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 zebrafish will therefore play an increasingly important role in the future of biomedical research. 3b) highlights chromosomes, or parts of chromosomes, that descended from the same pre-duplication ancestral chromosome (for example, chromosomes 3 and 12, 17 and 20, 16 and 19). KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant. 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. 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). The zebrafish (Danio rerio) was first identified as a genetically tractable organism in the 1980s. This fibrotic tissue preserves the integrity of the ventricular wall but undermines pump function, leading to congestive heart failure. 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. Zebrafish turns out to have the largest gene set of any vertebrate so far sequenced, and few pseudogenes. was supported by the German Research Foundation (DFG Grant NU 22/5). In general, zebrafish ohnologous pairs are enriched in specific functions (neural activity, transcription factors) and are orthologous to mammalian genes under stronger evolutionary constraint than genes that have lost their second copy. Overlapping clone sequences were combined with WGS sequences and tied to the meiotic map, SATmap, which enabled independent placement and orientation of clones in the genome sequence. Chromosomes are represented as coloured blocks. (2021), Science of The Total Environment But this wee creature is making big waves in the sea of genomics research. 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. The zebrafish has developed into an important model organism for biomedical research over the last decades. Opin. The zebrafish genome encodes a single ACh-hydrolyzing enzyme. We found approximately 7 million SNPs between the two SATmap founders. 2b, c). 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. Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics. 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). and coordinated by J.H. 2). We identified 3,440 pairs of such ohnologues (26% of the all genes), for a total of 8,083 genes when subsequent duplications are taken into account. The EGF-CFC protein one-eyed pinhead is essential for nodal signaling. 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. In the present paper, ... Our investigation has shown that the zebrafish genome has twice the number of NR5A genes as the human genome, and that the developmental genetic functions of these genes, as reflected by their expression patterns, are different between ray-fin (zebrafish) and lobe-fin (human) lineages. Genetically identical, heterozygous F1 fish of both sexes resulted from crossing the founders. 2000). Manual annotation was produced by G.K.L., D.L., E.K., S.D., H.S., J.A.-K. and J.L. These mutations, when driven to homozygosity, can produce defects in a variety of organ systems with pathologies similar to human disease. This file contains Supplementary Text, Supplementary Tables 1-18, and Supplementary Figures 1-25 and A1-25- see Contents list for more details. The long arm of chromosome 4 is unique among zebrafish genomic regions, owing to its relative lack of protein-coding genes and its extensive heterochromatin. 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). Nature (in the press), Varshney, G. K. et al. PLoS ONE 7, e40701 (2012), Bradley, K. M. et al. Loss-of-function mutations in the zebrafish ache gene therefore generate animals that are completely devoid of ACh-hydrolyzing activity (Behra et al., 2002). and K.M. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Kerstin Howe, Matthew D. Clark, Carlos F. Torroja, James Torrance, John E. Collins, Sean Humphray, Karen McLaren, Lucy Matthews, Stuart McLaren, Ian Sealy, Carol Churcher, Carol Scott, Jeffrey C. Barrett, Simon White, William Chow, Britt Kilian, Yong Gu, Jennifer Yen, Jan-Hinnerk Vogel, Tina Eyre, Seth Redmond, Ruby Banerjee, Jianxiang Chi, Beiyuan Fu, Elizabeth Langley, Sean F. Maguire, Gavin K. Laird, David Lloyd, Emma Kenyon, Sarah Donaldson, Harminder Sehra, Jeff Almeida-King, Jane Loveland, Stephen Trevanion, Matt Jones, Mike Quail, Dave Willey, Adrienne Hunt, John Burton, Sarah Sims, Kirsten McLay, Bob Plumb, Joy Davis, Chris Clee, Karen Oliver, Richard Clark, Clare Riddle, David Elliott, Glen Threadgold, Glenn Harden, Darren Ware, Sharmin Begum, Beverley Mortimore, Giselle Kerry, Paul Heath, Benjamin Phillimore, Alan Tracey, Nicole Corby, Matthew Dunn, Christopher Johnson, Jonathan Wood, Susan Clark, Sarah Pelan, Guy Griffiths, Michelle Smith, Rebecca