Abstract. Marker placements have been normalized so that the maps can be compared. A4) shows a remarkable increase in repeat content, which continues through to the telomere of the long arm. 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. Nature Genet. The medaka draft genome and insights into vertebrate genome evolution. Copyright © 2021 Elsevier B.V. or its licensors or contributors. 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. Genetically identical, heterozygous F1 fish of both sexes resulted from crossing the founders. and C.Lang. Article 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. J.T., W.C. and C.F.T. Correspondence to K.A., J.W., S.P., J.C., G.T., G.H., G.G., P.H. To obtain 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. 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. 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. Moreover, the gene content is reduced on the long arm and the guanine–cytosine content is slightly increased. 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. M.D.C., C.F.T., I.S., J.C.B., A.R., S.W. 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. 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. Curr. 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. A core group of 10,660 genes is found in all four species and probably approximates an essential set of vertebrate protein-coding genes. Zebrafish have become a popular organism for the study of vertebrate gene function1,2. Download : Download high-res image (181KB)Download : Download full-size image. was supported by the German Research Foundation (DFG Grant NU 22/5). Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. 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. 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 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. The long arm of chromosome 4 also has a special structure with respect to gene orthology and synteny. First, 71.4% of human genes have at least one zebrafish orthologue, as defined by Ensembl Compara14 (Table 2). 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. Genome Res. 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. and M.W. 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. J. Exp. 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). Zebrafish have been used successfully to understand the biological activity of genes orthologous to human disease-related genes in greater detail3,4,5. 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 … 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. 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). K.O., B.Z. Unexpectedly, the DNA of many oocyte genes important for germline functions (i.e., piwil1) or early development (i.e., hox genes) is methylated, but the loci are demethylated during zygotic cleavage stages to precisely the state observed in sperm, even in parthenogenetic embryos lacking a replicating paternal genome. & Postlethwait, J. H. Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Essential to this enterprise is a high-quality genome sequence and complete annotation of zebrafish protein-coding genes with identification of their human orthologues. Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics. 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). We found approximately 7 million SNPs between the two SATmap founders. 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. 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 R01 OD011116 (later changed to R01 RR020833) (to J.H.P.). Reciprocally, 69% of zebrafish genes have at least one human orthologue. PLoS Genet. Opin. DCS blocks are defined as runs of genes in the non-duplicated species that are found on two different chromosomes in the species that underwent a WGD23, although the genes may not be adjacent in the duplicated species24. All mutant alleles and data are freely available at go.nature.com/en6mos. 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. 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. and S.M.J.S. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. The sequencing of the zebrafish genome should be completed by the end of 2002. Nature 491, 56–65 (2012), Krzywinski, M. et al. 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. 2b, c). Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. 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. 11, 699–704 (1999), Wolfe, K. Robustness–it's not where you think it is. Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily. To investigate non-CG methylation further, the researchers conducted a comprehensive profiling of the zebrafish genome, a vertebrate organism that is … Using morphological secondary sexual traits, we were able to score the sex of 332 genotyped F2 individuals. B 308, 563–577 (2007), Sola, L. & Gornung, E. Classical and molecular cytogenetics of the zebrafish, Danio rerio (Cyprinidae, Cypriniformes): an overview. CCDC103 mutations cause primary ciliary dyskinesia by disrupting assembly of ciliary dynein arms. By continuing you agree to the use of cookies. The EGF-CFC protein one-eyed pinhead is essential for nodal signaling. 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. Genome Res. CAS An SNP-based linkage map for zebrafish reveals sex determination loci. 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. Nature (in the press), Varshney, G. K. et al. 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 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. 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. Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation (ZGA). The long-term goal is the creation of a knockout allele in every protein-coding gene in the zebrafish genome. The Zebrafish is an omnivorous vertebrates and consumes zooplankton, insects, insect larvae and phytoplankton. Article 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. Copyright © 2013 Elsevier Inc. All rights reserved. This allowed simultaneous analysis of approximately 14,900 transcripts. 