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Akata I, Edis G, Ozbey BG, Keskin E, Sahin E. Complete Genome Analyses of a Novel Flexivirus with Unique Genome Organization and Three Endornaviruses Hosted by the Mycorrhizal Fungus Terfezia claveryi. Curr Microbiol 2024; 81:210. [PMID: 38837067 DOI: 10.1007/s00284-024-03745-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/19/2024] [Indexed: 06/06/2024]
Abstract
The extensive use of high-throughput sequencing (HTS) has significantly advanced and transformed our comprehension of virus diversity, especially in intricate settings like soil and biological specimens. In this study, we delved into mycovirus sequence surveys within mycorrhizal fungus species Terfezia claveryi, through employing HTS with total double-stranded RNA (dsRNA) extracts. Our findings revealed the presence of four distinct members from the Alsuviricetes class, one flexivirus designated as Terfezia claveryi flexivirus 1 (TcFV1) and three endornaviruses (TcEV1, TcEV2, and TcEV3) in two different T. claveryi isolates. TcFV1, a member of the order Tymovirales, exhibits a unique genome structure and sequence features. Through in-depth analyses, we found that it shares sequence similarities with other deltaflexiviruses and challenges existing Deltaflexiviridae classification. The discovery of TcFV1 adds to the genomic plasticity of mycoviruses within the Tymovirales order, shedding light on their evolutionary adaptations. Additionally, the three newly discovered endornaviruses (TcEV1, TcEV2, and TcEV3) in T. claveryi exhibited limited sequence similarities with other endornaviruses and distinctive features, including conserved domains like DEAD-like helicase, ATPases Associated with Diverse Cellular Activities (AAA ATPase), and RNA dependent RNA polymerase (RdRp), indicating their classification as members of new species within the Alphaendornavirus genus. In conclusion, this research emphasizes the importance of exploring viral diversity in uncultivated fungi, bridging knowledge gaps in mycovirus ecology. The discoveries of a novel flexivirus with unique genome organization and endornaviruses in T. claveryi broaden our comprehension of mycovirus diversity and evolution, highlighting the need for continued investigations into viral populations in wild fungi.
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Affiliation(s)
- Ilgaz Akata
- Faculty of Science Department of Biology, Ankara University, Tandogan, 06100, Ankara, Turkey
| | - Gulce Edis
- Graduate School of Natural and Applied Sciences, Ankara University, Dışkapı, 06110, Ankara, Turkey
| | - Beste Gizem Ozbey
- Faculty of Science Department of Biology, Ankara University, Tandogan, 06100, Ankara, Turkey
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture Department of Fisheries and Aquaculture, Ankara University, Dışkapı, 06110, Ankara, Turkey
| | - Ergin Sahin
- Faculty of Science, Department of Biology, Dokuz Eylul University, Buca, 35390, Izmir, Turkey.
- Fauna and Flora Research and Application Center, Dokuz Eylul University, Buca, 35390, Izmir, Turkey.
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Sahin E, Edis G, Keskin E, Akata I. Molecular characterization of the complete genome of a novel ormycovirus infecting the ectomycorrhizal fungus Hortiboletus rubellus. Arch Virol 2024; 169:110. [PMID: 38664287 DOI: 10.1007/s00705-024-06027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/11/2024] [Indexed: 05/24/2024]
Abstract
Advancements in high-throughput sequencing and the development of new bioinformatics tools for large-scale data analysis play a crucial role in uncovering virus diversity and enhancing our understanding of virus evolution. The discovery of the ormycovirus clades, a group of RNA viruses that are phylogenetically distinct from all known Riboviria members and are found in fungi, highlights the value of these tools for the discovery of novel viruses. The aim of this study was to examine viral populations in fungal hosts to gain insights into the diversity, evolution, and classification of these viruses. Here, we report the molecular characterization of a newly discovered ormycovirus, which we have named "Hortiboletus rubellus ormycovirus 1" (HrOMV1), that was found in the ectomycorrhizal fungus Hortiboletus rubellus. The bipartite genome of HrOMV1, whose nucleotide sequence was determined by HTS and RLM-RACE, consists of two RNA segments (RNA1 and RNA2) that exhibit similarity to those of previously studied ormycoviruses in their organization and the proteins they encode. The presence of upstream, in-frame AUG triplets in the 5' termini of both RNA segments suggests that HrOMV1, like certain other ormycoviruses, employs a non-canonical translation initiation strategy. Phylogenetic analysis showed that HrOMV1 is positioned within the gammaormycovirus clade. Its putative RNA-dependent RNA polymerase (RdRp) exhibits sequence similarity to those of other gammaormycovirus members, the most similarity to that of Termitomyces ormycovirus 1, with 33.05% sequence identity. This protein was found to contain conserved motifs that are crucial for RNA replication, including the distinctive GDQ catalytic triad observed in gammaormycovirus RdRps. The results of this study underscore the significance of investigating the ecological role of mycoviruses in mycorrhizal fungi. This is the first report of an ormycovirus infecting a member of the ectomycorrhizal genus Hortiboletus.
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Affiliation(s)
- Ergin Sahin
- Faculty of Science, Department of Biology, Dokuz Eylul University, Buca, Izmir, 35390, Turkey.
- Fauna and Flora Research and Application Center, Dokuz Eylul University, Buca, Izmir, 35390, Turkey.
| | - Gulce Edis
- Graduate School of Natural and Applied Sciences, Ankara University, Dışkapı, Ankara, 06110, Turkey
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture Department of Fisheries and Aquaculture, Ankara University, Dışkapı, Ankara, 06110, Turkey
| | - Ilgaz Akata
- Faculty of Science Department of Biology, Ankara University, Tandogan, Ankara, 06100, Turkey
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3
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Zhao Y, Zhang X, Mu T, Wu X. Complete genome sequence of a novel partitivirus with a dsRNA3 segment, isolated from Fusarium commune strain CP-SX-3 causing strawberry root rot. Arch Virol 2024; 169:60. [PMID: 38430446 DOI: 10.1007/s00705-024-06004-8] [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: 11/12/2023] [Accepted: 01/24/2024] [Indexed: 03/03/2024]
Abstract
A novel partitivirus, Fusarium commune partitivirus 1 (FcoPV1), was identified in Fusarium commune strain CP-SX-3 isolated from diseased roots of strawberry with symptoms of root rot. The complete genome of FcoPV1 comprises three double-stranded RNAs (dsRNAs): dsRNA1 (1,825 nt), dsRNA2 (1,592 nt), and dsRNA3 (1,421 nt). dsRNA1 contains a single open reading frame (ORF1) encoding an RNA-dependent RNA polymerase (RdRp), and dsRNA2 contains a single ORF (ORF2) encoding a coat protein (CP). dsRNA3 is a possible satellite RNA that does not appear to encode a known protein. BLASTp analysis revealed that RdRp (86.59%) and CP (74.13%) encoded by the two ORFs (ORF1 and ORF2) had the highest sequence similarity to their counterparts in Fusarium equiseti partitivirus 1 (FePV1). Phylogenetic analysis based on the complete amino acid sequence of RdRp suggested that FcoPV1 should be considered a member of a new species in the proposed genus "Zetapartitivirus" within the family Partitiviridae. To the best of our knowledge, this is the first report of a zetapartitivirus infecting phytopathogenic F. commune.