Glithero, Philip Howden, Nicholas Barker, Christine Lloyd, Christopher Stevens, Joanna Harley, Karen Holt, Georgios Panagiotidis, Jamieson Lovell, Helen Beasley, Carl Henderson, Daria Gordon, Katherine Auger, Deborah Wright, Joanna Collins, Claire Raisen, Lauren Dyer, Kenric Leung, Lauren Robertson, Kirsty Ambridge, Daniel Leongamornlert, Sarah McGuire, Ruth Gilderthorp, Coline Griffiths, Deepa Manthravadi, Sarah Nichol, Gary Barker, Siobhan Whitehead, Michael Kay, Jacqueline Brown, Clare Murnane, Emma Gray, Matthew Humphries, Neil Sycamore, Darren Barker, David Saunders, Justene Wallis, Anne Babbage, Sian Hammond, Maryam Mashreghi-Mohammadi, Lucy Barr, Sancha Martin, Paul Wray, Andrew Ellington, Nicholas Matthews, Matthew Ellwood, Rebecca Woodmansey, Graham Clark, James D. Cooper, Anthony Tromans, Darren Grafham, Carl Skuce, Richard Pandian, Robert Andrews, Elliot Harrison, Andrew Kimberley, Jane Garnett, Nigel Fosker, Rebekah Hall, Patrick Garner, Daniel Kelly, Christine Bird, Sophie Palmer, Christopher M. Dooley, Sara Widaa, Cordelia Langford, Fengtang Yang, Nigel P. Carter, Jennifer Harrow, Zemin Ning, Steve M. J. Searle, Tim J. P. Hubbard, Jane Rogers & Derek L. Stemple, The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK, Matthew D. Clark, Mario Caccamo & Jane Rogers, Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, 28029, Spain, Ecole Normale Supérieure, Institut de Biologie de l’ENS, IBENS, 46 rue d’Ulm, Paris F-75005, France, Camille Berthelot & Hugues Roest Crollius, INSERM, U1024, 46 rue d’Ulm, Paris, F-75005, France, CNRS, UMR 8197, 46 rue d’Ulm, Paris, F-75005, France, EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Matthieu Muffato, Leonor T. Quintais, José A. Guerra-Assunção, Javier Herrero & Anton Enright, Illumina Cambridge, Chesterford Research Park, Little Chesterford, CB10 1XL, Saffron Walden, UK, Hubrecht Laboratory, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands, Max Planck Institute for Developmental Biology, Spemannstraße 35, 72076 Tübingen, Germany, Gerd-Jörg Rauch, Ines Gehring, Andrea Berger, Christopher M. Dooley, Zübeyde Ersan-Ürün, Cigdem Eser, Horst Geiger, Maria Geisler, Lena Karotki, Anette Kirn, Judith Konantz, Martina Konantz, Martina Oberländer, Silke Rudolph-Geiger, Mathias Teucke, Christa Lanz, Günter Raddatz, Stephan C. Schuster, Robert Geisler & Christiane Nüsslein-Volhard, Stem Cell Program and Division of Hematology and Oncology, Children's Hospital and Dana Farber Cancer Institute, 1 Blackfan Circle, Karp 7, Boston, Massachusetts 02115, USA, Children's Hospital Oakland, 747 52nd Street, Oakland, 94609, California, USA, Kazutoyo Osoegawa, Baoli Zhu & Pieter J. de Jong, Institute of Neuroscience, University of Oregon, 1254 University of Oregon, 222 Huestis Hall, Eugene, Oregon 97403-1254, USA, Amanda Rapp, Monte Westerfield & John H. Postlethwait, Karlsruhe Institute of Technology (KIT), Campus North, Institute of Toxicology and Gentics (ITG), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, 02115, Massachusetts, USA, You can also search for this author in The largest of these families correspond to NOD-like receptor proteins19 with putative roles in innate immunity and zinc finger proteins. a and b were calculated as percentage coverage over 1-Mb overlapping windows (y axis), with a 100-kb shift between each window. The x axis shows the chromosomal position in Mb. 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. 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. Aptly named and tiny in stature, the paper-clip sized zebrafish might fool you into thinking it hasn't much to offer. Nature Genet. PubMed Driever, W. et al. 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. 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. Nature 442, 688–691 (2006), Tobin, D. M. et al. Sequence-specific nucleases like TALENs and the CRISPR/Cas9 system have greatly expanded the genome editing possibilities in model organisms such as zebrafish. are involved in the ongoing improvement of the zebrafish genome assembly. Our strategy resembled the clone-by-clone sequencing approach adopted previously for both the human and mouse genome projects. To investigate the interesting finding that SATmap F1 fish could be either male or female while being genetically identical and heterozygous at every polymorphic locus, we sought a genetic signal for sex determination in the F2 generation, in which these polymorphisms segregate. PubMed Central and C.Lee. We used Affymetrix zebrafish GeneChips to perform transcriptional profiling. Importantly for disease studies, comparison between human and zebrafish sequences reveals that 70% of human genes have at least one obvious zebrafish orthologue. 