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

- Whole-genome sequencing of wild Siberian musk deer ( Moschus moschiferus ) provides insights into its genetic features.
- Worldwide, the population size of Siberian musk deer is threatened by severe illegal poaching for commercially valuable musk and meat, habitat losses, and forest fire.
- However, the genetic information of Siberian musk deer is largely unexplored..
- Results: Here, we produced 3.10 Gb draft assembly of wild Siberian musk deer with a contig N50 of 29,145 bp and a scaffold N50 of 7,955,248 bp.
- Our phylogenetic analysis reveals that wild Siberian musk deer is closer to Bovidae than to Cervidae..
- Comparative analyses showed that the genetic features of Siberian musk deer adapted in cold and high-altitude environments.
- We sequenced two additional genomes of Siberian musk deer constructed demographic history indicated that changes in effective population size corresponded with recent glacial epochs.
- Conclusions: Here, we present a high-quality draft genome of wild Siberian musk deer, which will provide a valuable genetic resource for further investigations of this economically important musk deer..
- Keywords: Wild Siberian musk deer ( Moschus moschiferus) genome, De novo assembly, Genetic features, Musk secretion.
- Musk deer (Moschus, Moschidae) are small hornless Pecora ungulates, occurring commonly at mountains and forests of central Asia, belong to Cetartiodactyla, Ruminantia [1, 2].
- At present, musk deer comprise seven species, including Anhui musk deer (M.
- anhuiensis), forest musk deer (M.
- berezovskii), Alpine musk deer (M..
- chrysogaster), black musk deer (M.
- musk deer (M.
- leucogaster), Kashmir musk deer (M..
- cupreus) and Siberian musk deer (M.
- Musk deer inhabits a fairly fixed area throughout its life and rarely changes [1].
- However, the population of musk deer has dramatically decreased due to illegal.
- 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 [22–40].
- Recent work has provided the first complete gen- ome sequence of the forest musk deer [49].
- Siberian musk deer is one of the seven species, widely occurs in Korea, Mongolia, Russia, China, Kazakhstan, Kyrgyzstan, Nepal, and Vietnam [50].
- However, the population size of Siberian musk deer is dwindling rapidly by the same rea- sons as other musk species, and they have been catego- rized as Vulnerable on the IUCN Red List [51].
- As a result of the extinction crisis of Siberian musk deer and eco- nomic and medical value of its musk, understanding the genetic basis and features, environment adaptions, and the musk secretion mechanism is necessary.
- However, the whole-genome sequencing of Siberian musk deer has not been performed, and their potential value has yet to be discovered..
- In this study, we perform high-quality whole-genome sequencing of three wild Siberian musk deer (WSMD) from Mongolia, and transcriptome sequencing of one mixture of tissue from a naturally died female WSMD..
- These genomic and transcriptome analyses provide evi- dence of Siberian musk deer genetic features and musk secretion..
- that of the forest musk deer (2.72Gb) [49].
- Genome comparison of Siberian musk deer and forest musk deer.
- We compared the genome assembly of the Siberian musk deer and forest musk deer recently reported by Fan et al..
- The continuity of our assembly was remarkably increased compared with that of the forest musk deer genome assembly, particularly in re- gard to the scaffold N50 (7.95 vs 2.85 Mb) and scaffold number (13,344 vs 79,206).
- Figure S1 and Table S4), which is less than the pre- dicted gene numbers of forest musk deer (24,352 genes) [49].
- Musk deer is a noc- turnal mammal with sensitive hearing, smell, and sight for its locating food and avoiding predators in darkness [6, 58]..
- This finding possibly avoids the Siberian musk deer from the DNA damage caused by UV radiation and hypoxia in high-altitude environments.
- 1 a The Venn diagram shows the number of orthologs shared among musk deer and other representative mammals.
- for Siberian musk deer recovered and peaked at ~ 0.30 Mya, during the Penultimate glaciation Mya) [60–62].
- Subsequently, a sharp decline in N e for Siberian musk deer coincided with the extreme cooling climate during the last glaciation.
- 20,000 years ago), it is likely that Siberian musk deer suffered from the effects of climate change, over-hunting, and habitat loss..
- To evaluate the genome completeness, gene annotation and excavating genes related to musk secretion, we se- quenced the transcriptome of a mixture tissue (including liver, kidney, lung, heart, skin, and stomach) which col- lected from a female Siberian musk deer.
- This result indicates that the mo- lecular components involved in the physiological activities of the siberian musk deer are not only concentrated in cells but also widely distributed in organelles, and play an im- portant role.
- b KEGG pathway enrichment of DEGs in the Siberian musk deer.
- In this study, we performed a draft genome of wild Si- berian musk deer using next generation sequencing technology.
- mouse (40.53%) (Additional file 1: Table S7) and forest musk deer .
- WSMD genome, which was less than the predicted gene numbers of forest musk deer (24,352 genes) [49].
- Previous studies on phylogenetic analysis based on whole-genome sequences revealed that forest musk deer as more closely related to Bovidae than to Cer- vidae, which is consistent with the results of the present study .
- Historically, the fossil records and some molecular phylogenetic studies regarded Siber- ian musk deer WSMD as the primitive species in Moschus .
- 27.3Mya) at which forest musk deer divided with Bovidae [39].
- These results were suggested that Siberian musk deer was not the most primitive musk deer..