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Affiliation(s)
- Yumeng Zhao
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
- Liaoning Institute of Pomology, Yingkou City, Liaoning, 115009, People's Republic of China
| | - Xinyi Zhang
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Tongyu Mu
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Xuehong Wu
- Department of Plant Pathology, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China.
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4
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Xu M, Liu H, Jia X, Zou X, Lu Y, Sui L, Li Q, Zhang Z, Liu J. The complete genome sequences of a negative single-stranded RNA virus and a double-stranded RNA virus coinfecting the entomopathogenic fungus Beauveria bassiana Vuillemin. Arch Virol 2024; 169:42. [PMID: 38332318 DOI: 10.1007/s00705-024-05985-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/11/2024] [Indexed: 02/10/2024]
Abstract
Beauveria bassiana Vuillemin is an entomopathogenic fungus that has been developed as a biological insecticide. B. bassiana can be infected by single or multiple mycoviruses, most of which are double-stranded RNA (dsRNA) viruses, while infections with single-stranded RNA (ssRNA) viruses, especially negative single-stranded RNA (-ssRNA) viruses, have been observed less frequently. In the present study, we sequenced and analyzed the complete genomes of two new different mycoviruses coinfecting a single B. bassiana strain: a -ssRNA virus which we have named "Beauveria bassiana negative-strand RNA virus 1" (BbNSRV1), and a dsRNA virus, which we have named "Beauveria bassiana orthocurvulavirus 1" (BbOCuV1). The genome of BbNSRV1 consists of a single segment of negative-sense, single-stranded RNA with a length of 6169 nt, containing a single open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) with 1949 aa (220.1 kDa). BLASTx analysis showed that the RdRp had the highest sequence similarity (59.79%) to that of Plasmopara viticola lesion associated mononegaambi virus 2, a member of the family Mymonaviridae. This is the first report of a -ssRNA mycovirus infecting B. bassiana. The genome of BbOCuV1 consists of two dsRNA segments, 2164 bp and 1765 bp in length, respectively, with dsRNA1 encoding a protein with conserved RdRp motifs and 70.75% sequence identity to the putative RdRp of the taxonomically unassigned mycovirus Fusarium graminearum virus 5 (FgV5), and the dsRNA2 encoding a putative coat protein with sequence identity 64.26% to the corresponding protein of the FgV5. Phylogenetic analysis indicated that BbOCuV1 belongs to a taxonomically unassigned group of dsRNA mycoviruses related to members of the families Curvulaviridae and Partitiviridae. Hence, it might be the member of a new family that remains to be named and formally recognized.
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Affiliation(s)
- Mengnan Xu
- Jilin Normal University, Siping, 136000, China
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of agriculture and rural affairs, Changchun, 130033, China
| | - Hongyu Liu
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of agriculture and rural affairs, Changchun, 130033, China
- Jilin Agricultural University, Changchun, 130118, China
| | - Xue Jia
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of agriculture and rural affairs, Changchun, 130033, China
- Jilin Agricultural University, Changchun, 130118, China
| | - Xiaowei Zou
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of agriculture and rural affairs, Changchun, 130033, China
| | - Yizhuo Lu
- Jilin Normal University, Siping, 136000, China
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of agriculture and rural affairs, Changchun, 130033, China
| | - Li Sui
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of agriculture and rural affairs, Changchun, 130033, China
| | - Qiyun Li
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of agriculture and rural affairs, Changchun, 130033, China
- Jilin Agricultural University, Changchun, 130118, China
- Jilin Agricultural Science and Technology University, Jilin, 132101, China
| | - Zhengkun Zhang
- Jilin Normal University, Siping, 136000, China.
- Institute of Plant Protection, Jilin Academy of Agricultural Sciences, Jilin Key Laboratory of Agricultural Microbiology, Key Laboratory of Integrated Pest Management on Crops in Northeast China, Ministry of agriculture and rural affairs, Changchun, 130033, China.
- Jilin Agricultural University, Changchun, 130118, China.
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5
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Erkmen S, Sahin E, Akata I. Full-length genome characterization of a novel mitovirus isolated from the root rot fungus Armillaria mellea. Virus Genes 2024; 60:65-70. [PMID: 38103104 DOI: 10.1007/s11262-023-02041-8] [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: 08/24/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Members of the genus Armillaria belong to the group of pathogenic and facultative saprotrophic fungi that are generally known as one of the causative agents of white root rot in infected plants including deciduous and evergreen trees and shrubs. Although several single-stranded RNA mycoviruses were previously described in different Armillaria species, there is no report on mitoviruses (one of the simplest RNA viruses of fungal hosts) known to infect Armillaria taxa. In this study, a new mitovirus denominated "Armillaria mellea mitovirus 1" (AmMV1) was identified in the sporophore samples of Armillaria mellea, commonly known as honey mushroom. AmMV1 has a genome length of 4440 nucleotides and a G + C content of 48%. It encompasses a single open reading frame (ORF) that encodes an RNA-dependent RNA polymerase (RdRp). Comparison through BLASTp analysis revealed that the RdRp domain of AmMV1 shares a sequence identity ranging from 33.43% to 43.27% with RdRp domains of Duamitovirus genus members, having the highest similarity (43.27%) to Rhizoctonia solani mitovirus 94. According to phylogenetic analysis, AmMV1 is classified as a member of the genus Duamitovirus belonging to the Mitoviridae family. This marks the initial instance of a mitovirus identified in Armillaria spp..
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Affiliation(s)
- Sıla Erkmen
- Faculty of Science, Department of Biology, Dokuz Eylul University, 35390, Buca, Izmir, Turkey
| | - Ergin Sahin
- Faculty of Science, Department of Biology, Dokuz Eylul University, 35390, Buca, Izmir, Turkey.
