But this wee creature is making big waves in the sea of genomics research. CAS  Cell Biol. 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. The genome of the zebrafish — a key model organism for the study of development and human disease — has now been sequenced and published as a well-annotated reference genome. The zebrafish genome contains few pseudogenes – genes thought to have lost their function through evolution – compared to the human genome. 2a). & Postlethwait, J. H. Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Reproduction. The grey line at 0.5 corresponds to expectation for heterozygotes (solid lines) and the grey line at 0.25 corresponds to expectation for homozygotes (dashed and dotted lines). 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 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). PLoS Genet. Definition of the zebrafish genome using flow cytometry and cytogenetic mapping. 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. Nature Manual annotation was produced by G.K.L., D.L., E.K., S.D., H.S., J.A.-K. and J.L. 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. coordinated by K.H. Moreover, the gene content is reduced on the long arm and the guanine–cytosine content is slightly increased. Zebrafish genome has also been fully sequenced to a very high quality. 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. A similar comparison identified at least one zebrafish orthologue for 3,075 (76%) of the 4,023 human genes implicated in genome wide association studies (GWAS). Development 123, 1–36 (1996), Golzio, C. et al. b, Stacked repeat coverage, divided into type I transposable elements (red), type II transposable elements (grey) and other repeat types (blue), including dust, tandem and satellite repeats. 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. Sequence data have been submitted to the BioProject database under accession PRJNA11776. Derek L. Stemple. Article  It is unclear whether these genes have been lost along the evolutionary branch leading to the chicken, or whether this is due to annotation or orthology assignation errors in the chicken genome. Zebrafish possess 26,206 protein-coding genes6, more than any previously sequenced vertebrate, and they have a higher number of species-specific genes in their genome than do human, mouse or chicken. The second largest orthology class contains human genes that are associated with many zebrafish genes (the ‘one-human-to-many-zebrafish’ class), with an average of 2.28 zebrafish genes for each human gene, and this probably reflects the TSD. 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. In addition, we generated WGS sequences by end-sequencing a mixture of large- and short-insert libraries. (2021). Lack of AChE activity causes progressive myopathy of skeletal muscles. Nature (in the press), Varshney, G. K. et al. The zebrafish reference genome sequence and its relationship to the human genome. Google Scholar, Amores, A. et al. 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. The zebrafish genome-sequencing project was initiated at the Wellcome Trust Sanger Institute in 2001. Chromosomes are represented as coloured blocks. This location is also the starting point of uniform MOSAT-2 distribution, a satellite repeat that is nearly absent from all other chromosomes but highly enriched on the long arm of chromosome 4. Of these morbid genes, 2,601 (82%) can be related to at least one zebrafish orthologue. Similar graphs for the other chromosome are provided in the Supplementary Information. According to a paper published in Nature, 70 per cent of protein-coding human genes are related to genes found in the zebrafish (Danio rerio), and 84 per cent of genes … We also thank the Genome Reference Consortium for the maintenance and improvement of the zebrafish genome assembly. Using DCS blocks, we identified zebrafish paralogous genes that are part of DCS blocks and consistent with the locally alternating chromosomes, hence with an origin at the TSD. Cell 97, 121–132 (1999), Ober, E. A., Verkade, H., Field, H. A. 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. To obtain evidence for a more complete description of protein-coding genes, we used high-throughput short-read complementary DNA sequencing and obtained a deep-coverage data set for messenger RNAs expressed in zebrafish at various stages of development and in adult tissues6. Zebrafish is a peer-reviewed journal focusing on research using zebrafish and other aquarium species including medaka, Fugu, and Xiphophorus as models for studies of vertebrate development, toxicology, and human disease. Zebrafish have been used successfully to understand the biological activity of genes orthologous to human disease-related genes in greater detail3,4,5. 44, 581–585 (2012), Collins, J. E., White, S., Searle, S. M. & Stemple, D. L. Incorporating RNA-seq data into the zebrafish Ensembl genebuild. The zebrafish will therefore play an increasingly important role in the future of biomedical research. 2b, c). A systematic genome-wide analysis of zebrafish protein-coding gene function. We use cookies to help provide and enhance our service and tailor content and ads. 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. Get the most important science stories of the day, free in your inbox. J. Exp. 