An Interrogation of Shared and Unique Copy Number Variants Across Genetically Distinct Zebrafish Strains.
An Interrogation of Shared and Unique Copy Number Variants Across Genetically Distinct Zebrafish Strains.
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对遗传上不同的斑马鱼品系的共享和独特拷贝数变异的询问。
DOI：
10.1089/zeb.2018.1644
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发表时间：
2019
期刊：
影响因子：
2
通讯作者：
Brown,KimH
中科院分区：
文献类型：
--
作者：
Holden,LindsayA;Wilson,Charles;Heineman,Zachary;Dobrinski,KimberlyP;Brown,KimH
斑马鱼（Danio rerio）是人类疾病的广泛使用的模型系统，但常见的实验室品系具有明显的行为和生理差异。伴随着这些已知的品系差异，常用的“野生型”斑马鱼品系具有共享和独特的单核苷酸多态性和拷贝数变异（CNV）。尽管如此，在研究设计中，基因组变异往往被忽略，实际使用的菌株往往没有得到充分的报告。本研究的目的是评估三种常见的实验室斑马鱼品系-AB、Tubingen（TU）和WIK-的CNV，并将这些数据作为斑马鱼群落的工具。在此，我们确定了1351 CNV区域内的最新的基因组组装（GRCz 11）覆盖1.9%的斑马鱼基因组（31.7 Mb）。在所有染色体上都发现了CNVs，2200个基因（5121个转录本）位于已鉴定的CNVs的±5 kb范围内，表明CNVs可能对附近的基因邻居起顺式调节作用。我们在UCSC基因组浏览器上创建了一个公共会话，以查看这项名为“danRer 11 zebrafish CNV across strains”的研究中的CNV，作为斑马鱼社区的工具。
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 likelycisregulatory 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.