- Fauna and Flora Research and Application Center, Dokuz Eylul University, 35390, Buca, Izmir, Turkey.
| | - Ilgaz Akata
- Faculty of Science, Department of Biology, Ankara University, 06100, Tandogan, Ankara, Turkey
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6
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Shi R, Mo X, Chen Z, Chen W, Yu S, Liu H, Li Y, Dai L, Li Y. Molecular characterization of a novel mycovirus from binucleate Rhizoctonia AG-A strain A46. Arch Virol 2024; 169:31. [PMID: 38233611 DOI: 10.1007/s00705-024-05963-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Abstract
The complete genome sequence of a positive-sense single-stranded RNA (+ ssRNA) virus, Rhizoctonia beny-like virus 1 (RBLV1), isolated from binucleate Rhizoctonia AG-A strain A46, was determined. The RBLV1 genome is 10,280 nt in length and contains a short stretch of adenines at the 3' terminus. It contains a single open reading frame (ORF) encoding a 376.30-kDa protein with viral helicase and RNA-dependent RNA polymerase (RdRp) motifs. The encoded protein exhibited the highest sequence similarity to Rhizoctonia cerealis beny-like virus 0928-1 (RcBeLV 0928-1, 45.25%), with a sequence coverage of 63%. Phylogenetic analysis based on ORF protein sequences revealed that RBLV1 is a novel unclassified mycovirus.
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Affiliation(s)
- Rui Shi
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, 650214, China
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, 650021, China
| | - Xiaohan Mo
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, 650021, China
| | - Zebin Chen
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, 650214, China
| | - Wurong Chen
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, 650214, China
| | - Shuhui Yu
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, 650214, China
| | - He Liu
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, 650214, China
| | - Yuchuan Li
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, 650214, China
| | - Lili Dai
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, 650214, China
| | - Yanqiong Li
- College of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan, 650214, China.
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7
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Zhang X, Shi H, Li J, Wu X. Complete genome sequence of a novel virus isolated from the phytopathogenic fungus Ceratobasidium sp. AG-A strain SHX-YJLC-1. Arch Virol 2023; 168:241. [PMID: 37668772 DOI: 10.1007/s00705-023-05868-6] [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: 05/31/2023] [Accepted: 07/30/2023] [Indexed: 09/06/2023]
Abstract
A novel mycovirus, Ceratobasidium bipartite virus 1 (CBV1), was identified in Ceratobasidium sp. AG-A strain SHX-YJLC-1 isolated from diseased potato stems. The complete genome of CBV1 consists of two double-stranded RNA (dsRNA) segments: dsRNA1 (2311 bp) and dsRNA2 (1761 bp). dsRNA1 contains a single open reading frame (ORF1) encoding an RNA-dependent RNA polymerase (RdRp), while dsRNA2 contains a single ORF (ORF2) encoding a hypothetical protein (HP) with unknown function. BLASTp analysis revealed that RdRp (75.04%) and HP (61.86%) encoded by the two ORFs have the highest sequence similarity to their counterparts in Rhizoctonia solani dsRNA virus 11 (RsRV11). The genome organization and phylogenetic analysis indicated that the closest relatives to CBV1 are members of the proposed family "Bipartitiviridae". Based on the collective results, CBV1 is inferred to be a new member of the proposed family "Bipartitiviridae". This is the first report on the complete genome sequence of the novel bipartitivirus CBV1, which infects Ceratobasidium sp. AG-A strain SHX-YJLC-1.
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Affiliation(s)
- Xinyi Zhang
- College of Plant Protection, China Agricultural University, Haidian District, 100193, Beijing, People's Republic of China
| | - Hao Shi
- College of Plant Protection, China Agricultural University, Haidian District, 100193, Beijing, People's Republic of China
| | - Jinting Li
- College of Plant Protection, China Agricultural University, Haidian District, 100193, Beijing, People's Republic of China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, 100193, Beijing, People's Republic of China.
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Sahin E, Ozbey Saridogan BG, Keskin E, Akata I. Identification and complete genome sequencing of a novel betapartitivirus naturally infecting the mycorrhizal desert truffle Terfezia claveryi. Virus Genes 2023; 59:254-259. [PMID: 36735175 DOI: 10.1007/s11262-023-01972-6] [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: 10/15/2022] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
Viruses that naturally infect fungal species and capable of establishing mycorrhizae are largely unknown. In this study, we identified and characterized a new partitivirus inhabiting the ascomycete, mycorrhizal desert truffle species Terfezia claveryi, and named it "Terfezia claveryi partitivirus 1" (TcPV1). The entire genome of TcPV1, sequenced by both high throughput sequencing of the total dsRNA extracts and by Sanger sequencing of the RLM-RACE PCR products comprised two dsRNA segments of 2404 bp and 2374 bp, respectively. Both dsRNA genome segments harbored a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp), and a capsid protein (CP), respectively. The BLASTp search of the RdRp and CP sequences revealed the highest sequence identities (41.92% and 24.13% identity, respectively) to those of Bipolaris maydis partitivirus 2 and Plasmopara viticola lesion associated partitivirus 5. Molecular phylogenetic analyses of the RdRp sequence showed that TcPV1 fall within a clade composed entirely of members of the genus Betapartitivirus, belonging to the family Partitiviridae. In light of this molecular evidence, TcPV1 is a new member of the genus Betapartitivirus. This is the first report of a new partitivirus hosted by the ascomycete, mycorrhizal fungus T. claveryi.
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Affiliation(s)
- Ergin Sahin
- Department of Biology, Faculty of Science, Dokuz Eylül University, Buca, 35390, İzmir, Turkey.
- Fauna and Flora Research and Application Center, Dokuz Eylül University, Buca, 35390, İzmir, Turkey.
| | | | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture, Department of Fisheries and Aquaculture, Ankara University, Dışkapı, 06110, Ankara, Turkey
| | - Ilgaz Akata
- Department of Biology, Faculty of Science, Ankara University, Tandogan, 06100, Ankara, Turkey
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Akata I, Edis G, Keskin E, Sahin E. Diverse partitiviruses hosted by the ectomycorrhizal agaric Hebeloma mesophaeum and the natural transmission of a partitivirus between phylogenetically distant, sympatric fungi. Virology 2023; 581:63-70. [PMID: 36913914 DOI: 10.1016/j.virol.2023.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Mycorrhizal fungi host diverse mycoviruses that contribute to our understanding of their diversity and evolution. Here we report on the identification and complete genome characterization of three novel partitiviruses naturally infecting the ectomycorrhizal fungus Hebeloma mesophaeum. During NGS derived viral sequence analyses, we identified a partitivirus that is conspecific with the previously reported partitivirus (LcPV1) described from a saprotrophic fungus Leucocybe candicans. The two distinct fungal specimens inhabited the same vicinity of a campus garden. RdRp sequences encoded by the LcPV1 isolates from both host fungi was found to be identical. Bio-tracking studies revealed that viral loads of LcPV1 drop significantly in L. candicans but not in H. mesophaeum within four years period. The physical proximity of the mycelial networks of both fungal specimens implied the occurrence of a virus transmission event with unknown mechanism. Nature of this virus transmission was discussed in relation to transient interspecific mycelial contact hypothesis.
