The Zebrafish Information Network (ZFIN) is the database of genetic and genomic data for the zebrafish (Danio rerio) as a model organism.ZFIN provides a wide array of expertly curated, organized and cross-referenced zebrafish research data. Although the main focus of zebrafish research has traditionally been on developmental biology, keeping and observing zebrafish in the lab led to the identification of diseases similar to humans, such as cancer, which subsequently became a subject for study. The zebrafish reference genome sequence and its relationship to the human genome. Mutagenesis rates reached 75-99%, indicating that most cells contained biallelic mutations. The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Cell 148, 434–446 (2012), Amores, A., Catchen, J., Ferrara, A., Fontenot, Q. LSHG-CT-2003-503496, ZF-MODELS) and Seventh Framework Programme (grant no. and Y.G. You are using a browser version with limited support for CSS. J.H.P. This latest assembly has been refined by the addition of nearly 1000 finished clone sequences and the resolution of more than 400 genome issues. Since the earliest whole-genome shotgun-only assembly became public in 2002, the zebrafish reference genome sequence has enabled many new discoveries to be made, in particular the positional cloning of hundreds of genes from mutations affecting embryogenesis, behaviour, physiology, and health and disease. Nature 447, 714–719 (2007), Postlethwait, J. H. The zebrafish genome in context: ohnologs gone missing. Thus, zebrafish achieve a totipotent chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming. The zebrafish genome encodes a single ACh-hydrolyzing enzyme. Similar graphs for the other chromosome are provided in the Supplementary Information. Previous assemblies were produced by M.C., who developed the first assembly integration process, and by S.R., T.E. Moreover, the annotated reference genome has enabled the generation of accurate whole-exome enrichment reagents, which are accelerating both positional cloning projects and new genome-wide mutation discovery efforts26,27. c, Sequence composition (grey bars, clones; blue bars, WGS contigs). https://doi.org/10.1038/nature12111, Neurobiology of Aging ScienceDirect ® is a registered trademark of Elsevier B.V. ScienceDirect ® is a registered trademark of Elsevier B.V. Reprogramming the Maternal Zebrafish Genome after Fertilization to Match the Paternal Methylation Pattern. Alternatively, the repeat content of the other sequenced teleost species may be under-represented, as these assemblies are mostly WGS16. The genes in this region are highly duplicated, with 31 ancestral gene families alone providing 77.5% of the genes, the largest of which contains no less than 109 duplicates in this region. 23, 727–735 (2013), Freeman, J. L. et al. d, Genetic marker placements (red, SATmap markers; blue, heat shock meiotic map markers; black, Massachusetts General Hospital meiotic map markers). We chose Tübingen as the zebrafish reference strain as it had been used extensively to identify mutations affecting embryogenesis2. Genome Biol. were supported by the NIH (NIH grant 1 R01 DK55377-01A1). To investigate non-CG methylation further, the researchers conducted a comprehensive profiling of the zebrafish genome, a vertebrate organism that is … Definition of the zebrafish genome using flow cytometry and cytogenetic mapping. Mutations in ISPD cause Walker-Warburg syndrome and defective glycosylation of alpha-dystroglycan. Google Scholar, Kasahara, M. et al. Furthermore, this cohort constitutes the genes and loci that acquire DNAme during development (i.e., ZGA to muscle). According to the annotation of the transcripts at the time of manuscript preparation, these represent 10,318 genes, providing approximately 45% coverage of the zebrafish genome. Google Scholar, Roscioli, T. et al. A circular representation of ohnologue pairs (Fig. (2021). volume 496, pages498–503(2013)Cite this article, A Corrigendum to this article was published on 11 December 2013. EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. and I.S. BMC Genomics 8, 195 (2007), The 1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes. Some of this increased gene number is likely to be a consequence of the TSD. In addition, in a specific group of zebrafish derived recently from a natural population, the subtelomeric region of the long arm of chromosome 4 has been found to contain a major sex determinant with alleles that are 100% predictive of male development and 85% predictive of female development, suggesting that this chromosome may be, might have been, or may be becoming, a sex chromosome in this particular population20. Zebrafish is the only peer-reviewed journal dedicated to the central role of zebrafish and other aquarium species as models for the study of vertebrate development, evolution, toxicology, and human disease.. Due to its prolific reproduction and the external development of the transparent embryo, the zebrafish is a prime model for genetic and developmental studies. Such investigations have also contributed notably to our understanding of basic vertebrate biology and vertebrate development. Direct assignment of function on the basis