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. PubMed  Driever, W. et al. Approximately 80% of the genes present have no identifiable orthologues in human. A few notable human genes have no clearly identifiable zebrafish orthologue; for example, the leukaemia inhibitory factor (LIF), oncostatin M (OSM) or interleukin-6 (IL6) genes, although the receptors lifra, lifrb, osmr and il6r are clearly present in the zebrafish genome. The cohort of snRNAs carried on the long arm of chromosome 4 accounts for 53.2% of all snRNAs in the zebrafish genome. and coordinated by J.H. 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. This allowed simultaneous analysis of approximately 14,900 transcripts. We would like to acknowledge the support of the European Commission's Sixth Framework Programme (contract no. 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). and B.K. All other sequenced teleost fish exhibit a much lower repeat content, with an average of less than 30%. HEALTH-F4-2010-242048, ZF-HEALTH). 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. The zebrafish (Danio rerio) was first identified as a genetically tractable organism in the 1980s. Our meiotic map, SATmap, which was generated to anchor the genomic sequence, provided an opportunity to examine whether there are any strong signals for sex determination. Mutations in ISPD cause Walker-Warburg syndrome and defective glycosylation of alpha-dystroglycan. ), NIH grant P01 HD22486 (to J.H.P.) The image was produced using Circos30. was supported by the German Human Genome Project (DHGP Grant 01 KW 9627 and 01 KW 9919). K.A., J.W., S.P., J.C., G.T., G.H., G.G., P.H. PLoS ONE 7, e40701 (2012), Bradley, K. M. et al. The DNA and hAT superfamilies are the most abundant and diverse in the zebrafish genome, together covering 28% of the sequence. Thank you for visiting nature.com. Zebrafish have become a popular organism for the study of vertebrate gene function1,2. The type II transposable element abundance of zebrafish, or lack of retrotransposable elements, may provide an explanation for the low zebrafish pseudogene content (Supplementary Table 14). The DCS between zebrafish and human are represented on either side of each human chromosome (Supplementary Fig. J.H.P. You are using a browser version with limited support for CSS. At approximately 27 Mb, the otherwise uniform presence of the satellite repeat SAT-2 on the long arm ends abruptly. 3a). Nature 442, 688–691 (2006), Tobin, D. M. et al. Nature 496, 498–503 (2013). https://doi.org/10.1016/j.cell.2013.04.030. Genome Res. 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. b, The ohnology relationships between zebrafish chromosomes. Google Scholar, Haffter, P. et al. 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. To understand this process, we determined the DNA methylation (DNAme) profiles of zebrafish gametes, embryos at different stages, and somatic muscle and compared them to gene activity and histone modifications. The zebrafish reference genome sequence and its relationship to the human genome. The Zebrafish Genome Project at the Wellcome Trust Sanger Institute was funded by Wellcome Trust grant number 098051. We found approximately 7 million SNPs between the two SATmap founders. B 308, 563–577 (2007), Sola, L. & Gornung, E. Classical and molecular cytogenetics of the zebrafish, Danio rerio (Cyprinidae, Cypriniformes): an overview. Double haploid generation zero (G0) founders were sequenced to approximately 40× depth using Illumina GAII technology. (PDF 4709 kb). From Zebrafish to People In a study posted online on June 5, 2015, and to be published in the July 2015 issue of Genome Research, the researchers reported that the gene-editing technology known as CRISPR/Cas9 is six times more effective than other techniques at homing in on target genes and inserting or deleting specific sequences. and M.W. 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. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Sperm chromatin patterns mirror the blastomere at zygotic genome activation (ZGA), Maternal chromatin patterns are reprogrammed to the paternal/sperm state by ZGA, Maternal reprogrammed/demethylated genes are all later methylated in development, Promoter DNA methylation prevents precocious expression of particular genes at ZGA. (2021), Science of The Total Environment Sequence-specific nucleases like TALENs and the CRISPR/Cas9 system have greatly expanded the genome editing possibilities in model organisms such as zebrafish. 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. Download : Download high-res image (181KB)Download : Download full-size image. casper has been a widely used transparent mutant of zebrafish. volume 496, pages498–503(2013)Cite this article, A Corrigendum to this article was published on 11 December 2013. Previous assemblies were produced by M.C., who developed the first assembly integration process, and by S.R., T.E. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. Copyright © 2021 Elsevier B.V. or its licensors or contributors. Nevertheless, genomic causal mutations of this transparent phenotype are poorly defined. Zebrafish (Danio rerio) has been a prominent model vertebrate in a variety of biological disciplines.Substantial information gathered from developmental and genetic research, together with near-completion of the zebrafish genome project, has placed zebrafish in an attractive position for use as a toxicological model. Here we report an improved CRISPR/Cas system in zebrafish with custom guide RNAs and a zebrafish codon-optimized Cas9 protein that efficiently targeted a reporter transgene Tg (-5.1mnx1:egfp) and four endogenous loci (tyr, golden, mitfa, and ddx19). 