An Interrogation of Shared and Unique Copy Number Variants Across Genetically Distinct Zebrafish Strains
| Autor: | Charles Wilson, Lindsay A. Holden, Kim H. Brown, Zachary Heineman, Kimberly P. Dobrinski |
|---|---|
| Rok vydání: | 2018 |
| Předmět: |
Fish Proteins
endocrine system animal structures DNA Copy Number Variations animal diseases Danio Model system Computational biology 03 medical and health sciences 0302 clinical medicine stomatognathic system Species Specificity Animals Copy-number variation Zebrafish 030304 developmental biology 0303 health sciences Genome biology fungi Original Articles biology.organism_classification Animal Science and Zoology 030217 neurology & neurosurgery Developmental Biology |
| Zdroj: | Zebrafish. 16(1) |
| ISSN: | 1557-8542 |
| Popis: | Zebrafish (Danio rerio) are a widely utilized model system for human disorders, but common laboratory strains have distinct behavioral and physiological differences. Accompanying these known strain differences, commonly used “wildtype” zebrafish strains have both shared and unique suites of single nucleotide polymorphisms and copy number variants (CNVs). Despite this, genomic variation is often ignored in study design, and the actual strain used is often not adequately reported. The goal of this study was to assess CNVs across three common laboratory strains of zebrafish—AB, Tubingen (TU), and WIK—and provide these data as a tool for the zebrafish community. Herein we identified 1351 CNV regions within the most recent genome assembly (GRCz11) covering 1.9% of the zebrafish genome (31.7 Mb). CNVs were found across all chromosomes, and 2200 genes (5121 transcripts) lie within ±5 kb of identified CNVs, pointing to likely cis regulatory actions of CNVs on nearby gene neighbors. We have created a Public Session accessible on the UCSC Genome Browser to view CNVs from this study titled “danRer11 zebrafish CNV across strains” as a tool for the zebrafish community. |
| Databáze: | OpenAIRE |
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