Genomic Resources for Zebrafish

Owned by Jonathan Knight
Last updated: Oct 06, 2021 by Doug Howe
10 min read

Table of Contents

Chemical Phenomics Initiative

https://my.vanderbilt.edu/chemicalphenomics / 

As a way of introduction, I do chemical genetics of zebrafish early development. https://medschool.vanderbilt.edu/chaz-hong-lab /

Briefly, in a manner analogous to classic mutagenesis screens, we conduct high-throughput chemical screens using zebrafish to discover small molecules that specifically perturb embryonic pattern formation.  Using the interdisciplinary chemical genetic approach, we have discovered exquisitely selective modulators of the Bone Morphogenetic Protein (BMP), Wnt and Hedgehog pathways, as well as important new signaling components that direct early vertebrate development. For example, I discovered dorsomorphin, the first small molecule inhibitor of BMP signaling. The technology from this effort is nearing an Investigational New Drug (IND) stage for several devastating human diseases, such as fibrodysplasia ossificans progressiva, and incurable pediatric cancers.

Importantly, from this effort, we also have discovered many compounds that have really interesting effects on zebrafish embryos, but we don’t know the mechanism of action. I hope to initiate a “crowd sourcing” to accelerate discovery and translation.  

Please do not hesitate to contact me with questions about this effort and how it might benefit the zebrafish community. I look forward to hearing from you.



Genome and Map Resources

The Sanger zebrafish homepage hosts all of the efforts of the zebrafish genome sequencing project, including the whole genome sequencing and assembly project with automated annotation in Ensembl and the clone mapping and sequencing project with manual annotation in Vega.

This site allows browsing of zebrafish BAC and PAC clones that were sequenced, analysed and manually annotated within the Sanger zebrafish genome project. Vega includes

    • manually annotated genes with poly A features
    • protein feature and domain annotation
    • mapping of unists markers
    • ab initio gene predictions
    • tRNA prediction
    • CpG island prediction and repeat masking

For Blast searches against all finished and unfinished clones go here.
The manual annotation is a joint effort between the Sanger Institute and ZFIN.

This site allows browsing of the latest zebrafish whole genome assembly Zv9

    • automatically annotated Ensembl genes
    • automatically annotated Ensembl EST genes
    • protein feature and domain annotation
    • Blast searches against all zebrafish ESTs, cDNAs and the WashU and IMCB EST clusters
    • Blast searches against all vertebrate proteins, Uniprot, all vertebrate cDNAs and ESTs
    • mapping of unists markers
    • mapping of the Affymetrix zebrafish probes
    • mapping of SNps in dbSNP
    • comparative analysis with other Ensembl species (human, mouse, rat, chicken, fugu, tetraodon)
    • BAC end placement
    • transcription start site predictions with Eponine
    • ab initio gene predictions
    • tRNA prediction
    • CpG island prediction and repeat masking

Additional DAS tracks with SNP and indel analysis derived from the comparison of the whole genome shotgun reads are available. Ensembl also offers completely customizable downloads with EnsMart
You can search Ensembl with BLAT.

Additional services available at the Sanger Institute

    • The WebFPC database hosts the physical map and allows searching and browsing for clone information. Please note that this database is not updated anymore. For up to date information on the clone path please check chromoview
    • The RepeatMasker service masks your sequence data with a choice of repeat libraries.
    • The miRBase service is the new home for microRNA data, incorporating the database and gene naming roles previously provided by the miRNA Registry, and including the new miRBase Target database.

  • Zebrafish Genome Browser at UCSC:

    A joint collaboration between UCSC and the Zebrafish Genome Initiative at Children's Hospital Boston provides several useful tracks of genome data, including:

    • Mapping & Sequencing: Position / Conigs / Scaffolds / RH Map / BAC End Pairs & Singles / Gap / GC Percent
    • Genes & Gene Prediction: RefSeq Genes / Ensembl Genes
    • mRNA & EST: ZF mRNAs & ESTs / spliced ESTs / WZ EST Clusters / nonZF mRNAs
    • Expression & Regulation: Affy ZF
    • Comparative Genomics: Fugu Chain & Net / Human Proteins / HG Blast
    • Variation & Repeats: RepeatMasker / SimpleRepeats

          Custom annotation tracks for the zebrafish research community include:

    • RH Map (about 9K sequences)
    • BAC End Clones (over 288K pairs, 23K singletons)
    • WZ ESTs (43K sequences, 76K alignments, 39K EST alignments)
    • Affymetrix Zebrafish Microarray Probe Alignments (15K probes)
    • Human Protein (over 40K alignments)

           The UCSC Browser for the Tropical 5D Zebrafish Line T5D (also known as Microsporidia Free 5-D line SPF 5-D)

  • Zebrafish Genome Resources at NCBI:

    This page provides information about genomic resources available from NCBI and the zebrafish research community, including sequence, mapping, clone information, and NCBI's independent gene annotation.

