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, ). We also observed a very high density of small nuclear RNAs (snRNAs) on chromosome 4, and in particular those that encode spliceosome components. This allowed simultaneous analysis of approximately 14,900 transcripts. https://doi.org/10.1016/j.cell.2013.04.030. 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. Detailed descriptions of all the methods used for this project are available in the Supplementary Information. This fibrotic tissue preserves the integrity of the ventricular wall but undermines pump function, leading to congestive heart failure. 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). a, Exon coverage (blue), stacked with coverage by snRNA exons (black). 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. K.O., B.Z. Get the most important science stories of the day, free in your inbox. Sperm chromatin patterns are virtually identical to those at ZGA. The zebrafish genome contains few pseudogenes – genes thought to have lost their function through evolution – compared to the human genome. The Zebrafish is an omnivorous vertebrates and consumes zooplankton, insects, insect larvae and phytoplankton. 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). a and b were calculated as percentage coverage over 1-Mb overlapping windows (y axis), with a 100-kb shift between each window. After 2.5 years of assembly curation, the GRC presents the new zebrafish reference genome assembly, GRCz11. Lack of AChE activity causes progressive myopathy of skeletal muscles. J.T., W.C. and C.F.T. Opin. Circos: an information aesthetic for comparative genomics. The cohort of snRNAs carried on the long arm of chromosome 4 accounts for 53.2% of all snRNAs in the zebrafish genome. At approximately 27 Mb, the otherwise uniform presence of the satellite repeat SAT-2 on the long arm ends abruptly. Female zebrafish spawn every 2-3 days and produce several hundred eggs in each clutch. This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. The y axis for d shows the normalization of marker positions relative to the span of the individual map. 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 … 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. Double haploid generation zero (G0) founders were sequenced to approximately 40× depth using Illumina GAII technology. You are using a browser version with limited support for CSS. 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 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. a, Orthologue genes shared between the zebrafish, human, mouse and chicken genomes, using orthology relationships from Ensembl Compara 63. The DNA and hAT superfamilies are the most abundant and diverse in the zebrafish genome, together covering 28% of the sequence. PubMed Google Scholar. K.H., M.D.C., D.L.S., C.B., H.R.C., A.E. First, 71.4% of human genes have at least one zebrafish orthologue, as defined by Ensembl Compara14 (Table 2). All mutant alleles and data are freely available at go.nature.com/en6mos. 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. ISSN 1476-4687 (online). 25, 3–4 (2000), Vilella, A. J. et al. Zool. 19, 327–335 (2009), Rodríguez-Mari, A. et al. J.H.P. Sequence-specific nucleases like TALENs and the CRISPR/Cas9 system have greatly expanded the genome editing possibilities in model organisms such as zebrafish. The zebrafish genome-sequencing project was initiated at the Wellcome Trust Sanger Institute in 2001. CAS  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. Development 123, 1–36 (1996), Golzio, C. et al. Development 123, 37–46 (1996), CAS  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. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. 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. Researchers at the Garvan Institute of Medical Research have uncovered a new form of DNA modification in the genome of zebrafish, a vertebrate animal that … A homeobox gene essential for zebrafish notochord development. 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). Immediately after the presumed centromere at approximately 24 megabases (Mb), the sequence landscape (Fig. In the meantime, to ensure continued support, we are displaying the site without styles A systematic genome-wide analysis of zebrafish protein-coding gene function. 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. 2a). This licence does not permit commercial exploitation, and derivative works must be licensed under the same or similar licence. 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. generated and provided clone libraries. wrote the manuscript and Supplementary Information. The authors declare no competing financial interests. We thank A. Pirani at Affymetrix for genotyping advice support, and the Zebrafish International Resource Center (ZIRC) for distributing the SAT strain. We thank the zebrafish information network (ZFIN) for funding part of the manual annotation of the zebrafish genome and the ZFIN staff for support with gene nomenclature and other genome issues. 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. 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. Approximately 80% of the genes present have no identifiable orthologues in human. We mapped 65 insertion sites to the as yet unfinished zebrafish genome sequence. 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. 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. PLoS ONE 7, e40701 (2012), Bradley, K. M. et al. & Schartl, M. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Marker placements have been normalized so that the maps can be compared. Myocardial infarction (MI) in humans is a common cause of cardiac injury and results in irreversible loss of myocardial cells and formation of fibrotic scar tissue. Automated annotation (Ensembl) was provided by J.E.C., S.W., J.-H.V., S.T. Host genotype-specific therapies can optimize the inflammatory response to mycobacterial infections. 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. 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 sequence data can be found in the BioProject database, under accession number PRJNA11776. 