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Belete MT, Kim SE, Gudeta WF, Igori D, Kwon JA, Lee SH, Moon JS. Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis. Virol J 2024; 21:86. [PMID: 38622686 PMCID: PMC11017662 DOI: 10.1186/s12985-024-02361-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Viruses have notable effects on agroecosystems, wherein they can adversely affect plant health and cause problems (e.g., increased biosecurity risks and economic losses). However, our knowledge of their diversity and interactions with specific host plants in ecosystems remains limited. To enhance our understanding of the roles that viruses play in agroecosystems, comprehensive analyses of the viromes of a wide range of plants are essential. High-throughput sequencing (HTS) techniques are useful for conducting impartial and unbiased investigations of plant viromes, ultimately forming a basis for generating further biological and ecological insights. This study was conducted to thoroughly characterize the viral community dynamics in individual plants. RESULTS An HTS-based virome analysis in conjunction with proximity sampling and a tripartite network analysis were performed to investigate the viral diversity in chunkung (Cnidium officinale) plants. We identified 61 distinct chunkung plant-associated viruses (27 DNA and 34 RNA viruses) from 21 known genera and 6 unclassified genera in 14 known viral families. Notably, 12 persistent viruses (7 DNA and 5 RNA viruses) were exclusive to dwarfed chunkung plants. The detection of viruses from the families Partitiviridae, Picobirnaviridae, and Spinareoviridae only in the dwarfed plants suggested that they may contribute to the observed dwarfism. The co-infection of chunkung by multiple viruses is indicative of a dynamic and interactive viral ecosystem with significant sequence variability and evidence of recombination. CONCLUSIONS We revealed the viral community involved in chunkung. Our findings suggest that chunkung serves as a significant reservoir for a variety of plant viruses. Moreover, the co-infection rate of individual plants was unexpectedly high. Future research will need to elucidate the mechanisms enabling several dozen viruses to co-exist in chunkung. Nevertheless, the important insights into the chunkung virome generated in this study may be relevant to developing effective plant viral disease management and control strategies.
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Affiliation(s)
- Mesele Tilahun Belete
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Amhara Agricultural Research Institute, Plant Biotechnology Research Division, Bahir Dar, Ethiopia
| | - Se Eun Kim
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Workitu Firmosa Gudeta
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Davaajargal Igori
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Biology, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, Mongolia
| | - Jeong A Kwon
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Su-Heon Lee
- School of Applied Bioscience, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 98411, Republic of Korea.
| | - Jae Sun Moon
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
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Iwai K, Kon T, Fujita Y, Abe H, Honma H, Kawasumi N, Kawakami H, Kawashimo M, Sakurai M, Fuji SI. Genetic diversity of viruses infecting cnidium plants ( Cnidium officinale) in Japan. Virusdisease 2023; 34:431-439. [PMID: 37780903 PMCID: PMC10533470 DOI: 10.1007/s13337-023-00835-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/01/2023] [Indexed: 10/03/2023] Open
Abstract
Cnidium vein yellowing virus (CnVYV), cnidium virus X (CnVX), cucumber mosaic virus (CMV) and cnidium virus 1 (CnV1) were detected at extremely high levels in Cnidium officinale plants showing viral symptoms collected from Iwate and Hokkaido Prefectures, Japan. The complete nucleotide sequence of the newly detected CnVYV and CnV1, and genetic diversity of the cnidium-infecting viruses (CnVYV, CnVX, and CnV1) indicated that South Korean and Japanese cnidium plants had close relationship with each other. All three viruses can infect vegetatively propagated perennials and are vertically transmitted once infection occurs. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00835-w.