A community resource for Zebrafish Genomics.

Bhartiya D, Maini J, Sharma M, Joshi P, Laddha SV, Jalali S, Patowary A, Purkanti R, Lalwani M, Singh AR, Chauhan R, Singh N, Bhardwaj A, Scaria V, Sivasubbu S. FishMap Zv8 update--a genomic regulatory map of zebrafish. Zebrafish. 2010 Jun;7(2):179-80.

Meli R, Prasad A, Patowary A, Lalwani MK, Maini J, Sharma M, Singh AR, Kumar G, Jadhav V, Scaria V, Sivasubbu S. FishMap: a community resource for zebrafish genomics. Zebrafish. 2008 Summer;5(2):125-30.

  • Zebrafish BLAST server at MGH:

    MGH site provides a BLAST search of a gene or marker of interest to the assembled sequence contigs of the zebrafish genomic shotgun sequence from the Sanger project.

Genomic Resources for Zebrafish#Primers

MGH site offers this tool which searches for a supercontig, scaffold, or finished BAC clone by name or accession number, derives all di- and tri- nucleotide repeat sequences in the supercontig, masks the sequence around the repeats for larger zebrafish repetitive sequences and then designs unique sequence primer pairs to amplify the simple sequence repeats. These are potentially polymorphic simple sequence repeats (SSRs) that can be used in genetic mapping/positional cloning projects. This site also offers a tool to search for marker primer pairs by chromosome coordinates (3MB chromosome segments max.)

The qPrimerDB database (real-time quantitative PCR Primer Database), https://biodb.swu.edu.cn/qprimerdb) is the most comprehensive qPCR primer database available to date, with a web front-end providing gene-specific and pre-computed primer pairs across 516 important organisms, including human, mouse, zebrafish, yeast, thale cress, rice, and maize. The qPrimerDB provides an interactive and information-rich web graphical interface to display search and BLAST results as table-based descriptions and associated links. In this database, we provide 9,273,735 of the best primer pairs for each gene based on primer pair coverage (PPC), as well as 68,653,054 alternative gene-specific primer pairs, which can be conveniently batch downloaded. We validated the specificity and efficiency of the qPCR primer pairs for 66 randomly selected genes in six different organisms through qPCR assays and gel electrophoresis. The qPrimerDB database represents a valuable, timesaving resource for gene expression analysis. This resource, which will be updated routinely.

Microarrays

The Trans-NIH Zebrafish Genome Initiative at Children's Hospital Boston aims to annotate zebrafish genes with human known genes for functional and comparative studies. This website provides a web service for retrieving annotated zebrafish genes represented on Affymetrix Zebrafish Genome Arrays and Roche-NimbleGen Zebrafish Expression Arrays to the research community.

  • Microarray expression at ZF-Espresso

  • Zebrafish Oligonucleotide Arrays :

The Norwegian Microarray Consortium offers their array products for academic use to customers world wide. One limitation is oligonucleotide arrays, which cannot provided to users in the US and Japan, due to licensing conditions. A moderate license fee will be added to the base price for oligonucleotide arrays sold to users in the UK, France, Germany, Italy, Austria, Belgium, Sweden, Switzerland, Luxembourg, and The Netherlands.


cDNA and EST Resources

NIH initiative for production of full length sequences and cDNA clones.
1819 ZGC clones recloned in pENTR223.1 In May 2008, ZGC has added 1819 full length ZGC clones recloned into a Gateway Entry vector (pENTR223.1;) for expression analysis and other applications.
These clones can be found by searching Entrez nucleotide for "NIH_ZGC_36".

The DFCI Zebrafish Gene Index (ZGI) integrates research data from international zebrafish gene research projects and represents a non-redundant view of all zebrafish genes and data on their expression patterns, cellular roles, functions, and evolutionary relationships.

This database consists of 4694 contigs or singletons obtained from ~18000 reads of cDNAs that were isolated from the microdissected otocysts of zebrafish embryos at 20-30 hours postfertilization, following subtraction with a pool of liver cDNAs from adult fishes.

Stock Centers

Mutagenesis Projects

  • Targeted mutations using zinc-finger nucleases (ZFNs):

The Lawson and Wolfe labs have compiled resources relating to their recent publication on targeted gene inactivation using ZFNs:
A list of plasmids and strains (available at addgene):
http://lawsonlab.umassmed.edu/PDFs/B1Hrec.pdf

Help on getting started with bacterial 1-hybrid screens:
http://lawsonlab.umassmed.edu/PDFs/B1HStart.pdf

An on-line search tool to identify and design library oligos:
http://pgfe.umassmed.edu/ZFPsearch.html

This project seeks to identify, phenotype and distribute a large number of mutant zebrafish lines. Mutations are identified from populations of chemically mutagenised animals using PCR of specific exons followed by re-sequencing. Mutants are analysed for morphological and molecular differences and distributed to the community. This is an open resource and is now open to requests from the community. The Zebrafish Mutation Resource Tracking page lists the mutants generated by the Sanger Zebrafish Mutation Resource and the ZF-HEALTH consortium.