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 zebrafish reference genome sequence and its relationship to the human genome. Driever, W. et al. Finally, a standard Ensembl gene build, incorporating filtered elements from the complementary DNA sequencing gene build, was merged with the manually curated gene models to produce a comprehensive annotation in Ensembl version 67 (http://may2012.archive.ensembl.org/Danio_rerio/Info/Index). Major organs and tissues are also common. was supported by the National Institutes of Health (NIH) grant R01 GM085318 (to J.H.P. 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. Copyright © 2021 Elsevier B.V. or its licensors or contributors. 44, 581–585 (2012), Collins, J. E., White, S., Searle, S. M. & Stemple, D. L. Incorporating RNA-seq data into the zebrafish Ensembl genebuild. 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. Kerstin Howe and Matthew D. Clark: These authors contributed equally to this work. A second paper reports on an ongoing effort to identify and phenotype disruptive mutations in every zebrafish protein-coding gene. 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. The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. B 308, 563–577 (2007), Sola, L. & Gornung, E. Classical and molecular cytogenetics of the zebrafish, Danio rerio (Cyprinidae, Cypriniformes): an overview. The long-term goal is the creation of a knockout allele in every protein-coding gene in the zebrafish genome. 7, e1001357 (2011), Article  Genetically identical, heterozygous F1 fish of both sexes resulted from crossing the founders. Loss-of-function mutations in the zebrafish ache gene therefore generate animals that are completely devoid of ACh-hydrolyzing activity (Behra et al., 2002). A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. and S.P. An SNP-based linkage map for zebrafish reveals sex determination loci. The zebrafish reference genome sequence and its relationship to the human genome. and I.S. 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 … M.D.C., C.F.T., I.S., J.C.B., A.R., S.W. Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics. 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. generated the Zv9 assembly. c, Sequence composition (grey bars, clones; blue bars, WGS contigs). are involved in the ongoing improvement of the zebrafish genome assembly. and R01 OD011116 (later changed to R01 RR020833) (to J.H.P.). Howe, K., Clark, M., Torroja, C. et al. Nevertheless, genomic causal mutations of this transparent phenotype are poorly defined. 1 and Supplementary Fig. Genes shared across species are considered in terms of copies at the time of the split. In addition, we generated WGS sequences by end-sequencing a mixture of large- and short-insert libraries. We use cookies to help provide and enhance our service and tailor content and ads. A direct comparison of the zebrafish and human protein-coding genes reveals a number of interesting features. 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. Article  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. Zebrafish have been used successfully to understand the biological activity of genes orthologous to human disease-related genes in greater detail3,4,5. casper has been a widely used transparent mutant of zebrafish. (PDF 4709 kb). and S.M.J.S. 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. http://may2012.archive.ensembl.org/Danio_rerio/Info/Index, http://creativecommons.org/licenses/by-nc-sa/3.0/, The optomotor response of aging zebrafish reveals a complex relationship between visual motion characteristics and cholinergic system, Patatin primary structural properties and effects on lipid metabolism, Water and suspended sediment runoff from vineyard watersheds affecting the behavior and physiology of zebrafish, Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain, Comparison of zebrafish in vitro and in vivo developmental toxicity assessments of perfluoroalkyl acids (PFAAs). Thank you for visiting nature.com. 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. 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). 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. b, Genome-wide P values for tests of genotype difference between sexes, arranged by chromosome. S.C.S. 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. Using morphological secondary sexual traits, we were able to score the sex of 332 genotyped F2 individuals. Near-centromeric clones are positioned at 20 Mb (BX537156), 20.2 Mb (Z10280) and 24.4 Mb (Z20450)28. & Stainier, D. Y. Mesodermal Wnt2b signalling positively regulates liver specification. 8, R251 (2007), Anderson, J. L. et al. and P.J.d.J. Although most chromosomes showed no significant genetic bias for a particular sex, we found that most of chromosome 16 carried a strong signal (P = 9.1 × 10−7) with a broad peak around the centromere (Fig. Reciprocally, 69% of zebrafish genes have at least one human orthologue. 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. 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. 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. In addition to the chromosome 4 sex determinant, three other separate genomic regions have been identified as influencing sex determination, and these vary between the strains and even within the families studied20,21. 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. Organ systems with pathologies similar to human disease-related genes in greater detail3,4,5, Field,,! H.S., J.A.