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Affiliation(s)
- Ilgaz Akata
- Ankara University Faculty of Science Department of Biology, 06100, Tandogan, Ankara, Turkey
| | - Gulce Edis
- Ankara University Science Institute, 06110, Dışkapı, Ankara, Turkey
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture Department of Fisheries and Aquaculture, Ankara University, 06110, Dışkapı, Ankara, Turkey
| | - Ergin Sahin
- Dokuz Eylül University Faculty of Science Department of Biology, 35390, Buca, İzmir, Turkey; Dokuz Eylül University Fauna and Flora Research and Application Center, 35390, Buca, İzmir, Turkey.
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10
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Sun A, Sun Y, Luo L, Zhao L, Li C, Yang G, Dong W. Molecular characterization of a novel mitovirus from Rhizoctonia solani AG-4 HGIII strain XMC-IF. Arch Virol 2022; 167:2821-2825. [PMID: 36261748 DOI: 10.1007/s00705-022-05599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/30/2022] [Indexed: 12/14/2022]
Abstract
The nucleotide sequence of a viral double-stranded RNA (dsRNA) from Rhizoctonia solani AG-4 HGIII strain XMC-IF (designated as "Rhizoctonia solani mitovirus 106", RsMV-106) was determined. The complete sequence was 2794 bp in length with a 57.50% A + U content and contained a large open reading frame (ORF) when the fungal mitochondrial genetic code was used. The ORF potentially encodes a 95.76-kDa protein containing a conserved domain of an RNA-dependent RNA polymerase (RdRp). BLASTp analysis revealed that the RdRp domain of RsMV-106 shared 47.52-73.24% sequence identity with those of viruses of the genus Duamitovirus and was most similar (73.24% identity) to that of Alternaria alternata mitovirus 1 (AaMV1). Phylogenetic analysis showed that RsMV-106 is a novel member of the genus Duamitovirus, family Mitoviridae. This is the first report of the full genome sequence of a mitovirus associated with R. solani AG-4 HGIII.
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Affiliation(s)
- Aili Sun
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Yang Sun
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Li Luo
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Lianjing Zhao
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Chengyun Li
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201, Kunming, Yunnan, China
| | - Genhua Yang
- State Key Laboratory for Protection and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
| | - Wenhan Dong
- Technology Department, Yunnan Agricultural University, 650201, Kunming, Yunnan, China.
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Kartali T, Zsindely N, Nyilasi I, Németh O, Sávai GN, Kocsubé S, Lipinszki Z, Patai R, Spisák K, Nagy G, Bodai L, Vágvölgyi C, Papp T. Molecular Characterization of Novel Mycoviruses in Seven Umbelopsis Strains. Viruses 2022; 14:v14112343. [PMID: 36366438 PMCID: PMC9694724 DOI: 10.3390/v14112343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 02/01/2023] Open
Abstract
The presence of viruses is less explored in Mucoromycota as compared to other fungal groups such as Ascomycota and Basidiomycota. Recently, more and more mycoviruses are identified from the early-diverging lineages of fungi. We have determined the genome of 11 novel dsRNA viruses in seven different Umbelopsis strains with next-generation sequencing (NGS). The identified viruses were named Umbelopsis ramanniana virus 5 (UrV5), 6a (UrV6a); 6b (UrV6b); 7 (UrV7); 8a (UrV8a); 8b (UrV8b); Umbelopsis gibberispora virus 1 (UgV1); 2 (UgV2) and Umbelopsis dimorpha virus 1a (UdV1a), 1b (UdV1b) and 2 (UdV2). All the newly identified viruses contain two open reading frames (ORFs), which putatively encode the coat protein (CP) and the RNA-dependent RNA polymerase (RdRp), respectively. Based on the phylogeny inferred from the RdRp sequences, eight viruses (UrV7, UrV8a, UrV8b, UgV1, UgV2, UdV1a, UdV1b and UdV2) belong to the genus Totivirus, while UrV5, UrV6a and UrV6b are placed into a yet unclassified but well-defined Totiviridae-related group. In UrV5, UgV1, UgV2, UrV8b, UdV1a, UdV2 and UdV1b, ORF2 is predicted to be translated as a fusion protein via a rare +1 (or -2) ribosomal frameshift, which is not characteristic to most members of the Totivirus genus. Virus particles 31 to 32 nm in diameter could be detected in the examined fungal strains by transmission electron microscopy. Through the identification and characterization of new viruses of Mucoromycota fungi, we can gain insight into the diversity of mycoviruses, as well as into their phylogeny and genome organization.
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Affiliation(s)
- Tünde Kartali
- ELKH-SZTE Fungal Pathogenicity Mechanisms Research Group, University of Szeged, 6726 Szeged, Hungary
- Correspondence: (T.K.); (T.P.)
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Ildikó Nyilasi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Orsolya Németh
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Gergő Norbert Sávai
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Zoltán Lipinszki
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), 6726 Szeged, Hungary
| | - Roland Patai
- Neuronal Plasticity Research Group, Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary
| | - Krisztina Spisák
- Neuronal Plasticity Research Group, Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary
- Theoretical Medicine Doctoral School, University of Szeged, 6722 Szeged, Hungary
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Tamás Papp
- ELKH-SZTE Fungal Pathogenicity Mechanisms Research Group, University of Szeged, 6726 Szeged, Hungary
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
- Correspondence: (T.K.); (T.P.)
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12
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A novel fungal negative-stranded RNA virus related to mymonaviruses in Auricularia heimuer. Arch Virol 2022; 167:2223-2227. [PMID: 35962823 DOI: 10.1007/s00705-022-05540-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 06/09/2022] [Indexed: 11/02/2022]
Abstract
Here, we report the characterization of a novel (-)ssRNA mycovirus isolated from Auricularia heimuer CCMJ1222, using a combination of RNA-seq, reverse transcription polymerase chain reaction, 5' and 3' rapid amplification of cDNA ends, and Sanger sequencing. Based on database searches, sequence alignment, and phylogenetic analysis, we designated the virus as "Auricularia heimuer negative-stranded RNA virus 1" (AhNsRV1). This virus has a monopartite RNA genome related to mymonaviruses (order Mononegavirales). The AhNsRV1 genome consists of 11,441 nucleotides and contains six open reading frames (ORFs). The largest ORF encodes a putative RNA-dependent RNA polymerase; the other ORFs encode hypothetical proteins with no conserved domains or known function. AhNsRV1 is the first (-)ssRNA virus and the third virus known to infect A. heimuer.
