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Zhou C, Zhang W, Wen Q, Bu P, Gao J, Wang G, Jin J, Song Y, Sun X, Zhang Y, Jiang X, Yu H, Peng C, Shen Y, Price M, Li J, Zhang X, Fan Z, Yue B. Comparative Genomics Reveals the Genetic Mechanisms of Musk Secretion and Adaptive Immunity in Chinese Forest Musk Deer. Genome Biol Evol 2019; 11:1019-1032. [PMID: 30903183 PMCID: PMC6450037 DOI: 10.1093/gbe/evz055] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2019] [Indexed: 02/05/2023] Open
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.
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Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Wenbo Zhang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Qinchao Wen
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Ping Bu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Jie Gao
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Guannan Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Jiazheng Jin
- Sichuan Engineering Research Center for Medicinal Animals, Xichang, P.R. China
| | - Yinjie Song
- Center of Infectious Diseases, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, P.R. China
| | - Xiaohong Sun
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Yifan Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Xue Jiang
- Sichuan Engineering Research Center for Medicinal Animals, Xichang, P.R. China
| | - Haoran Yu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Changjun Peng
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Yongmei Shen
- Sichuan Engineering Research Center for Medicinal Animals, Xichang, P.R. China
| | - Megan Price
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Jing Li
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
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Yang C, Meng Y, Yue B, Zhang X. Shanxi population of musk deer: species re-identification and genetic relationships with its sister species based on mitochondrial genomes. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1437821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Chengzhong Yang
- Chongqing Key Laboratory of Animal Biology, College of Life Sciences, Chongqing Normal University, Chongqing, P.R. China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Yang Meng
- The Natural History Museum of Sichuan University, College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
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Kim SI, Lee MY, Jeon HS, Han SH, An J. Complete mitochondrial genome of Siberian musk deer Moschus moschiferus (Artiodactyla: Moschidae) and phylogenetic relationship with other moschus species. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:860-861. [PMID: 33474012 PMCID: PMC7800829 DOI: 10.1080/23802359.2017.1407715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The Siberian musk deer, Moschus moschiferus, is an Endangered species in South Korea due to its decreasing population size caused by illegal hunting and habitat destruction. In this study, the complete mitochondrial genome of M. moschiferus was determined using next-generation sequencing. Total length of its mitogenome is 16,356 bp in length, encoding 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. Its AT contents are 62.4%, which are higher than its GC contents (37.7%) (A, 34.1%; C, 24.9%; G, 12.8%; and T, 28.3%). Phylogenetic relationship of genus Moschus showed topologies similar to those reported in previous studies. Sequence comparison between two M. moschiferus from South Korea indicated high sequence variations with 122 nucleotide differences. These results provide useful information necessary for further phylogenetic studies of Moschus species.
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Affiliation(s)
- Sang-In Kim
- School of Earth and Environmental Sciences, Seoul National University, Seoul, Republic of Korea
| | - Mu-Yeong Lee
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Hey Sook Jeon
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Sang-Hoon Han
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Junghwa An
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
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Pan T, Wang H, Hu C, Sun Z, Zhu X, Meng T, Meng X, Zhang B. Species Delimitation in the Genus Moschus (Ruminantia: Moschidae) and Its High-Plateau Origin. PLoS One 2015; 10:e0134183. [PMID: 26280166 PMCID: PMC4539215 DOI: 10.1371/journal.pone.0134183] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/06/2015] [Indexed: 11/29/2022] Open
Abstract
The authenticity of controversial species is a significant challenge for systematic biologists. Moschidae is a small family of musk deer in the Artiodactyla, composing only one genus, Moschus. Historically, the number of species in the Moschidae family has been debated. Presently, most musk deer species were restricted in the Tibetan Plateau and surrounding/adjacent areas, which implied that the evolution of Moschus might have been punctuated by the uplift of the Tibetan Plateau. In this study, we aimed to determine the evolutionary history and delimit the species in Moschus by exploring the complete mitochondrial genome (mtDNA) and other mitochondrial gene. Our study demonstrated that six species, M. leucogaster, M. fuscus, M. moschiferus, M. berezovskii, M. chrysogaster and M. anhuiensis, were authentic species in the genus Moschus. Phylogenetic analysis and molecular dating showed that the ancestor of the present Moschidae originates from Tibetan Plateau which suggested that the evolution of Moschus was prompted by the most intense orogenic movement of the Tibetan Plateau during the Pliocene age, and alternating glacial-interglacial geological eras.
