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Liu P, Jiang HY, Li LM, Zhou JB, Huang WZ, Chen JP. The assembled and annotated genome of the masked palm civet (Paguma larvata). Gigascience 2022; 11:6588112. [PMID: 35583674 PMCID: PMC9116208 DOI: 10.1093/gigascience/giac041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/11/2022] [Accepted: 03/29/2022] [Indexed: 12/15/2022] Open
Abstract
Background The masked palm civet (Paguma larvata) acts as an intermediate host of severe acute respiratory syndrome coronavirus (SARS-CoV), which caused SARS, and transfered this virus from bats to humans. Additionally, P. larvata has the potential to carry a variety of zoonotic viruses that may threaten human health. However, genome resources for P. larvata have not been reported to date. Findings A chromosome-level genome assembly of P. larvata was generated using PacBio sequencing, Illumina sequencing, and Hi-C technology. The genome assembly was 2.44 Gb in size, of which 95.32% could be grouped into 22 pseudochromosomes, with contig N50 and scaffold N50 values of 12.97 Mb and 111.81 Mb, respectively. A total of 21,582 protein-coding genes were predicted, and 95.20% of the predicted genes were functionally annotated. Phylogenetic analysis of 19 animal species confirmed the close genetic relationship between P. larvata and species belonging to the Felidae family. Gene family clustering revealed 119 unique, 243 significantly expanded, and 58 significantly contracted genes in the P. larvata genome. We identified 971 positively selected genes in P. larvata, and one known human viral receptor gene PDGFRA is positively selected in P. larvata, which is required for human cytomegalovirus infection. Conclusions This high-quality genome assembly provides a valuable genomic resource for exploring virus–host interactions. It will also provide a reliable reference for studying the genetic bases of the morphologic characteristics, adaptive evolution, and evolutionary history of this species.
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Affiliation(s)
- Ping Liu
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Hai-Ying Jiang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Lin-Miao Li
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Jia-Bin Zhou
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Wen-Zhong Huang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Jin-Ping Chen
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
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2
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Ecological traps and boosters of ixodid ticks: The differing ecological roles of two sympatric introduced mammals. Ticks Tick Borne Dis 2021; 12:101687. [PMID: 33631488 DOI: 10.1016/j.ttbdis.2021.101687] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 11/22/2022]
Abstract
The raccoon (Procyon lotor) and masked palm civet (Paguma larvata) are introduced species in Japan and have become abundant in human-inhabited environments. We surveyed tick infestations and tick ingestion by introduced raccoons and masked palm civets captured in Hayama, Kanagawa Prefecture, Japan between November 2018 and January 2020. We collected ticks from the body surface of animals and tick capitula from the gastrointestinal contents. We collected 18,357 ticks identified as Haemaphysalis flava, Haemaphysalis megaspinosa, Haemaphysalis longicornis, Ixodes ovatus, Ixodes tanuki, and Amblyomma testudinarium from 58 of 60 raccoons and 152 ticks, identified as H. flava and I. tanuki, from 16 of 41 masked palm civets. Furthermore, we obtained 16 capitula from 12 % of raccoons and 106 capitula from 63 % of masked palm civets. Raccoons harbored a greater number of ticks (all stages of H. flava and adult I. tanuki) compared with masked palmed civets, whereas the latter species ingested a greater number of nymphal and larval ticks. The results of this study extend our understanding of the ecological roles of two introduced wildlife species. The raccoon may act as an ecological booster, thereby increasing the success rate of bloodmeals and reproduction in ticks. In contrast, the masked palm civet may act as an ecological trap by effectively grooming to remove ticks and prevent bloodmeals.
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Yu Z, Wen X, Huang X, Yang R, Guo Y, Feng Y, Xiao L, Li N. Molecular characterization and zoonotic potential of Enterocytozoon bieneusi, Giardia duodenalis and Cryptosporidium sp. in farmed masked palm civets (Paguma larvata) in southern China. Parasit Vectors 2020; 13:403. [PMID: 32771043 PMCID: PMC7414269 DOI: 10.1186/s13071-020-04274-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Masked palm civets are known to play an important role in the transmission of some zoonotic pathogens. However, the distribution and zoonotic potential of Enterocytozoon bieneusi, Giardia duodenalis and Cryptosporidium spp. in these animals remain unclear. METHODS A total of 889 fecal specimens were collected in this study from farmed masked palm civets in Hainan, Guangdong, Jiangxi and Chongqing, southern China, and analyzed for these pathogens by nested PCR and DNA sequencing. RESULTS Altogether, 474 (53.3%), 34 (3.8%) and 1 (0.1%) specimens were positive for E. bieneusi, G. duodenalis and Cryptosporidium sp., respectively. Sequence analysis revealed the presence of 11 novel E. bieneusi genotypes named as PL1-PL11 and two known genotypes Peru8 and J, with PL1 and PL2 accounting for 90% of E. bieneusi infections. Phylogenetically, PL4, PL5, PL9, PL10 and PL11 were clustered into Group 1, while PL1, PL2, PL3, PL6, PL7 and PL8 were clustered into Group 2. Assemblage B (n = 33) and concurrence of B and D (n = 1) were identified among G. duodenalis-positive animals. Further multilocus genotyping of assemblage B has revealed that all 13 multilocus genotypes in civets formed a cluster related to those from humans. The Cryptosporidium isolate from one civet was identified to be genetically related to the Cryptosporidium bamboo rat genotype II. CONCLUSIONS To the best of our knowledge, this first report of enteric protists in farmed masked palm civets suggests that these animals might be potential reservoirs of zoonotic E. bieneusi and G. duodenalis genotypes.
