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

By Kerstin Howe, M. Clark, C. Torroja, J. Torrance, Camille Berthelot, Matthieu Muffato, J. Collins, S. Humphray, K. McLaren, L. Matthews and 162 more. Nature, 2013

4,740 citations recorded by the source corpus.

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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Citations in the corpus

RepeatModeler2: automated genomic discovery of transposable element families (2019, background): “The zebrafish, D. rerio, is dominated by class II, DNA-TIR transposons, but also exhibits a very diverse assortment of LTR retroelements with many unique families (Howe et al. 2013).”
The Genome 10K Project: A Way Forward (2015, unknown): “Teleosts (30,195, 60) Sturgeons (26, 1) Paddlefish (2, 0)”
Assessing genome assembly quality using the LTR Assembly Index (LAI) (2018, unknown): “3% (33)), and nematode (Caenorhabditis elegans, total LTR-RT 0.”
RepeatModeler2 for automated genomic discovery of transposable element families (2020, background): “The zebrafish, D. rerio, is dominated by class II, DNA-TIR transposons, but also exhibits a very diverse assortment of LTR retroelements with many unique families (42).”
The zebrafish (Danio rerio) as a model organism, with emphasis on applications for finfish aquaculture research (2014, methodology): “based also on high-throughput sequencing, recently, the sex determination factor has been identified in chromosome 16 (Howe et al. 2013).”
Ensembl 2014 (2013, methodology): “Manual annotation from Havana is additionally incorporated into our gene sets on alternate releases for zebraﬁsh (16) and for mouse, which also includes all current CCDS gene models.”
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation (2014, methodology): “Plot shows the proportion of RPFs or input reads aligned to the coding sequence of RefSeq genes at each position relative to the codon.”
Zebrafish: Development of a Vertebrate Model Organism (2018, methodology): “This effort was greatly aided by the sequencing of the zebrafish genome, beginning in 2001 at the Sanger Institute and completed in 2013 (Howe et al., 2013).”