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Affiliation(s)
- Tao Pan
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Hui Wang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Chaochao Hu
- School of Life Science, Nanjing Normal University, Nanjing, 230039, Jiangsu, China
| | - Zhonglou Sun
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Xiaoxue Zhu
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Tao Meng
- Guangxi Forest Inventory and Planning Institute, Nanning, 530011, Guangxi, China
| | - Xiuxiang Meng
- School of Environment and Natural Resources, Renmin University of China, Beijing, 100872, China
| | - Baowei Zhang
- Anhui Key Laboratory of Eco-engineering and Bio-technique, School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
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Li L, Wang BB, Ge YF, Wan QH. Major histocompatibility complex class II polymorphisms in forest musk deer (Moschus berezovskii) and their probable association with purulent disease. Int J Immunogenet 2014; 41:401-12. [PMID: 25053118 DOI: 10.1111/iji.12135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/20/2014] [Accepted: 06/12/2014] [Indexed: 11/26/2022]
Abstract
Genes of the major histocompatibility complex (MHC) family are crucial in immune responses because they present pathogenic peptides to T cells. In this study, we analysed the genetic variation in forest musk deer (Moschus berezovskii) MHC II genes and its potential association with musk deer purulent disease. In total, 53 purulent disease-susceptible and 46 purulent disease-resistant individuals were selected for MHC II exon 2 fragment analysis. Among them, 16 DQ alleles and four additional DR alleles were identified, with DQ exon 2 fragments displaying a low level of polymorphism. The nonsynonymous substitutions exceeded the synonymous substitutions in the peptide-binding sites of DQA2, DQB1 and DQB2. Then, 28 MHC II alleles were used to analyse the distribution patterns of purulent disease between the susceptible and resistant groups. Among them, three alleles (DQA1*01, DQA1*02 and DQA2*04) were found to be resistant, and five alleles (DRB3*07, DQA1*03, DQA1*04, DQA2*05 and DQA2*06) were found to increase susceptibility. Additionally, three haplotypes were found to be putatively associated with musk deer purulent disease. However, these three haplotypes were only found in the resistant or susceptible group, and their frequencies were low. The results from our study support a contributory role of MHC II polymorphisms in the development of purulent disease in forest musk deer.
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Affiliation(s)
- L Li
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
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Yang C, Xiang C, Zhang X, Yue B. The complete mitochondrial genome of the Alpine musk deer (Moschus chrysogaster). ACTA ACUST UNITED AC 2013; 24:501-3. [PMID: 23577614 DOI: 10.3109/19401736.2013.770504] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Though extensive efforts have been made to investigate the phylogeny of the Cetartiodactyla, the relationships within the Cetartiodactyla, especially the position of the family Moschidae among Ruminantia families, still remain controversial. To further clarify these relationships, we sequenced the mitochondrial genome of the Alpine musk deer (Moschus chrysogaster), which is an endemic endangered species from China. Then, we conducted molecular phylogenetic analyses of the Alpine musk deer and 49 other species on the basis of Bayesian and maximum likelihood methods. The results show that the Moschidae is the sister group of the Bovidae, both of which form a clade that clusters with the Cervidae. The cetaceans are nested within the Artiodactyla as the sister group of the Hippopotamidae. Among the musk deer, M. chrysogaster and M. berezovskii are more closely related to each other than to M. moschiferus.
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Affiliation(s)
- Chengzhong Yang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University , Chengdu 610064 , People's Republic of China
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Wang H, Zhu X, Pan T, Meng X, Li C, Zhou L, Zhang B. Mitochondrial genome of the Alpine musk deer Moschus chrysogaster (Artiodactyla: Ruminantia: Moschidae). MITOCHONDRIAL DNA 2013; 24:487-9. [PMID: 23560692 DOI: 10.3109/19401736.2013.770499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Alpine musk deer (Moschus chrysogaster) is an endangered species, which is distributed on the plateau and mountains, mainly in Neimenggu, Ningxia, Qinghai, Gansu, Sichuan, Tibet, Yunnan, Xinjiang, and other places. In this study, we determined the complete mitochondrial genome of M. chrysogaster. The circle genome was 16,354 bp and consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (CR). The CR was located between the tRNA(Pro) and tRNA(Phe) genes and is 924 bp in length. Overall base composition of the complete mitochondrial DNA was 34.0% A, 28.0% T, 25.1% C, and 12.9% G. The M. chrysogaster mitochondrial genome had 21 tRNA genes folded in the typical cloverleaf structure, with a unique exception of tRNA(Ser).
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Affiliation(s)
- Hui Wang
- School of Life Science, Anhui University , Hefei 230039 , People's Republic of China
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Zhu X, Shi W, Pan T, Wang H, Zhou L, Zhang B. Mitochondrial genome of the Anhui musk deer (Moschus anhuiensis). MITOCHONDRIAL DNA 2012. [PMID: 23198975 DOI: 10.3109/19401736.2012.744985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Anhui musk deer (Moschus anhuiensis) is an endangered species which is endemic to a narrow region in two National Nature Reserves in Dabie Mountains, Anhui Province, China. In this study, we determined the complete mitochondrial genome of M. anhuiensis. The results showed that the total length of the mitogenome was 16,351 bp as a circular DNA and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. Overall base composition of the complete mitochondrial DNA was 34.0% A, 28.1% T, 25.0% C, and 12.9% G. The M. anhuiensis mitochondrial genome had 21 tRNA genes folded in the typical cloverleaf structure, with a unique exception of tRNA(Ser). The mitochondrial genes from M. anhuiensis were overlapped in a total of 72 bp at seven locations, as well as interleaved with a total of 62 bp intergenic spacers.
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Affiliation(s)
- Xiaoxue Zhu
- School of Life Science, Anhui University, Hefei 230039, People's Republic of China
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Yang C, Li P, Zhang X, Guo Y, Gao Y, Xiong Y, Wang L, Qi W, Yue B. The complete mitochondrial genome of the Chinese Sika deer (Cervus nipponTemminck, 1838), and phylogenetic analysis among Cervidae, Moschidae and Bovidae. J NAT HIST 2012. [DOI: 10.1080/00222933.2012.693959] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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