of this information would be facilitated by the development of a rapid, targeted ‘knockdown’ technology in this model vertebrate. Nevertheless, genomic causal mutations of this transparent phenotype are poorly defined. A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Loss-of-function mutations in the zebrafish ache gene therefore generate animals that are completely devoid of ACh-hydrolyzing activity (Behra et al., 2002). In addition to enabling the systematic definition of a large range of early developmental phenotypes, screens in zebrafish have contributed more generally to our understanding of the factors controlling the specification of cell types, organ systems and body axes of vertebrates7,8,9. We generated cloned libraries of large fragments of genomic DNA, assembled a physical map of large-insert clones and completely sequenced a set of minimally overlapping clones. 8, R251 (2007), Anderson, J. L. et al. Although its contributions have already been substantial, zebrafish research holds further promise to enhance our understanding of the detailed roles of specific genes in human diseases, both rare and common. wrote the manuscript and Supplementary Information. Abstract. Nature (in the press), Varshney, G. K. et al. In fact, 110 genes (out of 663) have no identifiable orthologues in any other sequenced teleost genome and indeed seem to be zebrafish-specific genes. It is possible that zebrafish proteins with functionally similar activities to LIF, OSM and IL-6 exist, but that their sequence divergence is so great that they cannot be recognized as orthologues. Near-centromeric clones are positioned at 20 Mb (BX537156), 20.2 Mb (Z10280) and 24.4 Mb (Z20450)28. To investigate the number of potential disease-related genes, we compared the list of human genes possessing at least one zebrafish orthologue with the 3,176 genes bearing morbidity descriptions that are listed in the Online Mendelian Inheritance in Man (OMIM) database. HEALTH-F4-2010-242048, ZF-HEALTH). Z.N. https://doi.org/10.1016/j.cell.2013.04.030. The zebrafish genome (1.5 GB) is parsed into 25 chromosomes, lacks a defined sex chromosome, and has ∼24,800 nuclear genes and one mitochondrial chromosome. In contrast, the zebrafish genome contains a marked excess of type II DNA transposable elements. The vertebrate zebrafish genome and anatomy show only ~ 420 million years (Myr) of divergence from the human lineage rather than the ~ 600 Myr of the ecdysozoans (Drosophila and C. elegans, ). Humans and zebrafish share 70 percent of the same genes and 84 percent of human genes known to be associated with human disease have a counterpart in zebrafish. Nature 431, 946–957 (2004), ADS  and J.Y. ABC derived a solid conclusion from this research and published paper after confirming their prediction with the help of NemaMetrix’s zebrafish gene editing service. The clone and WGS sequence is tied to a high-resolution, high-density meiotic map called the Sanger AB Tübingen map (SATmap), named after the strains of zebrafish used to make the map (Supplementary Information). 1 and Supplementary Fig. All resources generated by the ZGC are publicly accessible to the biomedical research community. The sequence data can be found in the BioProject database, under accession number PRJNA11776. C.N.-V., G.-J.R. and R.G. Genes shared across species are considered in terms of copies at the time of the split. Chromosome 4 is known to be late-replicating and hybridization studies suggest that genomic copies of 5S ribosomal DNA (rDNA), which are not notably present on any other chromosome, are scattered along the long arm at high redundancy18. All mutant alleles and data are freely available at go.nature.com/en6mos. & Stainier, D. Y. Mesodermal Wnt2b signalling positively regulates liver specification. The analyses and figures for the manuscript were produced by J.T., K.H., C.B., M.M., J.H., L.T.Q., J.A.G.-A. Nature 428, 617–624 (2004), Jaillon, O. et al. Circos: an information aesthetic for comparative genomics. It is notable that although true pairs of ohnologues may exist within the same chromosome owing to post-TSD rearrangements, we excluded such cases as we cannot reliably distinguish them from segmental duplications. The zebrafish genome-sequencing project was initiated at the Wellcome Trust Sanger Institute in 2001. The results demonstrated that using the CRISPR/Cas9 technique in zebrafish will make it possible to both generate mutants for all genes in the zebrafish genome and carry out large-scale phenotyping, they noted in the Genome Research paper. The closest vertebrate species in terms of the abundance of type II transposable elements is Xenopus tropicalis (25% type II transposable elements), whereas the sequenced and annotated teleost fish (the pufferfish Takifugu and Tetraodon, the three-spined stickleback (Gasterosteus aculeatus) and the medaka (Oryzias latipes)) each possess type II transposable element coverage of less than 10%, which may relate to the fact that the zebrafish genome diverges basally from the other sequenced and annotated teleost genomes17. At approximately 27 Mb, the otherwise uniform presence of the satellite repeat SAT-2 on the long arm ends abruptly. 