Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa, 223-8522, Japan.
Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Minatojimaminami-machi 2-2-3, Kobe, Hyogo, 650-0047, Japan.
Sci Data. 2021 Jun 28;8(1):159. doi: 10.1038/s41597-021-00935-6.
Cynomolgus macaque (Macaca fascicularis) and common marmoset (Callithrix jacchus) have been widely used in human biomedical research. Long-standing primate genome assemblies used the human genome as a reference for ordering and orienting the assembled fragments into chromosomes. Here we performed de novo genome assembly of these two species without any human genome-based bias observed in the genome assemblies released earlier. We assembled PacBio long reads, and the resultant contigs were scaffolded with Hi-C data, which were further refined based on Hi-C contact maps and alternate de novo assemblies. The assemblies achieved scaffold N50 lengths of 149 Mb and 137 Mb for cynomolgus macaque and common marmoset, respectively. The high fidelity of our assembly is also ascertained by BAC-end concordance in common marmoset. Our assembly of cynomolgus macaque outperformed all the available assemblies of this species in terms of contiguity. The chromosome-scale genome assemblies produced in this study are valuable resources for non-human primate models and provide an important baseline in human biomedical research.
食蟹猴（Macaca fascicularis）和普通狨猴（Callithrix jacchus）被广泛应用于人类生物医学研究。在长期的灵长类动物基因组组装中，人类基因组被用作将组装片段排序和定向到染色体上的参考。在这里，我们进行了这两个物种的从头基因组组装，而在之前发布的基因组组装中没有观察到任何基于人类基因组的偏见。我们组装了 PacBio 长读长，并用 Hi-C 数据对生成的 contigs 进行支架构建，进一步根据 Hi-C 接触图谱和替代从头组装进行细化。组装获得的食蟹猴和普通狨猴的 scaffold N50 长度分别为 149Mb 和 137Mb。我们的组装在普通狨猴的 BAC 末端一致性方面也得到了高保真度的证实。与该物种的所有现有组装相比，我们组装的食蟹猴在连续性方面表现出色。本研究中产生的染色体级基因组组装为非人类灵长类模型提供了有价值的资源，并为人类生物医学研究提供了重要的基础。