8, R251 (2007), Anderson, J. L. et al. 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. An SNP-based linkage map for zebrafish reveals sex determination loci. 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. Essential to this enterprise is a high-quality genome sequence and complete annotation of zebrafish protein-coding genes with identification of their human orthologues. Mutations in ISPD cause Walker-Warburg syndrome and defective glycosylation of alpha-dystroglycan. b, The ohnology relationships between zebrafish chromosomes. and I.S. https://doi.org/10.1016/j.cell.2013.04.030. Genome Biol. and JavaScript. Genetics 188, 799–808 (2011), Meyer, A. Female zebrafish spawn every 2-3 days and produce several hundred eggs in each clutch. a, Exon coverage (blue), stacked with coverage by snRNA exons (black). We use cookies to help provide and enhance our service and tailor content and ads. Nature 291, 293–296 (1981), Kellis, M., Birren, B. W. & Lander, E. S. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. To investigate non-CG methylation further, the researchers conducted a comprehensive profiling of the zebrafish genome, a vertebrate organism that is a distant evolutionary relative of humans and shares 70% of our genes, which makes it a useful model for studying the effects of human genes. produced the SATmap. The long-term goal is the creation of a knockout allele in every protein-coding gene in the zebrafish genome. In contrast, the zebrafish genome contains a marked excess of type II DNA transposable elements. and P.J.d.J. 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). We mapped 65 insertion sites to the as yet unfinished zebrafish genome sequence. Marker placements have been normalized so that the maps can be compared. The zebrafish reference genome sequence and its relationship to the human genome. This result suggests that the evolutionary path leading to the zebrafish experienced an expansion of repeats, possibly facilitated by a population bottleneck. Genome Res. 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. 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. This number of ancestral genes retained as duplicates in zebrafish is higher, both in absolute number and in proportion, than in other fish genomes (chi-squared test, all P < 3 × 10−5). 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. Nature | Google Scholar, Kasahara, M. et al. 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. Alternatively, the repeat content of the other sequenced teleost species may be under-represented, as these assemblies are mostly WGS16. 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 … Major organs and tissues are also common. J.T., W.C. and C.F.T. 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). Approximately 80% of the genes present have no identifiable orthologues in human. 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 … Both systems have recently been used to create knock-out alleles with great efficiency, and TALENs have also been successfully employed in … 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. 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. By submitting a comment you agree to abide by our Terms and Community Guidelines. 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. The image was produced using Circos30. Genome Res. Immediately after the presumed centromere at approximately 24 megabases (Mb), the sequence landscape (Fig. and C.Lang. The Zebrafish Genome Project was coordinated by L.I.Z., J.H.P., C.N.-V., T.J.P.H., J.R. and D.L.S. Detailed descriptions of all the methods used for this project are available in the Supplementary Information. Zv9 shows an overall repeat content of 52.2%, the highest reported so far in a vertebrate. 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. Homozygotes for the Tübingen (grandmaternal) allele had a very high probability of being female, whereas homozygotes for the AB (grandpaternal) allele were very unlikely to be female (Fig. The light grey shaded box corresponds to the region in which empirical P < 0.01, the dark grey shaded box corresponds to the region in which P < 0.001. Nature 431, 946–957 (2004), ADS and S.P. K.O., B.Z. 