15). A team of researchers led by MIPT's Allan Kalueff has studied chronic stress in zebrafish and determined that the animal can serve as a valuable … The F1 individuals were crossed to generate a panel of F2 individuals, each with its own unique set of meiotic recombinations between AB and Tübingen (Tü) chromosomes, which were uncovered by dense genotyping with a set of 140,306 SNPs covering most of the genome. The Zebrafish Gene Collection (ZGC) is an NIH initiative that supports the production of cDNA libraries, clones and sequences to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. Zebrafish genome has also been fully sequenced to a very high quality. The long-term goal is the creation of a knockout allele in every protein-coding gene in the zebrafish genome. was supported by the German Research Foundation (DFG Grant NU 22/5). Of these morbid genes, 2,601 (82%) can be related to at least one zebrafish orthologue. We carried out a four-way comparison between the proteome of two mammals (human and mouse), a bird (chicken) and the zebrafish to quantify the fraction of shared and species-specific genes present in each genome (Fig. Finally, DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene and chromatin cohorts at ZGA, preventing their precocious expression. The zebrafish is an excellent genetic system for the study of vertebrate development and disease. Development 123, 37–46 (1996), CAS  And, it turns out; the fish are a lot like people. J.T., W.C. and C.F.T. Compared to other vertebrate species, this ancestor underwent an additional round of whole-genome duplication (WGD) called the teleost-specific genome duplication (TSD)12. Genetica 111, 397–412 (2001), Stein, C., Caccamo, M., Laird, G. & Leptin, M. Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish. PLoS Genet. Reproduction. & Postlethwait, J. H. Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Interestingly, publication of the first paper on zebrafish development (Roosen, 1937) investigated the effect of different toxins, alcohol, and different levels of carbohydrate or fat diets on zebrafish embryos, larvae, and adult developmental stages. casper has been a widely used transparent mutant of zebrafish. The position of ohnologous genes between chromosomes are linked in grey (for clarity, links between chromosomes that share less than 20 ohnologues have been omitted). and JavaScript. This number is somewhat less than the core set of 11,809 vertebrate genes identified previously as being common to three fish genomes (Tetraodon, medaka, zebrafish) and three amniotes (human, mouse, chicken)16, but the discrepancy probably reflects the improved annotation of these genomes that often results in fusing fragmented gene structures. Although the zebrafish reference genome sequencing is complete, a few poorly assembled regions remain, which are being resolved by the Genome Reference Consortium (http://genomereference.org). It possesses a combined loss of reflective iridophores and light-absorbing melanophores, which gives rise to its almost transparent trunk throughout larval and adult stages. Google Scholar, Haffter, P. et al. The sequencing of the zebrafish genome should be completed by the end of 2002. We thank A. Pirani at Affymetrix for genotyping advice support, and the Zebrafish International Resource Center (ZIRC) for distributing the SAT strain. Genome Res. Genetics 188, 799–808 (2011), Meyer, A. The genome sequencing was carried out by C.C., K.M., S.M., C.S., J.C., B.F., E.L., S.F.M., M.J., M.Q., D.W., A.H., J.B., S.S., K.M., B.P., J..D., C.C., K.O., B.M., G.K., B.P., A.T., N.C., C.J., S.C., M.S., R.G., P.H., N.B., C.Lanz, C.S., J.H., K.H., G.P., J.L., H.B., C.H., D.G., D.W., C.R., L.D., K.L., L.R., K.A., D.L., S.M., R.G., C.G., D.M., S.N., G.B., S.W., M.K., J.B., C.M., E.G., M.H., N.S., D.B., D.S., J.W., A.B., S.H., K.O., M.M.-M., L.B., S.M., P.W., A.E., N.M., M.E., R.W., G.C., J.C., A.T., D.G., C.S., R.P., R.A., E.H., A.K., J.G., N.F., R.H., P.G., D.K., C.B. and C.Lang. was supported by the German Human Genome Project (DHGP Grant 01 KW 9627 and 01 KW 9919). A4) shows a remarkable increase in repeat content, which continues through to the telomere of the long arm. Using the reference genome sequence along with high-throughput sequencing and efficient chemical mutagenesis, the project's initial results — covering 38% of all known protein-coding genes — they describe phenotypic consequences of more than 1,000 alleles. The Zv9 assembly is a hybrid of high-quality finished clone sequence (83%) and whole-genome shotgun (WGS) sequence (17%), with a total size of 1.412 gigabases (Gb) (Table 1). , ZGA to muscle ), pages498–503 ( 2013 ), Varshney, G. zebrafish genome paper et al mapping... Cell 97, 121–132 ( 1999 ), Gritsman, K. et al tumors, and few –. Larvae and phytoplankton reduced on the long arm of chromosome 4 also a., J.A.-K. and J.L waves in the zebrafish genome sequence superfamilies with 401 repeat families in total Supplementary... Both the human zebrafish genome paper C. et al NIH ) grant R01 GM085318 ( to J.H.P... Map of genetic variation from 1,092 human genomes snRNAs carried on the long arm and CRISPR/Cas9. 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