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13
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Complete nucleotide sequence of a novel alphapartitivirus from Rhizoctonia solani AG-4 HG III isolate SM03. Arch Virol 2022; 167:953-957. [PMID: 35112203 DOI: 10.1007/s00705-021-05261-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/23/2021] [Indexed: 11/02/2022]
Abstract
In this report, the full genome sequence of a novel mycovirus, designated as "Rhizoctonia solani partitivirus SM03" (RsPV-SM03), was determined in Rhizoctonia solani AG-4 HG III isolate SM03. RsPV-SM03 genome consists of two dsRNAs (dsRNA-1 and dsRNA-2), each of them contains one single open reading frame (ORF). ORF1 of dsRNA-1 encodes a putative RNA-dependent RNA polymerase (RdRp), while ORF2 of dsRNA-2 encodes a putative viral coat protein (CP). Phylogenetic analysis indicated that the RdRp and CP of RsPV-SM03 are closely related to those of other members of the genus Alphapartitivirus, family Partitiviridae, suggesting that RsPV-SM03 represents a novel species in the genus Alphapartitivirus.
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14
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Li Y, Xu P, Zhang L, Chen W, Ren Z, Yang G, Mo X. Complete nucleotide sequence of a novel mycovirus infecting Rhizoctonia fumigata AG-Ba isolate C-314 Baishi. Arch Virol 2022; 167:959-963. [PMID: 35112206 DOI: 10.1007/s00705-021-05269-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/31/2021] [Indexed: 11/02/2022]
Abstract
The complete nucleotide sequence of a novel mycovirus, designated as "Rhizoctonia fumigata bipartite virus 1" (RfBV1), from Rhizoctonia fumigata AG-Ba isolate C-314 Baishi was determined. The genome of RfBV1 is composed of two double-stranded RNAs (dsRNA). dsRNA-1 (2311 bp) contains one open reading frame (ORF), which codes for the putative RNA-dependent RNA polymerase (RdRp) of the virus. dsRNA-2 (1690 bp) contains one ORF, which encodes a putative protein whose function is unknown. Phylogenetic analysis indicated that the RdRp of RfBV1 clustered with several unassigned bipartite viruses belonging to the CThTV-like viruses group, but not the family Amalgaviridae or Partitiviridae. Our study suggests that RfBV1 is a novel mycovirus related to the CThTV-like viruses.
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Affiliation(s)
- Yanqiong Li
- College of Agriculture and Life Sciences, Kunming University, Kunming, 650214, Yunnan, China.,College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.,Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Ping Xu
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.,Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Lifang Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.,College of Bioresources and Food Engineering, Qujing Normal University, Qujing, 655011, Yunnan, China.,Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Wurong Chen
- College of Agriculture and Life Sciences, Kunming University, Kunming, 650214, Yunnan, China
| | - Zhen Ren
- College of Agriculture and Life Sciences, Kunming University, Kunming, 650214, Yunnan, China
| | - Genhua Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
| | - Xiaohan Mo
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China.
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15
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Complete genome sequence of a novel partitivirus infecting the phytopathogenic fungus Alternaria tenuissima. Arch Virol 2022; 167:635-639. [PMID: 35031860 DOI: 10.1007/s00705-021-05332-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/30/2021] [Indexed: 11/02/2022]
Abstract
In the present study, a novel double-stranded RNA (dsRNA) mycovirus designated as "Alternaria tenuissima partitivirus 2" (AttPV2), was isolated from Alternaria tenuissima strain BJ-SY-1, a phytopathogenic fungus causing muskmelon leaf blight in Beijing municipality of China. The genome of AttPV2 comprises two dsRNA segments. The larger segment is 1829 bp in length and has a single open reading frame (ORF), potentially encoding a 65.8-kDa RNA-dependent RNA polymerase (RdRp), and the smaller segment is 1681 bp in length and also contains a single ORF, encoding a putative coat protein (CP) with a molecular mass of 56.0 kDa. BLASTp analysis revealed that the RdRp and CP encoded by the two ORFs of AttPV2 have the highest sequence identity, 85.9% and 75.0%, respectively, to their counterparts in Colletotrichum eremochloae partitivirus 1 (CePV1). Phylogenetic analysis based on RdRp sequences showed that AttPV2 clustered most closely with CePV1, a member of the proposed genus "Epsilonpartitivirus" in the family Partitiviridae. Hence, we propose that AttPV2 is a new epsilonpartitivirus from A. tenuissima. To the best of our knowledge, this is the first report of an epsilonpartitivirus infecting A. tenuissima.
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16
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Kartali T, Nyilasi I, Kocsubé S, Patai R, Polgár TF, Zsindely N, Nagy G, Bodai L, Lipinszki Z, Vágvölgyi C, Papp T. Characterization of Four Novel dsRNA Viruses Isolated from Mucor hiemalis Strains. Viruses 2021; 13:v13112319. [PMID: 34835124 PMCID: PMC8625083 DOI: 10.3390/v13112319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
We previously screened the total nucleic acid extracts of 123 Mucor strains for the presence of dsRNA molecules without further molecular analyses. Here, we characterized five novel dsRNA genomes isolated from four different Mucor hiemalis strains with next-generation sequencing (NGS), namely Mucor hiemalis virus 1a (MhV1a) from WRL CN(M) 122; Mucor hiemalis virus 1b (MhV1b) from NRRL 3624; Mucor hiemalis virus 2 (MhV2) from NRRL 3616; and Mucor hiemalis virus 3 (MhV3) and Mucor hiemalis virus (MhV4) from NRRL 3617 strains. Genomes contain two open reading frames (ORF), which encode the coat protein (CP) and the RNA dependent RNA polymerase (RdRp), respectively. In MhV1a and MhV1b, it is predicted to be translated as a fusion protein via -1 ribosomal frameshift, while in MhV4 via a rare +1 (or-2) ribosomal frameshift. In MhV2 and MhV3, the presence of specific UAAUG pentanucleotide motif points to the fact for coupled translation termination and reinitialization. MhV1a, MhV2, and MhV3 are part of the clade representing the genus Victorivirus, while MhV4 is seated in Totivirus genus clade. The detected VLPs in Mucor strains were from 33 to 36 nm in diameter. Hybridization analysis revealed that the dsRNA molecules of MhV1a-MhV4 hybridized to the corresponding molecules.
