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

Li, Yang; Dalai, Menggen; Su, Rongguo; Lin, Weili; Erdenedalai, Myagmarsuren; Luvsantseren, Batkhuu; Chimedtseren, Chimedragchaa; Wang, Zhen; Hasi, Surong

doi:10.1186/s12864-020-6495-2

Cited by 12 publications

(9 citation statements)

References 103 publications

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“…All musk deer species (Moschus spp.) are assessed to be globally threatened due to poaching and habitat loss [19][20][21], with six being ranked as endangered and one as vulnerable (M. moschiferus) according to The IUCN Red List of Threatened Species v. 2015 [22]. The musk deer is characterized by the musk produced by the musk pod on the abdomen of adult males, and the musk is valuable for use in traditional Chinese medicine and perfumes [23].…”

Section: Introductionmentioning

confidence: 99%

Population genomics reveals moderate genetic differentiation between populations of endangered Forest Musk Deer located in Shaanxi and Sichuan

et al. 2022

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Background Many endangered species exist in small, genetically depauperate, or inbred populations, hence promoting genetic differentiation and reducing long-term population viability. Forest Musk Deer (Moschus berezovskii) has been subject to illegal hunting for hundreds of years due to the medical and commercial values of musk, resulting in a significant decline in population size. However, it is still unclear to what extent the genetic exchange and inbreeding levels are between geographically isolated populations. By using whole-genome data, we reconstructed the demographic history, evaluated genetic diversity, and characterized the population genetic structure of Forest Musk Deer from one wild population in Sichuan Province and two captive populations from two ex-situ centers in Shaanxi Province. Results SNP calling by GATK resulted in a total of 44,008,662 SNPs. Principal component analysis (PCA), phylogenetic tree (NJ tree), ancestral component analysis (ADMIXTURE) and the ABBA-BABA test separated Sichuan and Shaanxi Forest Musk Deer as two genetic clusters, but no obvious genetic differentiation was observed between the two captive populations. The average pairwise FST value between the populations in Sichuan and Shaanxi ranged from 0.05–0.07, suggesting a low to moderate genetic differentiation. The mean heterozygous SNPs rate was 0.14% (0.11%—0.15%) for Forest Musk Deer at the genomic scale, and varied significantly among three populations (Chi-square = 1.22, p < 0.05, Kruskal–Wallis Test), with the Sichuan population having the lowest (0.11%). The nucleotide diversity of three populations varied significantly (p < 0.05, Kruskal–Wallis Test), with the Sichuan population having the lowest genetic θπ (1.69 × 10–3). Conclusions Genetic diversity of Forest Musk Deer was moderate at the genomic scale compared with other endangered species. Genetic differentiation between populations in Sichuan and Shaanxi may not only result from historical biogeographical factors but also be associated with contemporary human disturbances. Our findings provide scientific aid for the conservation and management of Forest Musk Deer. They can extend the proposed measures at the genomic level to apply to other musk deer species worldwide.

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Section: Introductionmentioning

confidence: 99%

Population genomics reveals moderate genetic differentiation between populations of endangered Forest Musk Deer located in Shaanxi and Sichuan

et al. 2022

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“…Though often reported (e.g., Fu et al, 2020; Wang et al, 2020; Yi et al, 2020; Ludington & Sanders, 2021; Voelker et al, 2021; Okenmor et al, 2022), genome-wide alignment identity metrics like those produced by MuMmer4 are a broad and imperfect measure of assembly accuracy. Therefore, we endeavored to conduct a more in-depth analysis of accuracy by characterizing pairwise alignments of BUSCO sequences shared between assembly types.…”

Section: Discussionmentioning

confidence: 99%

Assessing the quality ofde novoparasite genomes assembled using only Oxford Nanopore Technologies MinION data