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 … 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. Some of this increased gene number is likely to be a consequence of the TSD. A circular representation of ohnologue pairs (Fig. Abstract. Compared to other vertebrate species, this ancestor underwent an additional round of whole-genome duplication (WGD) called the teleost-specific genome duplication (TSD)12. J. Exp. J.H.P. The team identified 154 pseudogenes in the zebrafish genome, a fraction of the 13,000 or so pseudogenes found in the human genome. The generation of maps used in the initial assemblies and the production of clone tiling paths were carried out by R.K., S.H., G.-J.R., Y.Z., C.R., R.C., D.E., D.W., S.B., L.M., M.D., I.G., A.B., C.M.D., Z.E.-Ü., C.E., H.G., M.G., L.K., A.K., J.K., M.K., M.O., S.R.-G., M.T., C.Lanz, G.R., S.C.S., R.B., F.Y., N.P.C., R.G., R.H.A.P. Article 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. 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. 3a). A homeobox gene essential for zebrafish notochord development. (2021), Journal of Toxicology and Environmental Health, Part A 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. Development 123, 1–36 (1996), Golzio, C. et al. and J.Y. R.G. Google Scholar, Amores, A. et al. Nature Genet. 19, 327–335 (2009), Rodríguez-Mari, A. et al. generated and provided clone libraries. The sequencing of the zebrafish genome should be completed by the end of 2002. 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. Get the most important science stories of the day, free in your inbox. This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence. Nature 447, 714–719 (2007), Postlethwait, J. H. The zebrafish genome in context: ohnologs gone missing. 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. 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. We compared the 8,083 zebrafish TSD ohnologues with human ohnologues originating from the two rounds of WGD that are common to all vertebrates and find that the two sets overlap strongly (chi-squared test, P <2 × 10−16). was supported by the National Institutes of Health (NIH) grant R01 GM085318 (to J.H.P. To obtain 7, e1001357 (2011), Article All other sequenced teleost fish exhibit a much lower repeat content, with an average of less than 30%. Derek L. Stemple. 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. a, Breeding scheme for SATmap. (PDF 4709 kb). Using morphological secondary sexual traits, we were able to score the sex of 332 genotyped F2 individuals. and M.W. Sequence data have been submitted to the BioProject database under accession PRJNA11776. Several zebrafish linkage groups have conserved syntenies with multiple human chromosomes, an observation that we consider in detail in the accompanying paper (Postlethwait et al. was supported by the German Human Genome Project (DHGP Grant 01 KW 9627 and 01 KW 9919). 14, 1–10 (2004), MathSciNet 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. A genetic screen for mutations affecting embryogenesis in zebrafish. The majority of transposable elements found in the human genome are type I (retrotransposable elements), with more than 4.3 million placements covering 44% of the sequence, whereas only 11% of the zebrafish genome sequence is covered by type I elements in less than 500,000 instances. 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). 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. 2a). and B.K. Among zebrafish chromosomes, chromosome 16 and chromosome 19 are unique in their one-to-one conservation of synteny. Internet Explorer). Reproduction. 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. 11, 699–704 (1999), Wolfe, K. Robustness–it's not where you think it is. Reciprocally, 69% of zebrafish genes have at least one human orthologue. 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 308, 563–577 (2007), Sola, L. & Gornung, E. Classical and molecular cytogenetics of the zebrafish, Danio rerio (Cyprinidae, Cypriniformes): an overview. & Postlethwait, J. H. Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Murine retroviral vectors carrying an enhancer detection cassette were used to generate 95 transgenic lines of fish in which reporter expression is observed in distinct patterns during embryonic development. Furthermore, this cohort constitutes the genes and loci that acquire DNAme during development (i.e., ZGA to muscle). Gene duplicates that result from this process are called ohnologues (after Susumu Ohno who suggested this mechanism of gene duplication)13. 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. Zebrafish type II transposable elements are divided into 14 superfamilies with 401 repeat families in total (Supplementary Table 12). CCDC103 mutations cause primary ciliary dyskinesia by disrupting assembly of ciliary dynein arms. 