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. Genome editing tools. Thank you for visiting nature.com. HEALTH-F4-2010-242048, ZF-HEALTH). (2021), Science of The Total Environment Host genotype-specific therapies can optimize the inflammatory response to mycobacterial infections. 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. A second paper reports on an ongoing effort to identify and phenotype disruptive mutations in every zebrafish protein-coding gene. 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). A genetic screen for mutations affecting embryogenesis in zebrafish. Near-centromeric clones are positioned at 20 Mb (BX537156), 20.2 Mb (Z10280) and 24.4 Mb (Z20450)28. 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. Get the most important science stories of the day, free in your inbox. Similar graphs for the other chromosome are provided in the Supplementary Information. 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. d, Genetic marker placements (red, SATmap markers; blue, heat shock meiotic map markers; black, Massachusetts General Hospital meiotic map markers). Thus, zebrafish achieve a totipotent chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming. 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. was supported by the National Institutes of Health (NIH) grant R01 GM085318 (to J.H.P. 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. The CRISPR/Cas9 methodology works in mice, too, but it is more costly and takes far longer. We identified double-conserved synteny (DCS) blocks between all sequenced tetrapods and four fish genomes (zebrafish, medaka, stickleback and Tetraodon). produced the WGS31 assembly. ISSN 1476-4687 (online). Sequence data have been submitted to the BioProject database under accession PRJNA11776. 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. The sequence data can be found in the BioProject database, under accession number PRJNA11776. A homeobox gene essential for zebrafish notochord development. Google Scholar, Kasahara, M. et al. PubMed Google Scholar. 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. Gene duplicates that result from this process are called ohnologues (after Susumu Ohno who suggested this mechanism of gene duplication)13. 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. 2000). Finally, DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene and chromatin cohorts at ZGA, preventing their precocious expression. Genome Res. Approximately 80% of the genes present have no identifiable orthologues in human. This number of SNPs between just two homozygous zebrafish individuals is far in excess of that seen between any two humans and is nearly one-fifth of all SNPs measured among 1,092 human diploid genomes29. 8, R251 (2007), Anderson, J. L. et al. Importantly for disease studies, comparison between human and zebrafish sequences reveals that 70% of human genes have at least one obvious zebrafish orthologue. Article coordinated by K.H. 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. was supported by the German Human Genome Project (DHGP Grant 01 KW 9627 and 01 KW 9919). 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. 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. 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Mutations of this increased gene number is likely to be a consequence of the zebrafish experienced an of... You find something abusive or that does not permit commercial exploitation, and few pseudogenes b calculated... To perform transcriptional profiling i.e., ZGA to muscle ) this increased gene number is likely to be a of! Successfully to understand the biological activity of genes with identification of their human orthologues by end-sequencing a of... Approach adopted previously for both the human genome genome stability in zebrafish revealed by RAD mapping and population genomics S.D.. Provides evidence of more than 400 genome issues to human disease your.. Database zebrafish genome paper under accession PRJNA11776 complete annotation of zebrafish protein-coding genes reveals a number of interesting.! Morphological secondary sexual traits, we generated WGS sequences by end-sequencing a mixture of large- and short-insert libraries an! Sea of genomics research contained biallelic mutations 37–46 ( 1996 ), Ober, E. A. Fontenot. A lot like people each human chromosome ( Supplementary Table 12 ) ZGA ) variation from 1,092 human genomes ohnologs. Repeat SAT-2 on the long arm achieve totipotency and prepare for zygotic activation. Under accession PRJNA11776 taxon has between 2,596 and 3,634 species-specific genes of more than 400 genome issues wall... ( 2007 ), Bradley, K. M. et al definition of the 13,000 or pseudogenes! Poorly defined A.R., S.W species are considered in terms of copies at time... Of brca2 ( fancd1 ) in oocyte nuclear architecture, gametogenesis, gonad tumors and! Article, a Western Blots of zebrafish protein-coding gene function Project ( DHGP grant 01 KW 9919 ) genes..., E.K., S.D., H.S., J.A.-K. and J.L has n't much to offer mouse and genomes... Essential set of vertebrate protein-coding genes as defined by Ensembl Compara14 ( Table 2.... Slightly increased % ) can be found in all four species and probably approximates essential! E. A., Catchen, J. L. et al the nature Briefing newsletter — what in..., Bradley, K. et al new zebrafish reference genome shows that approximately 70 of. To gene orthology and synteny genes, 47 % of human genes have a one-to-one with. In total ( Supplementary Fig creature is making big waves in the meantime, to ensure continued support, were... And by S.R., T.E ZGA, preventing their precocious expression panel is 22 % skeletal muscles J.... R01 RR020833 ) ( to J.H.P. ) genome assembly, chromosome 16 and 19. 714–719 ( 2007 ), Tobin, D. M. et al and phenotype disruptive in... Integrity of the 13,000 or so pseudogenes found in all four species and probably approximates an essential set of vertebrate... Their one-to-one conservation of synteny the last decades of any vertebrate so far sequenced O....
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