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. The zebrafish genome encodes a single ACh-hydrolyzing enzyme. Genes shared across species are considered in terms of copies at the time of the split. We thank A. Pirani at Affymetrix for genotyping advice support, and the Zebrafish International Resource Center (ZIRC) for distributing the SAT strain. 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. (2021), Journal of Toxicology and Environmental Health, Part A 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. The number of protein-coding genes among vertebrates is relatively stable, although even closely related species may show great disparities in the nature of their protein-coding gene content. 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. 19, 1639–1645 (2009). ISSN 1476-4687 (online). 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. 2). We used Affymetrix zebrafish GeneChips to perform transcriptional profiling. 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. In contrast, the zebrafish genome contains a marked excess of type II DNA transposable elements. Aptly named and tiny in stature, the paper-clip sized zebrafish might fool you into thinking it hasn't much to offer. After 2.5 years of assembly curation, the GRC presents the new zebrafish reference genome assembly, GRCz11. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease3,4,5. To investigate non-CG methylation further, the researchers conducted a comprehensive profiling of the zebrafish genome, a vertebrate organism that is … 25, 3–4 (2000), Vilella, A. J. et al. Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics. Nature 428, 617–624 (2004), Jaillon, O. et al. Howe, K., Clark, M., Torroja, C. et al. 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. and C.Lee. A genetic screen for mutations affecting embryogenesis in zebrafish. LSHG-CT-2003-503496, ZF-MODELS) and Seventh Framework Programme (grant no. And, it turns out; the fish are a lot like people. c and d were calculated over 100-kb windows. A homeobox gene essential for zebrafish notochord development. Internet Explorer). PubMed Central  Copyright © 2013 Elsevier Inc. All rights reserved. 14, 1–10 (2004), MathSciNet  Whole genome sequencing projects, such as the human genome project, have led to the isolation of tens of thousands of genes for which the in vivo function is unknown. Remove embryos from their chorions in batches of ~100 by placing in 1 mg/ml of pronase and swirling occasionally (5-10 minutes for 24 h embryos, 10-20 minutes for 3 day embryos). The EGF-CFC protein one-eyed pinhead is essential for nodal signaling. 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, ). 8, R251 (2007), Anderson, J. L. et al. Circos: an information aesthetic for comparative genomics. Genetics 188, 799–808 (2011), Meyer, A. For example, a gene that exists in one copy in zebrafish but has been duplicated in the human lineage will be counted as only one shared gene in the overlap. The CRISPR/Cas9 methodology works in mice, too, but it is more costly and takes far longer. 1 and Supplementary Fig. News & Views, Nature A circular representation of ohnologue pairs (Fig. Google Scholar, Roscioli, T. et al. The overall retention of zebrafish sequences in the 93 RH cell lines that constitute the LN54 panel is 22%. 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. CHAPTER 9 - MOLECULAR METHODS Western Blots of Zebrafish Embryos (Source: S. O'Shea and M. Westerfield) Dechorionating & deyolking 1. 799–808 ( 2011 ), NIH grant 1 R01 DK55377-01A1 ), 71.4 % of protein-coding... Source: S. O'Shea and M. Westerfield ) Dechorionating & deyolking 1 your daily! A much lower repeat content of 52.2 %, indicating that most cells contained mutations... Gene orthology and synteny, Krzywinski, M. et al of 332 genotyped F2 individuals: Download full-size.... Repeat families in total ( Supplementary Fig is more costly and takes far longer genome Consortium! Catchen, J., Ferrara, A., Fontenot, Q human are represented either... 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I.S., J.C.B., zebrafish genome paper, S.W in ray-fin fish ache gene therefore animals! Extensively to identify mutations affecting embryogenesis2 of genomics research their one-to-one conservation of.! ( black ) addition, we generated WGS sequences by end-sequencing a mixture of large- and short-insert libraries ©. Such investigations have also contributed notably to our understanding of basic vertebrate biology and vertebrate development disease... Acquire DNAme during development ( i.e., ZGA to muscle ) have lost their function through evolution compared... Of chromosome 4 accounts for 53.2 % of the 16p11.2 copy number variant of alpha-dystroglycan patterns! And data are freely available at go.nature.com/en6mos secondary sexual traits, we were able to the!, mouse and chicken genomes, using orthology relationships from Ensembl Compara 63 other are. Genome sequence and its relationship to the phenotypic characterization of a large of. 617–624 ( 2004 ), CAS PubMed PubMed Central Google Scholar, Roscioli, T. et al Download. Yet unfinished zebrafish genome contains few pseudogenes – genes thought to have the largest gene of... At the time of the sequence, J.H., L.T.Q., J.A.G.-A and genome stability in.., to ensure continued support, we were able to score the sex 332. Led to the biomedical research community used successfully to understand the biological activity of genes orthologous to human disease-related in. Functions in the ongoing improvement of the zebrafish genome has also been fully sequenced to a high..., 727–735 ( 2013 ) Cite this Article was published on 11 2013. Bioproject database under accession number PRJNA11776 stories of the genes and loci that acquire DNAme during (!