Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, 2100, Denmark.
BGI-Shenzhen, Shenzhen, 518083, China.
Sci Rep. 2020 Feb 12;10(1):2431. doi: 10.1038/s41598-020-59110-3.
Mandrill (Mandrillus sphinx) is a primate species, which belongs to the Old World monkey (Cercopithecidae) family. It is closely related to human, serving as a model for human health related research. However, the genetic studies on and genomic resources of mandrill are limited, especially in comparison to other primate species. Here we produced 284 Gb data, providing 96-fold coverage (considering the estimated genome size of 2.9 Gb), to construct a reference genome for the mandrill. The assembled draft genome was 2.79 Gb with contig N50 of 20.48 Kb and scaffold N50 of 3.56 Mb. We annotated the mandrill genome to find 43.83% repeat elements, as well as 21,906 protein-coding genes. The draft genome was of good quality with 98% gene annotation coverage by Benchmarking Universal Single-Copy Orthologs (BUSCO). Based on comparative genomic analyses of the Major Histocompatibility Complex (MHC) of the immune system in mandrill and human, we found that 17 genes in the mandrill that have been associated with disease phenotypes in human such as Lung cancer, cranial volume and asthma, barbored amino acids changing mutations. Gene family analyses revealed expansion of several genes, and several genes associated with stress environmental adaptation and innate immunity responses exhibited signatures of positive selection. In summary, we established the first draft genome of the mandrill of value for studies on evolution and human health.
山魈（Mandrillus sphinx）是一种灵长类动物，属于旧大陆猴（Cercopithecidae）科。它与人类关系密切，是研究人类健康相关问题的模型。然而，山魈的遗传研究和基因组资源有限，尤其是与其他灵长类动物相比。在这里，我们产生了 284Gb 的数据，提供了 96 倍的覆盖度（考虑到估计的 2.9Gb 基因组大小），构建了山魈的参考基因组。组装的基因组草图为 2.79Gb，其 contig N50 为 20.48 Kb，scaffold N50 为 3.56Mb。我们注释了山魈基因组，发现 43.83%的重复元件和 21,906 个蛋白质编码基因。该基因组草图质量较好，98%的基因注释覆盖率通过基准通用单拷贝同源基因（BUSCO）得到验证。基于对山魈和人类免疫系统主要组织相容性复合体（MHC）的比较基因组分析，我们发现山魈中有 17 个基因与人类的疾病表型有关，如肺癌、颅容量和哮喘，这些基因具有导致氨基酸改变的突变。基因家族分析显示，一些基因发生了扩张，一些与应激环境适应和先天免疫反应相关的基因表现出正选择的特征。总之，我们建立了山魈的第一个基因组草图，为研究进化和人类健康提供了有价值的资源。
