Abstract：
The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic.
We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse.
Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.
We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse.
Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.
摘要：
尼罗河大鼠（Avicanthisniloticus）是一种重要的动物模型，因为它具有强烈的昼夜节律，富含锥体的视网膜，以及在没有化学或遗传修饰的情况下发展饮食诱导的糖尿病的倾向。在这些方面与人类更相似，与广泛使用的小家鼠和褐家鼠模型相比，有望将研究成果更好地转化为临床。
我们报告2.5Gb，具有完全解析的亲本单倍型的染色体水平参考基因组组装，生成与脊椎动物基因组计划（VGP）。组装是高度连续的，重叠群N50为11.1Mb，脚手架N50为83Mb，和95.2％的序列分配给染色体。我们使用新的工作流程来鉴定3613个分段重复并量化重复的基因。比较分析揭示了尼罗河大鼠独特的基因组特征，包括一些影响与2型糖尿病和代谢功能障碍相关的基因。我们讨论了尼罗河大鼠中杂合或与家鼠高度分歧的14个基因。
我们的发现反映了这个组件中存在的基因组分辨率的异常水平，这将极大地扩展尼罗河大鼠作为模型生物的潜力。
我们报告2.5Gb，具有完全解析的亲本单倍型的染色体水平参考基因组组装，生成与脊椎动物基因组计划（VGP）。组装是高度连续的，重叠群N50为11.1Mb，脚手架N50为83Mb，和95.2％的序列分配给染色体。我们使用新的工作流程来鉴定3613个分段重复并量化重复的基因。比较分析揭示了尼罗河大鼠独特的基因组特征，包括一些影响与2型糖尿病和代谢功能障碍相关的基因。我们讨论了尼罗河大鼠中杂合或与家鼠高度分歧的14个基因。
我们的发现反映了这个组件中存在的基因组分辨率的异常水平，这将极大地扩展尼罗河大鼠作为模型生物的潜力。
