Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China.
Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China.
Genome Biol Evol. 2019 Apr 1;11(4):1019-1032. doi: 10.1093/gbe/evz055.
The Chinese forest musk deer (Moschus berezovskii; FMD) is an artiodactyl mammal and is both economically valuable and highly endangered. To investigate the genetic mechanisms of musk secretion and adaptive immunity in FMD, we compared its genome to nine other artiodactyl genomes. Comparative genomics demonstrated that eight positively selected genes (PSGs) in FMD were annotated in three KEGG pathways that were related to metabolic and synthetic activity of musk, similar to previous transcriptome studies. Functional enrichment analysis indicated that many PSGs were involved in the regulation of immune system processes, implying important reorganization of the immune system in FMD. FMD-specific missense mutations were found in two PSGs (MHC class II antigen DRA and ADA) that were classified as deleterious by PolyPhen-2, possibly contributing to immune adaptation to infectious diseases. Functional assessment showed that the FMD-specific mutation enhanced the ADA activity, which was likely to strengthen the immune defense against pathogenic invasion. Single nucleotide polymorphism-based inference showed the recent demographic trajectory for FMD. Our data and findings provide valuable genomic resources not only for studying the genetic mechanisms of musk secretion and adaptive immunity, but also for facilitating more effective management of the captive breeding programs for this endangered species.
中国林麝（Moschus berezovskii；FMD）是一种偶蹄目哺乳动物，具有重要的经济价值和高度濒危性。为了研究 FMD 麝香分泌和适应性免疫的遗传机制，我们将其基因组与其他九个偶蹄目基因组进行了比较。比较基因组学表明，FMD 中的 8 个正选择基因（PSGs）被注释到与麝香代谢和合成活性相关的三个 KEGG 途径中，这与之前的转录组研究相似。功能富集分析表明，许多 PSGs 参与了免疫系统过程的调节，表明 FMD 中免疫系统的重要重组。在两个 PSGs（MHC 类 II 抗原 DRA 和 ADA）中发现了 FMD 特异性错义突变，这些突变被 PolyPhen-2 归类为有害突变，可能有助于对传染病的免疫适应。功能评估表明，FMD 特异性突变增强了 ADA 的活性，这可能增强了对病原体入侵的免疫防御。基于单核苷酸多态性的推断表明了 FMD 最近的人口轨迹。我们的数据和发现不仅为研究麝香分泌和适应性免疫的遗传机制提供了有价值的基因组资源，而且为这一濒危物种的圈养繁殖计划提供了更有效的管理。
