Corrigendum: The zebrafish reference genome sequence and its relationship to the human genome

1] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK [2].
Nature (Impact Factor: 42.35). 04/2013; 496(7446). DOI: 10.1038/nature12111
Source: PubMed

ABSTRACT Zebrafish have become a popular organism for the study of vertebrate gene function. 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 disease. 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. 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. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. 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.

Download full-text


Available from: Camille Berthelot, Aug 30, 2015
    • "There are considerable strengths in using the zebrafish model to define mechanisms associated with developmental toxicant exposure and the developmental origins of adult health and disease including ex utero fertilization and embryonic development , rapid embryogenesis, and a relatively short life span. Paired with these biological strengths are the structural and functional homology of the zebrafish CNS to humans and the conserved genetic, molecular, and endocrine pathways making the zebrafish a powerful model to assess the later life alterations caused by an embryonic atrazine exposure (de Esch et al., 2012; Howe et al., 2013). There are a few recent studies that are now utilizing the zebrafish to examine the contributions of toxicant exposure to the DOHaD hypothesis. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Atrazine is an herbicide applied to agricultural crops and is indicated to be an endocrine disruptor. Atrazine is frequently found to contaminate potable water supplies above the maximum contaminant level of 3μg/L as defined by the U. S. Environmental Protection Agency. The developmental origin of adult disease hypothesis suggests that toxicant exposure during development can increase the risk of certain diseases during adulthood. However, the molecular mechanisms underlying disease progression are still unknown. In this study, zebrafish embryos were exposed to 0, 0.3, 3, or 30μg/L atrazine throughout embryogenesis. Larvae were then allowed to mature under normal laboratory conditions with no further chemical treatment until 7 days post fertilization (dpf) or adulthood and neurotransmitter analysis completed. No significant alterations in neurotransmitter levels was observed at 7 dpf or in adult males, but a significant decrease in 5-Hydroxyindoleacetic acid (5-HIAA) and serotonin turnover was seen in adult female brain tissue. Transcriptomic analysis was completed on adult female brain tissue to identify molecular pathways underlying the observed neurological alterations. Altered expression of 1853, 84, and 419 genes in the females exposed to 0.3, 3, or 30μg/L atrazine during embryogenesis were identified, respectively. There was a high level of overlap between the biological processes and molecular pathways in which the altered genes were associated. Moreover, a subset of genes was down regulated throughout the serotonergic pathway. These results provide support of the developmental origins of neurological alterations observed in adult female zebrafish exposed to atrazine during embryogenesis. Copyright © 2015. Published by Elsevier Ireland Ltd.
    Toxicology 04/2015; 333. DOI:10.1016/j.tox.2015.04.016 · 3.75 Impact Factor
  • Source
    • "4.1. Using zebrafish to model human neurobehavioral disorders 82% of human related disease genes are present in the zebrafish genome (Howe et al., 2013). And zebrafish physiology is very similar to ours (Bakkers, 2011; Gestri et al., 2012). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Obsessive-Compulsive Disorder (OCD) is the tenth most disabling illness of any kind. OCD stands as a paradigm for complex neurobehavioral disorders due to its polygenic origin. It presents heterogenic clinical presentation, variable disease onset, progression and treatment responses, what makes its understanding a major neuropsychiatric challenge. Like with other neurobehavioral disorders, animal models are essential tools for decoding OCD genetic complexity, understanding its biological base and discovering novel treatments and diagnostic methods. 20 years of rodent OCD modeling have helped to understand the disease better, but multiple questions remain regarding OCD. Innovative whole genome sequencing (WGS) approaches might provide important answers on OCD risk associated genes. However, exploiting those large data sets through the use of traditional animal models is costly and time consuming. Zebrafish might be an appropriate animal model to streamline the pipeline of gene functional validation. This animal model shows several advantages versus rodent models, such as faster and cheaper genetic manipulation, strong impact on the 3Rs implementation, behavioral phenotypic reproducibility of OCD-like behaviors (obsessions and compulsions) and feasibility to develop high-throughput assays for novel OCD drug therapies discovery. In conclusion, zebrafish could be an innovative and relevant model for understanding OCD. Copyright © 2015 Elsevier B.V. All rights reserved.
    European journal of pharmacology 03/2015; 759. DOI:10.1016/j.ejphar.2015.03.027 · 2.68 Impact Factor
  • Source
    • "In particular, by conducting comparative genome analysis, information on conservation of gene sequences can be obtained and there is a possibility to find evidences for genome evolution (Clark et al., 2001). Eukaryote genome sequencing has been endeavored through various international genome sequencing projects for more than 100 species with so far accomplished ones for whole genomes of human (IHGSC, 2004), chicken (ICGSC, 2004) and zebrafish (Howe et al., 2013). In addition, genome sequencing has been completed for the organism possessing the most compact genome among vertebrates, the Japanese pufferfish (Fugu) (Takifugu rubripes) (Aparicio et al., 2002). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Tumor necrosis factor (TNF) and its superfamily (TNFSF) members are important inflammatory cytokines. Although fish have fourteen TNFSF genes, their genomic location and existence are yet to be described and confirmed in the Japanese pufferfish (Fugu) (Takifugu rubripes). Therefore, we conducted in silico identification, synteny analysis of TNFSF genes from Fugu with that of zebrafish and human TNFSF loci and their expression analysis in various tissues. We identified ten novel TNFSF genes, viz. TNFSF5 (CD40L), TNFSF6 (FasL), three TNFSF10 (TRAIL) (-1, 2 and 3), TNFSF11 (RANKlg), TNFSF12 (TWEAK), two TNFSF13B (BAFF) (1 and 2) and TNFSF14 (LIGHT) belonging to seven TNFSFs in Fugu. Several features such as existence of TNF family signature, conservation of genes in TNF loci with human and zebrafish chromosomes and phylogenetic clustering with other teleost TNFSF orthologs confirmed their identity. Fugu TNFSF genes were constitutively expressed in all eight different tissues with most of them expressed highly in liver. Fugu TNFSF10 gene has three homologs present on chromosomes 10 (TNFSF10-1), 8 (TNFSF10-2) and 2 (TNFSF10-3). Moreover, a phylogenetic analysis containing all available vertebrate (mammals, birds, reptiles, amphibians and fish) TNFSF10 orthologs showed that Fugu TNFSF10-1 and 10-3 are present in all vertebrates, whereas TNFSF10-2 was not related to any mammalian and avian orthologs. Viral double-stranded RNA mimic poly (I:C) caused an elevated expression of three Fugu TNFSF10 genes in head kidney cells at 4h indicating probable role of these genes to induce apoptosis in virus-infected cells. In conclusion, Fugu possesses genes belonging to nine TNFSFs including the newly identified seven and previously reported two, TNFSF New (TNF-N) and TNFSF2 (TNF-α). Our findings would add up information to TNFSF evolution among vertebrates. Copyright © 2015. Published by Elsevier B.V.
    Marine Genomics 03/2015; 22. DOI:10.1016/j.margen.2015.03.003 · 1.97 Impact Factor
Show more