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Affiliation(s)
- Zhengjie Yu
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xi Wen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Xitong Huang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Ruohong Yang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Yaqiong Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China
| | - Na Li
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong, 510642, China.
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Endo Y, Lin LK, Yamazaki K, Pei KJC, Chang SW, Chen YJ, Ochiai K, Yachimori S, Anezaki T, Kaneko Y, Masuda R. Introduction and Expansion History of the Masked Palm Civet, Paguma larvata, in Japan, Revealed by Mitochondrial DNA Control Region and Cytochrome b Analysis. MAMMAL STUDY 2020. [DOI: 10.3106/ms2020-0016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Yu Endo
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Liang-Kong Lin
- Department of Life Science, Tunghai University, Taichung 407, Taiwan
| | - Koji Yamazaki
- Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Kurtis Jai-Chyi Pei
- National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
| | - Shih-Wei Chang
- Division of Zoology, Endemic Species Research Institute, Nantou 55244, Taiwan
| | - Yen-Jean Chen
- Department of Zoology, National Museum of Natural Science, Taichung 404, Taiwan
| | - Keiji Ochiai
- Natural History Museum and Institute, Chiba 260-8682, Japan
| | | | - Tomoko Anezaki
- Gunma Museum of Natural History, Tomioka 370-2345, Japan
| | - Yayoi Kaneko
- Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Ryuichi Masuda
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan
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Nishizawa T, Sugimoto Y, Takeda T, Kodera Y, Hatano Y, Takahashi M, Okamoto H. Identification and whole genome characterization of novel anelloviruses in masked palm civets (Paguma larvata): Segregation into four distinct clades. Virus Res 2018; 256:183-191. [PMID: 30149046 DOI: 10.1016/j.virusres.2018.08.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
The members of the family Anelloviridae are small and single-stranded DNA viruses with marked diversity in sequence and length, which ubiquitously infect many vertebrates, including mammals, birds and reptiles. The anelloviruses isolated from mammals are currently classified into 11 assigned and four proposed genera; some anelloviruses remain unassigned. The present study was conducted to identify anelloviruses in wild-caught masked palm civets (Paguma larvata) in Japan using a rolling-circle amplification method. Thirteen novel anellovirus strains were identified from 8 of 10 masked palm civets and their entire genomic sequences (2039-2535 nucleotides) were determined; they were classifiable into four distinct clades. Comparative analyses of all reported anelloviruses for which the entire or near-entire genomic sequences have been determined, including the 13 strains obtained in the present study, revealed that anelloviruses can provisionally be classified into 20 clades, which may correspond to 20 genera (including 11 assigned and four proposed genera) by a >70% amino acid sequence difference in open reading frame 1 (ORF1). This study suggested that novel anelloviruses of marked diversity are circulating in animals worldwide, and that the rolling-circle amplification method would be useful for identifying novel anelloviruses and other viruses with a circular DNA genome.
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Affiliation(s)
- Tsutomu Nishizawa
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Yuji Sugimoto
- Nikko Branch, Tochigi Hunter Association, Nikko, Tochigi, 321-2522, Japan
| | - Tsutomu Takeda
- Center for Weeds and Wildlife Management, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Yuuji Kodera
- Center for Weeds and Wildlife Management, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan
| | - Yumi Hatano
- Sakakibara Heart Institute Clinic, Shinjuku-ku, Tokyo, 163-0804, Japan
| | - Masaharu Takahashi
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Tochigi, 329-0498, Japan.