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Affiliation(s)
- Kazuma Iwai
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Tatsuya Kon
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Yuito Fujita
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Haruki Abe
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Hiroshi Honma
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Naoki Kawasumi
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Hiroko Kawakami
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Midori Kawashimo
- Botanical Raw Materials Division, Tsumura & Co., 3586 Yoshiwara, Ami-machi, Inashiki-gun, Ibaraki 300-1192 Japan
| | - Miki Sakurai
- Botanical Raw Materials Division, Tsumura & Co., 3586 Yoshiwara, Ami-machi, Inashiki-gun, Ibaraki 300-1192 Japan
| | - Shin-ichi Fuji
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
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Complete Genome Sequences of Two Apple Stem Grooving Viruses in Cnidium officinale in Korea. Microbiol Resour Announc 2023; 12:e0090222. [PMID: 36475761 PMCID: PMC9872693 DOI: 10.1128/mra.00902-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We determined the whole-genome sequences of two apple stem grooving viruses (ASGV) detected in infected Cnidium officinale plants. The analyzed ASGV genomes were 6,494 nucleotides long and encoded two overlapping open reading frames. Phylogenetic analysis revealed the two ASGV isolates to be most closely related to the ASGV isolate Xinjiang-3.
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Jiang X, Luan Y, Chai M, Yang Y, Wang Y, Deng W, Li Y, Cheng X, Wu X. The N-Terminal α-Helix of Potato Virus X-Encoded RNA-Dependent RNA Polymerase Is Required for Membrane Association and Multimerization. Viruses 2022; 14:v14091907. [PMID: 36146714 PMCID: PMC9504981 DOI: 10.3390/v14091907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Positive-sense single-stranded RNA viruses replicate in virus-induced membranous organelles for maximum efficiency and immune escaping. The replication of potato virus X (PVX) takes place on the endoplasmic reticulum (ER); however, how PVX-encoded RNA-dependent RNA polymerase (RdRp) is associated with the ER is still unknown. A proline-kinked amphipathic α-helix was recently found in the MET domain of RdRp. In this study, we further illustrate that the first α-helix of the MET domain is also required for ER association. Moreover, we found that the MET domain forms multimers on ER and the first α-helix is essential for multimerization. These results suggest that the RdRp of PVX adopts more than one hydrophobic motif for membrane association and for multimerization.
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Affiliation(s)
- Xue Jiang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yameng Luan
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Mengzhu Chai
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yingshuai Yang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yuting Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Wenjia Deng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yonggang Li
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaofei Cheng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (X.C.); (X.W.)
| | - Xiaoyun Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
- Correspondence: (X.C.); (X.W.)
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Gudeta WF, Belete MT, Igori D, Kim SE, Moon JS. Complete genome sequence of cnidium closterovirus 1, a novel member of the genus Closterovirus infecting Cnidium officinale. Arch Virol 2022; 167:1491-1494. [PMID: 35474497 DOI: 10.1007/s00705-022-05448-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/17/2022] [Indexed: 11/02/2022]
Abstract
The genome of a novel virus identified in Cnidium officinale is composed of a monopartite ssRNA of 16,755 nucleotides that shares 68.73% (query coverage, 20%) sequence identity with carrot yellow leaf virus (CYLV, accession no. FJ869862.1). It contains 11 putative open reading frames and has an organization typical of closteroviruses. It shares 30-50% nucleotide sequence identity with other closteroviruses. The heat shock protein 70-like protein (HSP70), putative RNA-dependent RNA polymerase (RdRp), and coat protein (CP) show 39-66%, 16-60%, and 24-41% amino acid sequence identity, respectively, to the homologous proteins of previously identified closteroviruses. Molecular and HSP70-based phylogenetic analysis of the genome and encoded protein sequences suggested that this virus is a novel member of the genus Closterovirus in the family Closteroviridae, which we have tentatively named "cnidium closterovirus 1" (CnClV1).
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Affiliation(s)
- Workitu Firomsa Gudeta
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.,Ethiopian Institute of Agricultural Research (EIAR), Holeta, Ethiopia
| | - Mesele Tilahun Belete
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Davaajargal Igori
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,Department of Biology, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, Mongolia
| | - Se Eun Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Jae Sun Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea. .,Biosystems and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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