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Affiliation(s)
- Tünde Kartali
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
- Correspondence: (T.K.); (T.P.)
| | - Ildikó Nyilasi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Roland Patai
- Neuronal Plasticity Research Group, Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary; (R.P.); (T.F.P.)
| | - Tamás F. Polgár
- Neuronal Plasticity Research Group, Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary; (R.P.); (T.F.P.)
- Theoretical Medicine Doctoral School, University of Szeged, 6722 Szeged, Hungary
| | - Nóra Zsindely
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (G.N.); (L.B.)
| | - László Bodai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (G.N.); (L.B.)
| | - Zoltán Lipinszki
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), 6726 Szeged, Hungary;
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary; (I.N.); (S.K.); (N.Z.); (C.V.)
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences and Department of Microbiology, University of Szeged, 6726 Szeged, Hungary
- Correspondence: (T.K.); (T.P.)
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17
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Li Y, Sun Y, Yu L, Chen W, Liu H, Yin L, Guang Y, Yang G, Mo X. Complete genome sequence of a novel mitovirus from binucleate Rhizoctonia AG-K strain FAS2909W. Arch Virol 2021; 167:271-276. [PMID: 34773510 DOI: 10.1007/s00705-021-05277-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/02/2021] [Indexed: 11/30/2022]
Abstract
The full-length AU-rich (63.14%) 2,794-nucleotide sequence of Rhizoctonia mitovirus K1 (RMV-K1) isolated from the binucleate AG-K strain FAS2909W was determined. The positive strand of RMV-K1 contains a large open reading frame (ORF) when the fungal mitochondrial genetic code is used. This ORF was predicted to encode an RdRp protein exhibiting the highest sequence identity (41.77%) to Rhizoctonia solani mitovirus 30. Phylogenetic analysis showed that RMV-K1 is a novel member of the genus Mitovirus, family Mitoviridae.
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Affiliation(s)
- Yanqiong Li
- College of Agriculture and Life Sciences, Kunming University, Kunming, 650214, Yunnan, China.,Yunnan Agricultural University, Kunming, 650201, Yunnan, China.,Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China
| | - Yang Sun
- Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Lei Yu
- College of Agriculture and Life Sciences, Kunming University, Kunming, 650214, Yunnan, China
| | - Wurong Chen
- College of Agriculture and Life Sciences, Kunming University, Kunming, 650214, Yunnan, China
| | - He Liu
- College of Agriculture and Life Sciences, Kunming University, Kunming, 650214, Yunnan, China
| | - Lifang Yin
- College of Agriculture and Life Sciences, Kunming University, Kunming, 650214, Yunnan, China
| | - Yingxia Guang
- College of Agriculture and Life Sciences, Kunming University, Kunming, 650214, Yunnan, China
| | - Genhua Yang
- Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
| | - Xiaohan Mo
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming, 650021, Yunnan, China.
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18
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Zhang M, He Z, Huang X, Shu C, Zhou E. Genome Organizations and Functional Analyses of a Novel Gammapartitivirus from Rhizoctonia solani AG-1 IA Strain D122. Viruses 2021; 13:v13112254. [PMID: 34835059 PMCID: PMC8623816 DOI: 10.3390/v13112254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
Here, we describe a novel double-stranded (ds) RNA mycovirus designated Rhizoctonia solani dsRNA virus 5 (RsRV5) from strain D122 of Rhizoctonia solani AG-1 IA, the causal agent of rice sheath blight. The RsRV5 genome consists of two segments of dsRNA (dsRNA-1, 1894 bp and dsRNA-2, 1755 bp), each possessing a single open reading frame (ORF). Sequence alignments and phylogenetic analyses showed that RsRV5 is a new member of the genus Gammapartitivirus in the family Partitiviridae. Transmission electron microscope (TEM) images revealed that RsRV5 has isometric viral particles with a diameter of approximately 20 nm. The mycovirus RsRV5 was successfully removed from strain D122 by using the protoplast regeneration technique, thus resulting in derivative isogenic RsRV5-cured strain D122-P being obtained. RsRV5-cured strain D122-P possessed the traits of accelerated mycelial growth rate, increased sclerotia production and enhanced pathogenicity to rice leaves compared with wild type RsRV5-infection strain D122. Transcriptome analysis showed that three genes were differentially expressed between two isogenic strains, D122 and D122-P. These findings provided new insights into the molecular mechanism of the interaction between RsRV5 and its host, D122 of R. solani AG-1 IA.
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Affiliation(s)
- Meiling Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (M.Z.); (Z.H.); (X.H.)
- School of Biological and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Zhenrui He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (M.Z.); (Z.H.); (X.H.)
| | - Xiaotong Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (M.Z.); (Z.H.); (X.H.)
| | - Canwei Shu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (M.Z.); (Z.H.); (X.H.)
- Correspondence: (C.S.); (E.Z.)
| | - Erxun Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (M.Z.); (Z.H.); (X.H.)
- Correspondence: (C.S.); (E.Z.)
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19
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Sahin E, Keskin E, Akata I. Molecular characterization of the complete genome of a novel partitivirus hosted by the saprobic mushroom Leucocybe candicans. Arch Microbiol 2021; 203:5825-5830. [PMID: 34427724 DOI: 10.1007/s00203-021-02540-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/30/2021] [Accepted: 08/18/2021] [Indexed: 12/29/2022]
Abstract
Virus communities of uncultivated fungi stay largely unknown. In the current study, we characterized a new partitivirus species detected in the basidiomycetous, saprobic mushroom Leucocybe candicans, named "Leucocybe candicans partitivirus 1" (LcPV1). The full-length genome of LcPV1, determined using deep sequencing and RLM-RACE approaches, consists of two dsRNA segments with each having the same size of 1984 bp. Both dsRNA genome segments comprise a single open reading frame (ORF), encoding an RNA-dependent RNA polymerase (RdRp), and a capsid protein (CP), respectively. Based on BLASTp search, the sequences of the RdRp and CP show the highest identity (50.09% and 35.71% similarity, respectively) to those of partitiviruses reported from an oomycetous, plant pathogenic, stramenopile algae Plasmopara viticola and basidiomycetous, plant pathogenic fungus Ceratobasidium sp., respectively. Phylogenetic analyses performed based on the RdRp and CP sequences revealed that LcPV1 falls within a cluster that includes different alphapartitivirus species from the family Partitiviridae. In this study, we propose that LcPV1 is a new member of a species belonging to the genus Alphapartitivirus. To our knowledge, this is the first study reporting on a new fungal virus (mycovirus) identified in the basidiomycetous, saprobic mushroom Leucocybe candicans.