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Graham CF, Glenn TC, McArthur AG, Boreham DR, Kieran T, Lance S, Manzon RG, Martino JA, Pierson T, Rogers SM, Wilson JY, Somers CM. Impacts of degraded
DNA
on restriction enzyme associated
DNA
sequencing (
RADS
eq). Mol Ecol Resour 2015; 15:1304-15. [DOI: 10.1111/1755-0998.12404] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Carly F. Graham
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Travis C. Glenn
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Andrew G. McArthur
- M.G. DeGroote Institute for Infectious Disease Research Department of Biochemistry and Biomedical Sciences DeGroote School of Medicine McMaster University 1280 Main Street West Hamilton Ontario L8S 4K1 Canada
| | - Douglas R. Boreham
- Medical Sciences Northern Ontario School of Medicine Greater Sudbury Ontario P0M Canada
| | - Troy Kieran
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Stacey Lance
- Savannah River Ecology Laboratory University of Georgia Athens GA 30602 USA
| | - Richard G. Manzon
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Jessica A. Martino
- Department of Biology University of Regina Regina Saskatchewan S4S 0A2 Canada
| | - Todd Pierson
- College of Public Health University of Georgia Athens GA 30602 USA
| | - Sean M. Rogers
- Department of Biological Sciences University of Calgary Calgary Alberta T2N 1N4 Canada
| | - Joanna Y. Wilson
- Department of Biology McMaster University Hamilton Ontario L8S 4M1 Canada
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Geng QF, Liu J, Sun L, Liu H, Ou-Yang Y, Cai Y, Tang XS, Zhang HW, Wang ZS, An SQ. Development and characterization of polymorphic microsatellite markers (SSRs) for an endemic plant, Pseudolarix amabilis (Nelson) Rehd. (Pinaceae). Molecules 2015; 20:2685-92. [PMID: 25658143 PMCID: PMC6272200 DOI: 10.3390/molecules20022685] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 01/21/2015] [Accepted: 01/29/2015] [Indexed: 11/16/2022] Open
Abstract
Pseudolarix (Pinaceae) is a vulnerable (sensu IUCN) monotypic genus restricted to southeastern China. To better understand levels of genetic diversity, population structure and gene flow among populations of P. amabilis, we developed five compound SSR markers and ten novel polymorphic expressed sequence tags (EST) derived microsatellites. The results showed that all 15 loci were polymorphic with the number of alleles per locus ranging from two to seven. The expected and observed heterozygosities varied from 0.169 to 0.752, and 0.000 to 1.000, respectively. The inbreeding coefficient ranged from −0.833 to 1.000. These markers will contribute to research on genetic diversity and population genetic structure of P. amabilis, which in turn will contribute to the species conservation.
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Affiliation(s)
- Qi-Fang Geng
- School of Life Science, Nanjing University, Nanjing 210093, China; E-Mails: (Q.-F.G.); (J.L.); (L.S.); (Y.O.-Y.); (Y.C.)
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China
| | - Jun Liu
- School of Life Science, Nanjing University, Nanjing 210093, China; E-Mails: (Q.-F.G.); (J.L.); (L.S.); (Y.O.-Y.); (Y.C.)
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China
| | - Lin Sun
- School of Life Science, Nanjing University, Nanjing 210093, China; E-Mails: (Q.-F.G.); (J.L.); (L.S.); (Y.O.-Y.); (Y.C.)
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China
| | - Hong Liu
- International Center for Tropical Botany, Department of Earth and Environment, Florida International University, Miami, FL 33199, USA; E-Mail:
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Yan Ou-Yang
- School of Life Science, Nanjing University, Nanjing 210093, China; E-Mails: (Q.-F.G.); (J.L.); (L.S.); (Y.O.-Y.); (Y.C.)
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China
| | - Ying Cai
- School of Life Science, Nanjing University, Nanjing 210093, China; E-Mails: (Q.-F.G.); (J.L.); (L.S.); (Y.O.-Y.); (Y.C.)
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China
| | - Xin-Sheng Tang
- College of Life and Environment Sciences, Huangshan University, Huangshan 245041, China; E-Mail:
| | - Hong-Wei Zhang
- Administration of Zhejiang Qingliangfeng National Nature Reserve, Lin’an 311321, China; E-Mail:
| | - Zhong-Sheng Wang
- School of Life Science, Nanjing University, Nanjing 210093, China; E-Mails: (Q.-F.G.); (J.L.); (L.S.); (Y.O.-Y.); (Y.C.)
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China
- Authors to whom correspondence should be addressed; E-Mails: (Z.-S.W.); (S.-Q.A.); Tel.: +86-25-8968-2705 (Z.-S.W.); +86-25-8968-4560 (S.-Q.A.)
| | - Shu-Qing An
- School of Life Science, Nanjing University, Nanjing 210093, China; E-Mails: (Q.-F.G.); (J.L.); (L.S.); (Y.O.-Y.); (Y.C.)
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China
- Authors to whom correspondence should be addressed; E-Mails: (Z.-S.W.); (S.-Q.A.); Tel.: +86-25-8968-2705 (Z.-S.W.); +86-25-8968-4560 (S.-Q.A.)
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Tsujino R, Yumoto T. Habitat preferences of medium/large mammals in human disturbed forests in Central Japan. Ecol Res 2014. [DOI: 10.1007/s11284-014-1159-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kamada S, Murakami T, Masuda R. Multiple Origins of the Japanese MartenMartes melampusIntroduced Into Hokkaido Island, Japan, Revealed by Microsatellite Analysis. MAMMAL STUDY 2013. [DOI: 10.3106/041.038.0410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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The genetic structure of raccoon introduced in Central Europe reflects multiple invasion pathways. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0595-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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