Herzog,

Wu,

Hawdon

et al. 2023

Preprint

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Parasitic nematode infections represent a significant burden of disease in impoverished populations. High prevalence of infection coupled with widespread geographic distributions means populations of parasitic nematodes likely harbor high levels of genetic diversity that are not reflected in currently available genomic resources. Comparative genomic studies of parasitic nematodes have identified novel drug and vaccine targets and yielded unprecedented insights into helminth biology, highlighting the potential of high-quality reference genomes. Few genomic resources exist for parasitic nematodes, however, and most species are represented by only a single genome. This is partly due to challenges associated with generating genomic data for these parasites. Many species are small in size and yet have relatively large and complex genomes, making their genomes difficult and expensive to sequence and assemble. Short-read sequence data has primarily been used to generate genomic data for parasitic nematodes, but whole genome assemblies based on short-read data are highly discontiguous. Recent improvements in the accuracy of Oxford Nanopore Technologies (ONT) long-read data makes it an appealing approach for improving existing reference genomes and generating novel genome assemblies from uncharacterized species. This study targets three species of parasitic nematodes to compare the current gold standard hybridde novogenome assembly approach to one that relies on long-read ONT MinION data only. Hybrid assemblies were found to be more contiguous, but nonetheless, MinION data alone were used successfully to generate highly contiguous, complete, and accurate assemblies for all species quickly and inexpensively.Significant StatementHigh quality helminth genome assemblies are invaluable tools for identifying novel drug and vaccine targets and monitoring the effectiveness of control campaigns, but generating regionally relevant reference-quality genomes from a broad diversity of populations and species can be challenging when relying on traditional approaches. This study demonstrates that Oxford Nanopore Technologies MinION long-read data alone can be used to quickly and inexpensively generate highly contiguous, complete, and accurate whole genome assemblies for parasitic nematodes. These findings highlight an accessible method for increasing the resources available for comparative helminth genomics and a path toward incorporating genomic epidemiology as a routine component of assessing control campaign effectiveness.Data Availability StatementQuality-controlled MinION and Illumina data for each species are deposited in the NCBISequence Read Archive (SRA) under the BioProject accession number XXXX. Final assemblies for each species are publicly available on WormBase ParaSite.

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“…The analysis of molecular phylogeny indicated that Bovidae and Moschidae diverged from a common ancestor ( Fan Z. et al, 2018 ; Zhou et al, 2019 ; Yi et al, 2020 ). After comparison with all tissues of cows, we found that the mRNA expression pattern of the musk gland was the closest to that of the prostate.…”

Section: Discussionmentioning

confidence: 99%

Integrated multi-omics analysis reveals insights into Chinese forest musk deer (Moschus berezovskii) genome evolution and musk synthesis

Hong

Feng

et al. 2023

Front. Cell Dev. Biol.

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Among the artiodactyls, male animals belonging to the Family Moschidae have a unique tissue, the musk gland, with the capability of musk synthesis. However, the genetic basis of musk gland formation and musk production are still poorly understood. Here, musk gland tissues from two juvenile and three adult Chinese forest musk deer (Moschus berezovskii) were utilized to analyze genomic evolution events, evaluate mRNA profiles and investigate cell compositions. By performing genome reannotation and comparison with 11 ruminant genomes, three expanded gene families were identified in the Moschus berezovskii genome. Transcriptional analysis further indicated that the musk gland displayed a prostate-like mRNA expression pattern. Single-cell sequencing revealed that the musk gland is composed of seven distinguishable cell types. Among them, sebaceous gland cells and luminal epithelial cells play important roles in musk synthesis, while endothelial cells master the regulation of cell-to-cell communication. In conclusion, our study provides insights into musk gland formation and the musk-synthesizing process.

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

Cited by 12 publications

References 103 publications

Population genomics reveals moderate genetic differentiation between populations of endangered Forest Musk Deer located in Shaanxi and Sichuan

Population genomics reveals moderate genetic differentiation between populations of endangered Forest Musk Deer located in Shaanxi and Sichuan

Assessing the quality ofde novoparasite genomes assembled using only Oxford Nanopore Technologies MinION data

Integrated multi-omics analysis reveals insights into Chinese forest musk deer (Moschus berezovskii) genome evolution and musk synthesis

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