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Affiliation(s)
- Ergin Sahin
- Faculty of Science Department of Biology, Ankara University, 06100, Ankara, Tandogan, Turkey.
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Faculty of Agriculture Department of Fisheries and Aquaculture, Ankara University, 06110, Ankara, Dışkapı, Turkey
| | - Ilgaz Akata
- Faculty of Science Department of Biology, Ankara University, 06100, Ankara, Tandogan, Turkey
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Molecular characterization of a new mitovirus hosted by the ectomycorrhizal fungus Albatrellopsis flettii. Arch Virol 2021; 166:3449-3454. [PMID: 34554305 DOI: 10.1007/s00705-021-05250-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 08/09/2021] [Indexed: 10/20/2022]
Abstract
The complete genome of a novel mycovirus, Albatrellopsis flettii mitovirus 1 (AfMV1), hosted by the basidiomycetous ectomycorrhizal fungus Albatrellopsis flettii (Morse ex Pouzar) Audet, was sequenced and analyzed. The full-length cDNA sequence, obtained from a dsRNA replication intermediate of the AfMV1 genome, is 3037 bp in length with a predicted G+C content of 40.66%. Sequence analysis revealed that a single large open reading frame (ORF) is present on the positive strand when the mold mitochondrial genetic code is applied. The single ORF encodes a putative RNA-dependent RNA polymerase of 859 amino acids with a predicted molecular weight of 97.05 kDa that shares the closest similarity with the corresponding protein of Entomophthora muscae mitovirus 7, with 43.38% sequence identity. Phylogenetic analysis showed that AfMV1 could be classified as a new member of the genus Mitovirus within the family Mitoviridae. This is the first report of the complete genome sequence of a new mitovirus, AfMV1, isolated from the basidiomycetous ectomycorrhizal fungus A. flettii.
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21
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Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA strain 9-11. Arch Virol 2021; 166:3229-3232. [PMID: 34524536 DOI: 10.1007/s00705-021-05219-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/11/2021] [Indexed: 10/20/2022]
Abstract
The complete genome sequence of a double-stranded RNA (dsRNA) virus, Rhizoctonia solani dsRNA virus 11 (RsRV11), isolated from Rhizoctonia solani AG-1 IA strain 9-11 was determined. The RsRV11 genome is 9,555 bp in length and contains three conserved domains: structural maintenance of chromosomes (SMC) superfamily, phosphoribulokinase (PRK), and RNA-dependent RNA polymerase (RdRp). The RsRV11 genome has two non-overlapping open reading frames (ORFs). ORF1 is predicted to encode a 204.12-kDa protein that shares low but significant amino acid sequence similarity with a putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008). ORF2 potentially encodes a 132.41-kDa protein that contains the conserved domain of the RdRp. Phylogenetic analysis indicated that RsRV11 clustered with RsRV-HN008 in a separate clade from other virus families. This implies that RsRV11 and RsRV-HN008 should be included in a new mycovirus taxon close to the family Megabirnaviridae and that RsRV11 is a new mycovirus.
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22
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Sahin E, Keskin E, Akata I. The unique genome organization of two novel fusariviruses hosted by the true morel mushroom Morchella esculenta. Virus Res 2021; 302:198486. [PMID: 34146607 DOI: 10.1016/j.virusres.2021.198486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/05/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Two putative mycoviruses belonging to the proposed family "Fusariviridae" were identified in Morchella esculenta by sequencing of double-stranded RNAs extracted from the morel mushroom. These viruses were tentatively named "Morchella esculenta fusarivirus 1″ (MeFV1) and "Morchella esculenta fusarivirus 2″ (MeFV2). Including the poly(A) tail the complete genomes of MeFV1 and MeFV2 are composed of 9096 and 9011 nucleotides (nt) respectively. Both genomes contain four non-overlapping open reading frames (ORFs) in which the largest and the smallest ORFs are ORF2 and ORF3 for both genomes respectively. The ORF1 of MeFV1 and MeFV2 are preceded by the 5' untranslated regions (UTRs) of 27 and 37 nt respectively and encode 341 and 339 aa long proteins that do not exhibit significant similarity to any of the protein sequences present in GenBank database. The 1502 and 1511 aa long proteins encoded by ORF2 of MeFV1 and MeFV2 share 84.42% sequence identity to each other and are 58.54% and 58.57% identical to the RNA-dependent RNA polymerase (RdRp) of Morchella importuna fusarivirus 1 (MiFV1) respectively. Interestingly, a Promethin/LDAF1 protein domain that is associated with the endoplasmic reticulum (ER) and lipid droplet (LD) membranes was identified at the N terminal regions of MeFV1 and MeFV2 RdRps, implying that the replication of these viruses is linked to the lipid membranes. The ORF3 and ORF4 of MeFV1 and MeFV2 encode proteins (268 and 333 aa long, and 645 and 647 aa long respectively) that only share significant sequence similarities with the proteins encoded by the ORF2 and ORF3 of MiFV1 respectively. The 3' UTRs of MeFV1 and MeFV2 are 162 and 159 nt long respectively and both of them have 51 nt long terminal poly(A) traits. To our knowledge, MeFV1 and MeFV2 are the first fusariviruses identified in M. esculenta and this is the first study reporting on the presence of Promethin/LDAF1 domain in viral RdRps.
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Affiliation(s)
- Ergin Sahin
- Ankara University Faculty of Science Department of Biology 06100 Tandogan, Ankara, Turkey; Dokuz Eylül University Faculty of Science Department of Biology 35390 Buca, İzmir, Turkey.