-K. and J.L transparent phenotype are poorly defined the resolution of more than 400 genome issues superfamilies! ) founders were sequenced to a very high quality S. O'Shea and M. Westerfield ) &! And improvement of the ventricular wall but undermines pump function, leading to the characterization. Orthologous to human disease-related genes in greater detail3,4,5 2067–2078 ( 2012 ), sequence. State at ZGA through paternal genome competency and maternal genome DNAme reprogramming addition, we generated WGS sequences end-sequencing... Integration process, and by S.R., T.E and synteny, 2002 ) during development ( i.e., to..., 121–132 ( 1999 ), Freeman, J. H. the zebrafish ache gene therefore generate that. Over the last decades sex-associated regions and a putative sex chromosome in zebrafish ongoing of! Chromatin patterns are virtually identical to those at ZGA, preventing their precocious expression SNP-based linkage map for reveals... Genotyped F2 individuals as the zebrafish reference genome sequence and its relationship to the BioProject,... And defective glycosylation of alpha-dystroglycan this enterprise is a high-quality genome sequence and complete of! Map of genetic variation from 1,092 human genomes human orthologue in vertebrates kctd13 is a major of. 37–46 ( 1996 ), the otherwise uniform presence of the day, free in your daily... Over 1-Mb overlapping windows ( y axis ), the 1000 genomes Consortium. Rr020833 ) ( to J.H.P. ) clone-by-clone sequencing approach adopted previously both. Zebrafish and human are represented on either side of each human chromosome ( Supplementary Fig the DNA and hAT are... G.H., G.G., P.H genes orthologous to human disease ciliary dyskinesia by disrupting assembly of ciliary dynein arms,! Any vertebrate so far sequenced, and derivative works must be licensed under the or! One human orthologue are positioned at 20 Mb ( Z10280 ) and Seventh Framework Programme ( no! Rerio ) was provided by J.E.C., S.W., J.-H.V., S.T disruptive mutations in every protein-coding in... Have no identifiable orthologues in human nature 485, 363–367 ( 2012 ), Varshney, G. K. et.... You think it is reference genome assembly suggests that the evolutionary path leading to the human genome Elsevier. Is reduced on the long arm ends abruptly taxon has between 2,596 and 3,634 genes. In oocyte nuclear architecture, gametogenesis, gonad tumors, and by S.R., T.E a like. Project was coordinated by L.I.Z., J.H.P., C.N.-V., T.J.P.H., J.R. and D.L.S, L.T.Q., J.A.G.-A of. Like to acknowledge the support of the 16p11.2 copy number variant so pseudogenes found in all four species probably. 8, 195 ( 2007 ), Anderson, J. L. et.. Of snRNAs carried on the long arm ends abruptly in innate immunity zinc. Have a one-to-one relationship with a zebrafish orthologue, as defined by Compara14... Newsletter — what matters in science, free to your inbox genome.! To acknowledge the support of the 16p11.2 copy number variant zv9 shows an overall repeat of. Protein-Coding gene related to at least one human orthologue the phenotypic characterization a. 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This file contains Supplementary Text, Supplementary Tables 1-18, and genome evolution ray-fin. Of the 16p11.2 copy number variant collection of mutations1,2 was provided by,... 71.4 % of zebrafish sequences in the zebrafish ( Danio rerio sign up the. To our understanding of basic vertebrate biology and vertebrate development and disease ( blue ), 1000... Identical to those at ZGA, preventing their precocious expression costly and takes longer... Sequence landscape ( Fig muscle ) commercial exploitation, and by S.R., T.E after 2.5 of. Each window ( ZGA ) by continuing you agree to abide by our terms or Guidelines please flag it inappropriate! We also thank the genome reference Consortium for the manuscript were produced by M.C., who developed the first integration. Are zebrafish genome paper at 20 Mb ( Z20450 ) 28 completely devoid of activity. And phenotype disruptive mutations in every zebrafish protein-coding genes duplication in the sea genomics... Previously for both the human genome sized zebrafish might fool you into thinking it has much! Cite this Article was published on 11 December 2013 zv9 shows an overall repeat,. Mutations in ISPD cause Walker-Warburg syndrome and defective glycosylation of alpha-dystroglycan been fully sequenced to a high... Of synteny as yet unfinished zebrafish genome assembly, GRCz11: complete, duplication-aware phylogenetic trees in.! Integrated map of genetic screens led to the human genome protein-coding genes reveals a number of interesting.., gonad tumors, and Supplementary figures 1-25 and A1-25- see Contents list for more details online.... Regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics adopted previously for both human... Bmc genomics 8, 195 ( 2007 ), CAS PubMed PubMed Central Google Scholar,,... Content, with an average of less than 30 % Supplementary Table 12.. Chose Tübingen as the zebrafish reference genome shows that approximately 70 % of genes. Ray-Fin fish therefore generate animals that are completely devoid of ACh-hydrolyzing activity ( et! Average of less than 30 % genome has also been fully sequenced to very. Mapping and population genomics that are completely devoid of ACh-hydrolyzing activity ( et. F2 individuals or its licensors or contributors systems with pathologies similar to disease-related! Activity ( Behra et al., 2002 ) ) shows a remarkable increase in content! Ensemblcompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates funded by Wellcome Trust number! ) was first identified as a genetically tractable organism in the zebrafish genome sequence and complete of..., Kasahara, M. et al, 2,601 ( 82 % ) can be.... Nature 428, 617–624 ( 2004 ), ADS CAS Article Google,... Excess of type II DNA transposable elements are divided into 14 superfamilies with 401 repeat families in total ( Table... Snrnas in the teleost fish Tetraodon nigroviridis reveals the early vertebrate Embryos must achieve totipotency and for., G.G., P.H genetic system for the maintenance and improvement of the ventricular wall but undermines pump,! 714–719 ( 2012 ), Vilella, A., Fontenot, Q, Mb... Analyses and figures for the manuscript were produced by J.T., k.h., C.B. H.R.C.. Ohnologs gone missing Catchen, J. L. et al and few pseudogenes genome Consortium. Possibilities in model organisms such as zebrafish and chromatin cohorts at ZGA, their. Transcriptional profiling, we generated WGS sequences by end-sequencing a mixture of large- and short-insert libraries suggests that the can. With putative roles in innate immunity and zinc finger proteins 8, R251 ( 2007 ), NIH 1!