Comparative Genomics Reveals the Genetic Mechanisms of Musk Secretion and Adaptive Immunity in Chinese Forest Musk Deer

Abstract

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.

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features

“…However, Moschidea is a sister group of Bovidae or of Cervidae, has obtained different results in different analyses [28,[31][32][33][34]. Previous studies on phylogenetic analysis based on whole-genome sequences revealed that forest musk deer as more closely related to Bovidae than to Cervidae, which is consistent with the results of the present study [35,36,76]. Historically, the fossil records and some molecular phylogenetic studies regarded Siberian musk deer WSMD as the primitive species in Moschus [25,37,38].…”

“…These categories seem to be help musk deer living at high altitudes avoid high levels of ultraviolet radiation and forage in darkness. The previous study based on the forest musk genome has identified eight PSGs genes enriched in the phototransduction pathway and retinol metabolism pathways [35]. Our results and theirs did not have overlap candidate genes.…”

“…Other studies have shown that testosterone plays an important role in the seasonal development of musk glands [92], and oxytocin may regulate the function of muskrat scented glands by the locally expressed receptors [94]. Studies based on transcriptome [42,43] and genetic analysis [35] have shown that a considerable number of genes involved in musk metabolism pathways, such as steroid biosynthesis, flavone and flavonol biosynthesis, terpenoid backbone biosynthesis, aldosterone-regulated sodium reabsorption was played a significant role in musk secretion. In this study, we identified 21 up-regulation DEGs which were closely associated with metabolism and response of steroid, terpenoid and hormone which were coincident with the previous reports [35,42,43].…”

“…Studies based on transcriptome [42,43] and genetic analysis [35] have shown that a considerable number of genes involved in musk metabolism pathways, such as steroid biosynthesis, flavone and flavonol biosynthesis, terpenoid backbone biosynthesis, aldosterone-regulated sodium reabsorption was played a significant role in musk secretion. In this study, we identified 21 up-regulation DEGs which were closely associated with metabolism and response of steroid, terpenoid and hormone which were coincident with the previous reports [35,42,43]. Although there have been several studies on the secretion of musk, the genetic mechanisms of musk secretion are still poorly understood.…”

“…In recent years, there has been significant progress in the studies of musk deer ecology, taxonomy, evolution history by paleontological, morphological, ecological and ethological and molecular analysis [22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40]. The musk composition and secretory mechanism of musk have been explored by various aspects, including microsatellite, mtDNA marker, and transcriptome sequencing data [41][42][43][44][45][46].…”