Generating an accurate and complete genome annotation for an organism is complex because the cells within each tissue can express a unique set of transcript isoforms from a unique set of genes. A comprehensive genome annotation should contain information on what tissues express what transcript isoforms at what level. This tissue-level isoform information can then inform a wide range of research questions as well as experiment designs. Long-read sequencing technology combined with advanced full-length cDNA library preparation methods has now achieved throughput and accuracy where generating these types of annotations is achievable. Here, we show this by generating a genome annotation of the mouse (Mus musculus). We used the nanopore-based R2C2 long-read sequencing method to generate 64 million highly accurate full-length cDNA consensus reads—averaging 5.4 million reads per tissue for a dozen tissues. Using the Mandalorion tool, we processed these reads to generate the Tissue-level Atlas of Mouse Isoforms which is available as a trackhub for the UCSC Genome Browser and contains at least one full-length isoform for the vast majority of expressed genes in each tissue.

中文翻译：

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小鼠多组织基因组注释图谱的生成和分析


为生物体生成准确而完整的基因组注释很复杂，因为每个组织内的细胞都可以从一组独特的基因中表达一组独特的转录本亚型。全面的基因组注释应包含有关哪些组织在什么水平表达哪些转录本亚型的信息。然后，这种组织水平的亚型信息可以为广泛的研究问题和实验设计提供信息。长读长测序技术与先进的全长 cDNA 文库制备方法相结合，现已在生成这些类型的注释时实现了通量和准确性。在这里，我们通过生成小鼠 （Mus musculus） 的基因组注释来显示这一点。我们使用基于纳米孔的 R2C2 长读长测序方法生成了 6400 万个高度准确的全长 cDNA 共有读长——十几个组织每个组织平均 540 万个读长。使用 Mandalorion 工具，我们处理了这些读数以生成小鼠亚型的组织水平图谱，该图谱可作为 UCSC 基因组浏览器的跟踪中心使用，并且包含每个组织中绝大多数表达基因的至少一种全长亚型。