- To adapt to environments of the high mountain for- ests, Siberian musk deer may have been formed some characteristics under natural selection.
- It is worth noting that musk deer has sensitive smell and hearing to locating food in darkness.
- Studies have shown that due to the small body size and small appetite musk deer could not get enough food in one time to obtain more en- ergy [77].
- Therefore, musk deer often choose high-energy and digestible good, especially in the cold winter and spring when the food is scarce [78].
- We found that the ex- pansion gene families were significantly enriched in energy metabolism pathways and GO terms which might help Siberian musk deer to optimize their energy storage and production in the forest.
- These categories seem to be help musk deer living at high altitudes avoid high levels of ultraviolet radiation and forage in darkness.
- Taken to- gether, these results provide evidence for musk deer to adapt to the environments.
- As we known that musk deer is famous for secreting musk.
- Siberian musk deer once inhabited most of Asia, but today they are sharply declining and being endangered status due to overharvesting, natural disaster, and dis- eases.
- In this study, we report the first whole genome se- quencing, assembly, and annotation of the wild Siberian musk deer.
- A mixture tissue sample (including liver, kidney, lung, heart, skin, and stomach) was collected from a female Siberian musk deer the nat- urally died.
- All collected samples were approved by the Mongolian Musk Deer Breeding Center and completed with the help of staff..
- The genome of forest musk deer assembled by Fan et al..
- We performed whole-genome alignment between the Siberian musk deer and forest musk deer assembly using mummer4 (nucmer -l 100 -c 500 --maxmatch) [56].
- Gene families among the musk deer and other mam- mals were constructed with the TreeFam pipeline [111] (Additional file 1: Table S10), as described in detail by Li et al.
- Based on the CDS alignment of single-copy orthologs, positively selected genes (PSGs) in the musk deer were identified by codeml in PAML (v4.9) [116].
- Taking the musk deer as the foreground and other species as the background, the branch-site model (model = 2, NSsite = 2) with dN/dS ≤ 1 (fix_omega = 1, omega = 1) and dN/dS >.
- Genomes of two additional musk deer (s190119001 and s180119002) were re-sequenced with the standard Illu- mina HiSeq protocol (2 × 150 bp).
- We would like to special thanks to all the breeders of musk deer in Mongolia..
- Ecology of the Himalayan musk deer in Sagarmatha National Park, Nepal.
- Review of the distribution, status and conservation of musk deer in China.
- Changes in distribution area of Korean musk deer (Moschus moschiferus parvipes) from 1950s to 1999 in South Korea.
- mtDNA analysis confirms the endangered Kashmir musk deer extends its range to Nepal.
- De novo assembly of Chinese forest musk deer (Moschus berezovskii) transcriptome from next- generation mRNA sequencing.
- The musk chemical composition and microbiota of Chinese forest musk deer males.
- Musk deer (Moschus moschiferus): reinvestigation of main lipid components from preputial gland secretion.
- Musk deer Moschus cupreus persist in the eastern forests of Afghanistan.
- The distribution, status and conservation of the Himalayan musk deer Moschus chrysogaster.
- Status, habitat use and conservation of Alpine musk deer (Moschus chrysogaster) in Uttarakhand Himalayas, India.
- Conservation status and causes of decline of musk deer ( Moschus spp.
- No licence to kill: the population and harvest of musk deer and trade in musk in the Russian federation and Mongolia.
- The musk deer in China.
- Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples.
- Molecular phylogeny of musk deer: a genomic view with mitochondrial 16S rRNA and cytochrome b gene.
- Comparative genomics reveals the genetic mechanisms of musk secretion and adaptive immunity in Chinese forest musk deer.
- Mitochondrial DNA sequences imply Anhui musk deer a valid species in genus Moschus.
- The earliest musk deer of the genus Moschus and their significance in clarifying of evolution and relationships of the family Moschidae.
- Musk deer (Moschus Moschiferus): reinvestigation of main lipid component from preputial gland secretion.
- Illumina-based de novo transcriptome sequencing and analysis of Chinese forest musk deer.
- De novo assembly of Chinese forest musk deer (Moschus berezovskii) transcriptome form next- generation mRNA sequencing.
- Studies on the genetic diversity of forest musk deer ( Moschus berezovskii ) and linkage analysis between the performance of musk productivity and AFLP markers.
- Genetic diversity of captive forest musk deer (Moschus berezovskii) inferred from the mitochondrial DNA control region.
- Assement of genetic diversity in the captive forest musk deer ( Moschus berezovskii ) and linkage analysis between the performance of musk productivity and DNA molecular markers.
- Comparative analysis of the gut microbiota composition between captive and wild forest musk deer.
- Comparative analysis of the gut microbial communities in forest and alpine musk deer using high-throughout sequencing.
- The draft genome sequence of forest musk deer (Moschus berezovskii)..
- Mongolian Musk deer ( Moschus moschiferus Linnaeus , 1758)..
- The draft genome sequence of forest musk deer ( Moschus berezovskii.
- The reproductive performance of female forest musk deer (Moschus berezovskii) in captivity..
- On the structure and affinities of the Musk-Deer (Moschus moschifer- us Linn.
- Sex hormones play roles in determining musk composition during the early stages of musk secretion by musk deer (Moschus berezovskii).
- Sex hormones play roles in determining musk composition during the early stages of musk secretion by musk deer ( Moshus berezovskii

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