Detailed information on the mutants resulting from the large insertional mutagenesis screen described in Amsterdam, et al. (2004) Identification of 315 genes essential for early zebrafish development. Proceeding of the National Academy of Sciences 101: 12792-12797

Gene Trap, Enhancer Trap, Insertion Mutagenesis and CreloxP System Resources

  • Zfishbook: real-time database of gene-break transposon mutagenesis projects in the zebrafish (Steve Ekker laboratory).

  • Digital Fish: flip trap database and digital atlas (Scott Fraser laboratory).
  • CreZoo: database for zebrafish Cre driver and responder lines (Michael Brand laboratory).
  • zTrap: Tol2-mediated gene and enhancer traps that express GFP or Gal4 in specific cells, tissues, and organs (Koichi Kawakami laboratory).
  • Zebrafish Enhancer Trap Database: Gal4FF enhancer trap lines enriched for brain selective expression maintained at NICHD (Harold Burgess laboratory).
  • ZInC: zebrafish insertion mutation collection (Shuo Lin/Shawn Burgess laboratories).
  • Engert lab neural enhancer trap line resource: This neural enhancer trap line resource is a collection of Gal4 expressing enhancer trap lines which have been registered to the ZBrain for expression comparison and annotation. Full resolution stacks can be downloaded from the website and lines can be ordered from the Engert lab.

TALENs/CRISPRs

E-CRISP is a software tool to design and evaluate target sites for use with the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) system. The web application uses fast algorithms to identify sgRNA target sequences in any nucleotide sequence for use in CRISPR/Cas mediated genome editing. E-CRISP analyzes target specificity of the putative designs and assesses their genomic context (e.g. exons, transcripts, CpG islands). The design process incorporates different options of how CRISPR constructs can be used in experimental applications

E-TALEN is a web service to design TALENs for introducing knock-out mutations, for endogenous tagging and targeted excision repair. The tool can be used to design TALENs against a single target but also for up to 50 target genes in parallel. E-TALEN guides the user through end-to-end de-novo design process for specific sequences or genomic loci. In addition, it can also be used to evaluate existing TALEN designs.

 Identifies gRNA target sequences from an input sequence and checks for off-target binding.

CRISPRz is a curated database of validated CRISPR targets in zebrafish maintained by Shawn Burgess' lab at NHGRI/NIH. The database contains target sites from the Burgess lab's large-scale mutagenesis project, as well as those reported in the literature. A search form allows users to search by various identifiers in order to determine if a validated CRISPR target exists for a gene of interest.

  • CHOPCHOP:

               CHOPCHOP is a web tool for selecting target sites for CRISPR/Cas9, CRISPR/Cpf1, CRISPR/Cas13 or NICKASE/TALEN-directed mutagenesis.


Morpholinos

Pathways

This site allows browsing, editing, downloading and publishing of zebrafish pathways that are annotated for computational analysis and illustrated for human consumption.

      • includes metabolic, signaling, regulatory and disease pathways
      • browse and search for pathways by title or gene content
      • download pathways as images for presentations
      • download pathway for data visualization and analysis
      • edit pathways using a built-in drawing tool
      • publish new pathways based on your knowledge and research
      • add literature references to important pathway components or steps
      • discuss, share and collaborate on pathways with colleagues globally
      • compete with others to curate the highest ranking pathways

WikiPathways is also accessible programmatically through a web service API, which supports search, download, and data mapping.

Neurobehavioral / Physiological Models


  • Zebrafish Neurophenome Project (ZNP): 

ZNP is a comprehensive resource for neurobehavioral and physiological data of adult zebrafish models. ZNP incorporates validated and curated data from work published in this field, to improve the accessibility of current knowledge to researchers interested in using adult zebrafish models.

  • Zebrafish Brain-Behavior Axis Database (ZBBAD)

    By gathering these literatures we tried to provide a package of neural studies on Zebrafish with behavioral outcomes and overseeing an intervention on the brain. The studies on zebrafish have different approaches, from neural disease and dysfunctionalities to the specific role of a neural factor. Near a half of the researchers used zebrafish to understand the brain functions, mechanisms, and their related gene expression patterns. However, some studies tried to improve imaging or other assessing tools. We included studies with any exposure, impacts the zebrafish's brain or behavior to gather all the recent methods and works in brain_behavior axes.

Gene Expression Resources

Regeneration database that provides easy access to a large number of RNA-Seq datasets through custom-made plots of expression levels, differential expression analyses, correlations of genes and comparisons of the different datasets. 

Tomo-seq is a high-resolution genome-wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages, produced using RNA Tomography.

White Papers