Lok Si, Lau Timothy N H, Trost Brett, Tong Amy H Y, Paton Tara, Wintle Richard F, Engstrom Mark D, Gunn Anne, Scherer Stephen W
The Centre for Applied Genomics, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, 686 Bay Street, Rm 13.9713, Suite 03-6577, Toronto, ON, M5G 0A4, Canada.
Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada.
Sci Rep. 2024 Sep 16;14(1):21023. doi: 10.1038/s41598-024-67270-9.
The muskox (Ovibos moschatus), an integral component and iconic symbol of arctic biocultural diversity, is under threat by rapid environmental disruptions from climate change. We report a chromosomal-level haploid genome assembly of a muskox from Banks Island in the Canadian Arctic Archipelago. The assembly has a contig N50 of 44.7 Mbp, a scaffold N50 of 112.3 Mbp, a complete representation (100%) of the BUSCO v5.2.2 set of 9225 mammalian marker genes and is anchored to the 24 chromosomes of the muskox. Tabulation of heterozygous single nucleotide variants in our specimen revealed a very low level of genetic diversity, which is consistent with recent reports of the muskox having the lowest genome-wide heterozygosity among the ungulates. While muskox populations are currently showing no overt signs of inbreeding depression, environmental disruptions are expected to strain the genomic resilience of the species. One notable impact of rapid climate change in the Arctic is the spread of emerging infectious and parasitic diseases in the muskox, as exemplified by the range expansion of muskox lungworms, and the recent fatal outbreaks of Erysipelothrix rhusiopathiae, a pathogen normally associated with domestic swine and poultry. As a genomics resource for conservation management of the muskox against existing and emerging disease modalities, we annotated the genes of the major histocompatibility complex on chromosome 2 and performed an initial assessment of the genetic diversity of this complex. This resource is further supported by the annotation of the principal genes of the innate immunity system, genes that are rapidly evolving and under positive selection in the muskox, genes associated with environmental adaptations, and the genes associated with socioeconomic benefits for Arctic communities such as wool (qiviut) attributes. These annotations will benefit muskox management and conservation.
麝牛（Ovibos moschatus）是北极生物文化多样性的重要组成部分和标志性象征，正受到气候变化导致的快速环境破坏的威胁。我们报告了来自加拿大北极群岛班克斯岛的一头麝牛的染色体水平单倍体基因组组装。该组装的重叠群N50为44.7兆碱基对，支架N50为112.3兆碱基对，完整代表了9225个哺乳动物标记基因的BUSCO v5.2.2集（100%），并锚定到麝牛的24条染色体上。对我们样本中杂合单核苷酸变异的列表显示遗传多样性水平非常低，这与最近关于麝牛在有蹄类动物中具有全基因组最低杂合度的报道一致。虽然目前麝牛种群没有明显的近亲繁殖衰退迹象，但环境破坏预计会使该物种的基因组恢复力受到压力。北极快速气候变化的一个显著影响是麝牛中新兴传染病和寄生虫病的传播，麝牛肺线虫的范围扩大以及最近猪丹毒杆菌（一种通常与家猪和家禽相关的病原体）的致命爆发就是例证。作为针对现有和新出现疾病模式对麝牛进行保护管理的基因组学资源，我们注释了2号染色体上主要组织相容性复合体的基因，并对该复合体的遗传多样性进行了初步评估。先天免疫系统的主要基因、在麝牛中快速进化且处于正选择状态的基因、与环境适应相关的基因以及与北极社区社会经济利益相关的基因（如羊毛（qiviut）属性）的注释进一步支持了这一资源。这些注释将有利于麝牛的管理和保护。
