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: 41.46). 04/2013; 496(7446). DOI: 10.1038/nature12111
Source: PubMed


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.

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    • "Nevertheless, all the studies are focused on direct exposure of embryos or pregnant females, neglecting the risk of adult male exposure to the toxic during fertile life. Since George Streisinger firstly proposed zebrafish (Danio rerio) as model species (Streisinger et al., 1986) it has become more and more used in developmental biology and human disease (including cardiovascular one (Bakkers, 2011)), due to its high fecundity, rapid life cycle, transparence during development and high gene homology with humans (71%) (Howe et al., 2013; Asnani and Peterson, 2014). Moreover, it has become widely used in ecotoxicology as reviewed by Dai and colleagues (Dai et al., 2014) and more specifically for the study of the effects of BPA (Little and Seebacher, 2015; Cypher et al., 2015; Lam et al., 2011; Tse et al., 2013). "
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    • "The study by Howe et al. also revealed a comparable number of species specific genes for zebrafish, human and mouse when duplicated genes are regarded as one gene (Howe et al., 2013). Teleost fish have undergone an additional round of whole genome duplication and although many of these duplicated ohnologs got subsequently lost, about 30% of all zebrafish genes still have one (Howe et al., 2013). The degree of conservation changes from gene to gene, and it remains to be determined in many cases whether both or only one of these duplicates are found in a given cell type. "
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