We report the construction and analysis of a new reference genome assembly for Rattus norvegicus, the laboratory rat, a widely used experimental animal model organism. The assembly has been adopted as the rat reference assembly by the Genome Reference Consortium and is named GRCr8. The assembly has employed 40× Pacific Biosciences (PacBio) HiFi sequencing coverage and scaffolding using optical mapping and Hi-C. We used genomic DNA from a male BN/NHsdMcwi (BN) rat of the same strain and from the same colony as the prior reference assembly, mRatBN7.2. The assembly is at chromosome level with 98.7% of the sequence assigned to chromosomes. All chromosomes have increased in size compared with the prior assembly and k-mer analysis indicates that the subject animal is fully inbred and that the genome is represented as a single haploid assembly. Notable increases are observed in Chromosomes 3, 11, and 12 in the prospective rDNA regions. In addition, Chr Y has increased threefold in size and is more consistent with the rat karyotype than previous assemblies. Several other chromosomes have grown by the incorporation of sizable discrete new blocks. These contain highly repetitive sequences and encode numerous previously unannotated genes. In addition, centromeric sequences are incorporated in most chromosomes. Genome annotation has been performed by NCBI RefSeq, which confirms improvement in assembly quality and adds more than 1100 new protein coding genes. PacBio Iso-Seq data have been acquired from multiple tissues of the subject animal and are released concurrently with the new assembly to aid further analyses.

中文翻译：

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从长读长和长距离支架构建和评估新的大鼠参考基因组组装 GRCr8


我们报道了实验室大鼠 Rattus norvegicus 的新参考基因组组装的构建和分析，Rattus norvegicus 是一种广泛使用的实验动物模式生物。该组装已被基因组参考联盟 （Genome Reference Consortium） 采用为大鼠参考组装，并被命名为 GRCr8。该组件采用了 40× Pacific Biosciences （PacBio） HiFi 测序覆盖率和使用光学映射和 Hi-C 的支架。我们使用了来自雄性 BN/NHsdMcwi （BN） 大鼠的基因组 DNA，该大鼠与先前的参考组装体 mRatBN7.2 相同菌株和相同的菌落。组装在染色体水平上，98.7% 的序列分配给染色体。与先前的组装相比，所有染色体的大小都增加了，并且 k-mer 分析表明实验体动物是完全近亲繁殖的，并且基因组表示为单个单倍体组装。在前瞻性 rDNA 区域的 3 、 11 和 12 号染色体中观察到显著增加。此外，Chr Y 的大小增加了三倍，并且比以前的组装体更符合大鼠核型。其他几条染色体通过掺入相当大的离散新块而生长。这些包含高度重复的序列，并编码许多以前未注释的基因。此外，着丝粒序列掺入大多数染色体中。NCBI RefSeq 进行了基因组注释，证实了组装质量的改进，并添加了 1100 多个新的蛋白质编码基因。PacBio Iso-Seq 数据已从实验动物的多个组织中采集，并与新组装同时发布，以帮助进一步分析。