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完成斑马鱼基因组的 de novo 组装和重新注释

Javan Okendo¹, Sergey Koren², Arang Rhie²

¹Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

bioRxiv : the preprint server for biology

|December 3, 2025

概括

斑马鱼的基因组组件已经使用先进的测序得到了显著改进,增加了1.3亿个基并增强了基因注释. 这种新的参考基因组 (GRCz12) 为脊椎动物研究和变异分析提供了更完整的资源.

科学领域:

基因组学就是基因组学.
进行比较基因组学.
分子生物学分子生物学

背景情况:

斑马鱼 (Danio rerio) 是脊椎动物研究中的一个关键模型生物.
以前的基因组参考组件 (例如GRCz11) 包含了重要的未解决的基因组区域.
长读测序和组装算法的进步使得基因组结构更加完整.

研究的目的:

为了生成一个更完整和连续的参考基因组组合为斑马鱼.
改进斑马鱼蛋白质编码和非编码RNA的注释.
建立斑马鱼泛基因组资源,以进行增强的变种分析.

主要方法:

从同卵性斑马鱼菌株 (图宾根和AB) 的长读测序使用de novo基因组组装.
整合Iso-SeqcDNA序列,以改善RefSeq注释.
产生40个草稿单元型来构建斑马鱼大基因组.

主要成果:

与GRCz11.11相比,新的GRCz12组件更加连续,结合了7%的序列和1亿3千万个以前未组装的DNA基数.
RefSeq注释显示mRNAs (68%),lncRNAs (47%) 和misc_RNAs (1099%) 的数量大幅增加.
两个组合 (GRCz12tu和GRCz12ab) 获得了参考基因组地位,以及一个新的斑马鱼泛基因组资源.

结论:

斑马鱼GRCz12参考基因组在组装完整性和注释方面显著改进.
开发的斑马鱼泛基因组资源有助于更全面的变种发现和分析.
这些进展为未来的斑马鱼研究提供了更强大的基因组基础.

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