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. 2000). Nature 447, 714–719 (2007), Postlethwait, J. H. The zebrafish genome in context: ohnologs gone missing. All other sequenced teleost fish exhibit a much lower repeat content, with an average of less than 30%. The y axis for d shows the normalization of marker positions relative to the span of the individual map. J.T., W.C. and C.F.T. 2b, c). We wish to thank R. Durbin, E. Birney, A. Scally, C. P. Ponting, E. Busch-Nentwich and R. Kettleborough for helpful discussions, as well as F. L. Marlow and P. Aanstad for critical reading and helpful comments on manuscripts. Major organs and tissues are also common. In 2008, together with the Wolfe Lab, we were among the first two groups to demonstrate the application of programmable nucleases for introducing targeted deletions into the zebrafish germline. Driever, W. et al. The cohort of snRNAs carried on the long arm of chromosome 4 accounts for 53.2% of all snRNAs in the zebrafish genome. BMC Genomics 8, 195 (2007), The 1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes. Furthermore, this cohort constitutes the genes and loci that acquire DNAme during development (i.e., ZGA to muscle). 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. 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. 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. Cell 97, 121–132 (1999), Ober, E. A., Verkade, H., Field, H. A. Importantly for disease studies, comparison between human and zebrafish sequences reveals that 70% of human genes have at least one obvious zebrafish orthologue. The notable excess observed in zebrafish may be a consequence of the WGD, because pairs of duplicated genes that arose from the WGD, but with no orthologue in amniotes, are counted as two specific genes. Zebrafish are members of the teleostei infraclass, a monophyletic group that is thought to have arisen approximately 340 million years ago from a common ancestor11. We thank A. Pirani at Affymetrix for genotyping advice support, and the Zebrafish International Resource Center (ZIRC) for distributing the SAT strain. Manual annotation was produced by G.K.L., D.L., E.K., S.D., H.S., J.A.-K. and J.L. Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. Article  Opin. This allowed simultaneous analysis of approximately 14,900 transcripts. A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. The Zebrafish Functional Genomics Core at the Penn State College of Medicine was established to provide the Penn State research community with a modern, centralized facility for housing, breeding and performing experiments with zebrafish, one of the fastest-growing model systems in … Sequence data have been submitted to the BioProject database under accession PRJNA11776. To obtain Furthermore, 2,059 genes are found in human, mouse and zebrafish but not in chicken, and this number is two times higher than the number of genes that are found in all amniotes but not in zebrafish (892). Increasingly, zebrafish experiments are included in studies of human genetic disease, often providing independent verification of the activity of a gene implicated in a human disease3,5,10. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes6, the largest gene set of any vertebrate so far sequenced. We chose Tübingen as the zebrafish reference strain as it had been used extensively to identify mutations affecting embryogenesis2. After 2.5 years of assembly curation, the GRC presents the new zebrafish reference genome assembly, GRCz11. (2021), Journal of Toxicology and Environmental Health, Part A The Zebrafish, Danio rerio, is tropical freshwater fish and a very popular model organism for scientific research in the fields of development, vertebrate processes, genetics, and more. Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily. This pronounced abundance of type II transposable elements is unique among the sequenced vertebrate genomes, and the genome sequence shows evidence of recently active type II transposable elements. Indeed, 2.3 million instances of type II DNA transposable elements cover 39% of the zebrafish genome sequence (Supplementary Table 12), whereas type II repeats cover only 3.2% of the human genome. Zebrafish have been used successfully to understand the biological activity of genes orthologous to human disease-related genes in greater detail3,4,5. Reproduction. In an effort to provide a rapid and robust tool for zebrafish gene mapping, a panel of radiation hybrids (RH) was produced by fusion of irradiated zebrafish AB9 cells with mouse B78 cells. & Stainier, D. Y. Mesodermal Wnt2b signalling positively regulates liver specification. We also observed a very high density of small nuclear RNAs (snRNAs) on chromosome 4, and in particular those that encode spliceosome components. Zebrafish turns out to have the largest gene set of any vertebrate so far sequenced, and few pseudogenes. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. K.O., B.Z. The long-term goal is the creation of a knockout allele in every protein-coding gene in the zebrafish genome. S.C.S. & Schartl, M. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Thank you for visiting nature.com. Genome Res. 44, 714–719 (2012), CAS  Lack of AChE activity causes progressive myopathy of skeletal muscles. HEALTH-F4-2010-242048, ZF-HEALTH). Article  We identified double-conserved synteny (DCS) blocks between all sequenced tetrapods and four fish genomes (zebrafish, medaka, stickleback and Tetraodon). 14, 1–10 (2004), MathSciNet  We mapped 65 insertion sites to the as yet unfinished zebrafish genome sequence. wrote the manuscript and Supplementary Information. This latest assembly has been refined by the addition of nearly 1000 finished clone sequences and the resolution of more than 400 genome issues. Google Scholar, Kettleborough, R. N. W. et al. A paper published last month in Nature unveiled the long-awaited sequence of the zebrafish genome, revealing that zebrafish, mice and human have 12,719 genes in … Consistent with the conservation of synteny, chromosome 16 and chromosome 19 possess clusters of orthologues of genes associated with the mammalian major histocompatibility complex (MHC) as well as the hoxab and hoxaa clusters, respectively, which are each orthologous to the human HOXA cluster25. Similarly, the zebrafish genome has no BRCA1 orthologue, but does have an orthologue of the BRCA1-associated BARD1 gene, which encodes an associated and functionally similar protein and a brca2 gene, which plays an important role in oocyte development, probably reflecting its role in DNA damage repair15. are involved in the ongoing improvement of the zebrafish genome assembly. coordinated by K.H. 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. All resources generated by the ZGC are publicly accessible to the biomedical research community. 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. Black ) less than 30 % Article was published on 11 December 2013 using morphological secondary sexual traits, were! For the study of vertebrate protein-coding genes characterization of a large collection of mutations1,2 more details G.K.L.,,. 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