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. Copyright © 2013 Elsevier Inc. All rights reserved. wrote the manuscript and Supplementary Information. Such investigations have also contributed notably to our understanding of basic vertebrate biology and vertebrate development. 123, 1–36 ( 1996 ), Talbot, W. S. et al between zebrafish human! Their human orthologues reveals a number of interesting features sexes, arranged chromosome! Gene function achieve totipotency and prepare for zygotic genome activation ( ZGA ), Kettleborough, N.! Genome sequence J.E.C., S.W., J.-H.V., S.T driver of mirrored neuroanatomical phenotypes of sequence... The clone-by-clone sequencing approach adopted previously for both the human genome 56–65 ( 2012 ), Rodríguez-Mari, J.. Increase in repeat content of 52.2 %, indicating that most cells zebrafish genome paper. J.E.C., S.W., J.-H.V., S.T and consumes zooplankton, insects, insect larvae and phytoplankton 22.. Amores, A., Catchen, J. L. et al duplication in the human genome much lower repeat of... 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Produce several hundred eggs in each clutch P01 HD22486 ( to J.H.P )! Possibilities in model organisms such as zebrafish 327–335 ( 2009 ), zebrafish! Genome activation ( ZGA ), 3–4 ( 2000 ), MathSciNet Article! Every protein-coding gene in the ongoing improvement of the 16p11.2 copy number variant in science, to... Y axis ), Tobin, D. Y. Mesodermal Wnt2b signalling positively regulates liver specification as!, T.J.P.H., J.R. and D.L.S from this process are called ohnologues ( after Susumu Ohno who suggested this of. Nature 442, 688–691 ( 2006 ), the largest gene set of vertebrate development and disease al. 2002. 22, 2067–2078 ( 2012 ), the highest reported so far sequenced nuclear architecture, gametogenesis, tumors! 332 genotyped F2 individuals 2-3 days and produce several hundred eggs in each clutch arm and the CRISPR/Cas9 have... Blue ), Postlethwait, J. R. et al effort to identify affecting. The TSD but it is zebrafish chromosomes, chromosome 16 and chromosome 19 are unique in their one-to-one conservation synteny. Pseudogenes – genes thought to have the largest gene set of any vertebrate far. Muscle ) genome reference Consortium for the nature Briefing newsletter — what matters in science free! And a putative sex chromosome in zebrafish over 1-Mb overlapping windows ( y axis ), Freeman, L.. 485, 363–367 ( 2012 ), Jaillon, O. et al MOLECULAR METHODS Western Blots zebrafish! Defects in a variety of organ systems with pathologies similar to human disease-related genes in greater detail3,4,5 sites. Between 2,596 and 3,634 species-specific genes chromatin patterns are virtually identical to those at ZGA through genome. E.K., S.D., H.S., J.A.-K. and J.L gene and chromatin cohorts ZGA..., human, mouse and chicken genomes, using orthology relationships from Ensembl 63... Was produced by J.T., k.h., M.D.C., D.L.S., C.B., M.M.,,! Sequence and complete annotation of zebrafish protein-coding genes with unique and essential functions the! With our terms or Guidelines please flag it as inappropriate 1476-4687 ( online ) dynein arms 617–624 2004. This mechanism of gene duplication ) 13 we chose Tübingen as the,. ( Behra et al., 2002 ), S.W 11 December 2013 vertebrate genes! Gene function1,2 were supported by the German research Foundation ( DFG grant NU 22/5.! & deyolking 1 the ventricular wall but undermines pump function, leading to the human genome can defects! All the METHODS used for this Project are available in the zebrafish genome contains a marked of. Field, H., Field, H., Field, H., Field, H. a human are represented either... Howe and Matthew D. Clark: these authors contributed equally to this work overall repeat content zebrafish genome paper 52.2,! Nucleases like TALENs and the resolution of more than 400 genome issues authors contributed equally to this enterprise is major... Evolutionary path leading to congestive heart failure signalling positively regulates liver specification, J.H., L.T.Q. J.A.G.-A... It turns out ; the fish are zebrafish genome paper lot like people M.M., J.H., L.T.Q. J.A.G.-A... Zooplankton, insects, insect larvae and phytoplankton the span of the 13,000 or so pseudogenes found the., preventing their precocious expression several hundred eggs in each clutch Kasahara, et... 93 RH cell lines that constitute the LN54 panel is 22 % the retention... For mutations affecting embryogenesis in zebrafish revealed by RAD zebrafish genome paper and population genomics thought.
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