross-species experiments demonstrate that valuable insight into both the molecular mechanisms and evolutionary conservation of epigenetic processes may be obtained via transgenic experiments, which can then be used to guide further investigations and experiments in the species of interest.

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Nonhuman primates’ tissue banks: resources for all model organism research

Mammalian Genome ◽

10.1007/s00335-021-09925-w ◽

2021 ◽

Author(s):

Claire Witham ◽

Sara Wells

Keyword(s):

Nonhuman Primates ◽

Ex Vivo ◽

Model Organism ◽

Translation Studies ◽

Model Organisms ◽

Laboratory Animals ◽

Tissue Banks ◽

Post Mortem ◽

Wide Range ◽

Research Programmes

AbstractBiobanks containing tissue and other biological samples from many model organisms provide easy and faster access to ex vivo resources for a wide-range of research programmes. For all laboratory animals, collecting and preserving tissue at post-mortem is an effective way of maximising the benefits of individual animals and potentially reducing the numbers required for experimentation in the future. For primate tissues, biobanks represent the scarcest of these resources but quite possibly those most valuable for preclinical and translation studies.

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Accurate allele frequencies from ultra-low coverage pool-seq samples in evolve-and-resequence experiments

10.1101/244004 ◽

2018 ◽

Author(s):

Susanne Tilk ◽

Alan Bergland ◽

Aaron Goodman ◽

Paul Schmidt ◽

Dmitri Petrov ◽

...

Keyword(s):

Allele Frequency ◽

Model Organism ◽

Software Tool ◽

Allele Frequencies ◽

Model Organisms ◽

Sequencing Data ◽

High Coverage ◽

Next Generation Sequencing Technology ◽

Low Coverage ◽

Pooled Samples

AbstractEvolve-and-resequence (E+R) experiments leverage next-generation sequencing technology to track the allele frequency dynamics of populations as they evolve. While previous work has shown that adaptive alleles can be detected by comparing frequency trajectories from many replicate populations, this power comes at the expense of high-coverage (>100x) sequencing of many pooled samples, which can be cost-prohibitive. Here, we show that accurate estimates of allele frequencies can be achieved with very shallow sequencing depths (<5x) via inference of known founder haplotypes in small genomic windows. This technique can be used to efficiently estimate frequencies for any number of bi-allelic SNPs in populations of any model organism founded with sequenced homozygous strains. Using both experimentally-pooled and simulated samples of Drosophila melanogaster, we show that haplotype inference can improve allele frequency accuracy by orders of magnitude for up to 50 generations of recombination, and is robust to moderate levels of missing data, as well as different selection regimes. Finally, we show that a simple linear model generated from these simulations can predict the accuracy of haplotype-derived allele frequencies in other model organisms and experimental designs. To make these results broadly accessible for use in E+R experiments, we introduce HAF-pipe, an open-source software tool for calculating haplotype-derived allele frequencies from raw sequencing data. Ultimately, by reducing sequencing costs without sacrificing accuracy, our method facilitates E+R designs with higher replication and resolution, and thereby, increased power to detect adaptive alleles.

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