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Ankara University Faculty of Agriculture Department of Fisheries and Aquaculture 06110 Dışkapı, Ankara, Turkey
| | - Ilgaz Akata
- Ankara University Faculty of Science Department of Biology 06100 Tandogan, Ankara, Turkey
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Molecular characterization of a new endornavirus inhabiting the ectomycorrhizal fungus Hygrophorus penarioides. Braz J Microbiol 2021; 52:1167-1172. [PMID: 33900612 DOI: 10.1007/s42770-021-00500-8] [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: 01/09/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022] Open
Abstract
Viruses hosted by uncultivated fungi have been poorly studied. We carried out studies to characterize a large dsRNA segment (~20 kbp) detected in the basidiomycetous, ectomycorrhizal fungus Hygrophorus penarioides. The dsRNA was gel-purified and its randomly amplified cDNA fragments were used for high throughput sequencing (HTS). Reads were de novo assembled and BLASTx analysis revealed sequence similarity to viruses of the family Endornaviridae. The 5' and 3' terminal sequences of the dsRNA segment were determined by performing RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE). The full-length cDNA sequence of the putative endornavirus comprises 16,785 nt and contains a single, long open reading frame which encodes for a polyprotein of 5522 aa with conserved domains for cysteine-rich region, helicase, glycosyltransferase, and RNA-dependent RNA polymerase. The virus was named Hygrophorus penarioides endornavirus 1 (HpEnV1). A BLASTp search performed using the polyprotein sequence revealed that the most closely related, fully sequenced endornavirus to HpEnV1 is Ceratobasidium endornavirus B.
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24
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Chiba Y, Tomaru Y, Shimabukuro H, Kimura K, Hirai M, Takaki Y, Hagiwara D, Nunoura T, Urayama SI. Viral RNA Genomes Identified from Marine Macroalgae and a Diatom. Microbes Environ 2021; 35. [PMID: 32554943 PMCID: PMC7511793 DOI: 10.1264/jsme2.me20016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Protists provide insights into the diversity and function of RNA viruses in marine systems. Among them, marine macroalgae are good targets for RNA virome analyses because they have a sufficient biomass in nature. However, RNA viruses in macroalgae have not yet been examined in detail, and only partial genome sequences have been reported for the majority of RNA viruses. Therefore, to obtain further insights into the distribution and diversity of RNA viruses associated with marine protists, we herein examined RNA viruses in macroalgae and a diatom. We report the putative complete genome sequences of six novel RNA viruses from two marine macroalgae and one diatom holobiont. Four viruses were not classified into established viral genera or families. Furthermore, a virus classified into Totiviridae showed a genome structure that has not yet been reported in this family. These results suggest that a number of distinct RNA viruses are widespread in a broad range of protists.
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Affiliation(s)
- Yuto Chiba
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba.,Faculty of Science, International College of Arts and Science, Yokohama City University
| | - Yuji Tomaru
- Japan Fisheries Research and Education Agency, National Research Institute of Fisheries and Environment of the Inland Sea
| | - Hiromori Shimabukuro
- Japan Fisheries Research and Education Agency, National Research Institute of Fisheries and Environment of the Inland Sea
| | | | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, JAMSTEC
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, JAMSTEC
| | - Daisuke Hagiwara
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba.,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Syun-Ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba.,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba.,Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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25
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Sahin E, Akata I. Full-length genome characterization of a novel alphapartitivirus detected in the ectomycorrhizal fungus Hygrophorus penarioides. Virus Genes 2021; 57:94-99. [PMID: 33392985 DOI: 10.1007/s11262-020-01814-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/17/2020] [Indexed: 12/25/2022]
Abstract
Virus populations of ectomycorrhizal fungi remain poorly studied. In the present study, we characterized a new partitivirus isolated from the basidiomycetous, ectomycorrhizal fungus Hygrophorus penarioides, named "Hygrophorus penarioides partitivirus 1" (HpPV1). The whole genome of HpPV1, determined by merging deep sequencing and RLM-RACE approaches, comprised two dsRNA segments of 2053 bp and 2072 bp, respectively. Both dsRNA genome segments included a single open reading frame (ORF), encoding a putative RNA-dependent RNA polymerase (RdRp), and a capsid protein (CP), respectively. Based on BLASTp search, the sequences of the RdRp and CP exhibits the highest similarity (67.49% and 75.61% identity, respectively) to those of partitiviruses identified from an ascomycetous ectomycorrhizal fungus Sarcosphaera coronaria. Phylogenetic analyses performed based on the CP and RdRp sequences demonstrated that HpPV1 clusters within a clade that includes members of the genus Alphapartitivirus, belonging to the family Partitiviridae. Here, we propose that HpPV1 is a new member of the genus Alphapartitivirus. This is the first study reporting on a new partitivirus identified from the basidiomycetous, ectomycorrhizal fungus Hygrophorus penarioides.
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Affiliation(s)
- Ergin Sahin
- Department of Biology, Faculty of Science, Ankara University, Tandogan, 06100, Ankara, Turkey.
| | - Ilgaz Akata
- Department of Biology, Faculty of Science, Ankara University, Tandogan, 06100, Ankara, Turkey
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26
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Sahin E, Keskin E, Akata I. Novel and diverse mycoviruses co-inhabiting the hypogeous ectomycorrhizal fungus Picoa juniperi. Virology 2020; 552:10-19. [PMID: 33032032 DOI: 10.1016/j.virol.2020.09.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]
Abstract
Viruses hosted by ectomycorrhizal fungi remain poorly studied. In this study, we detected eight new fungal viruses co-infecting a single isolate of the hypogeous ectomycorrhizal fungus Picoa juniperi using high-throughput sequencing. Phylogenetic analysis of one identified virus abbreviated as PjMTV1 revealed its closest relatives as members of the newly proposed family "Megatotiviridae". Phylogenetic analyses of two identified viruses abbreviated as PjV1 and PjV2 showed that these viruses are associated with members of the proposed family "Fusagraviridae". Phylogenetic analysis of the identified one another virus abbreviated as PjYV1 demonstrated that this virus is related to the members of the proposed family Yadokariviridae. The remaining four identified virus-like contigs were determined as segments of the bipartite dsRNA mycoviruses from the family Partitiviridae. The mycoviruses reported in this study are the first viruses described in Picoa juniperi, and PjMTV1 characterized herein is the secondly reported member of the newly proposed family "Megatotiviridae".
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Affiliation(s)
- Ergin Sahin
- Ankara University Faculty of Science Department of Biology, 06100, Tandogan, Ankara, Turkey.
| | - Emre Keskin
- Evolutionary Genetics Laboratory (eGL), Ankara University Faculty of Agriculture Department of Fisheries and Aquaculture, 06110, Dışkapı, Ankara, Turkey
| | - Ilgaz Akata
- Ankara University Faculty of Science Department of Biology, 06100, Tandogan, Ankara, Turkey
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27
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Li X, Sui K, Xie J, Hai D, Yin W, Sossah FL, Jiang D, Song B, Li Y. Molecular characterization of a novel fusarivirus infecting the edible fungus Auricularia heimuer. Arch Virol 2020; 165:2689-2693. [PMID: 32812093 DOI: 10.1007/s00705-020-04781-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/20/2020] [Indexed: 11/28/2022]
Abstract
Here, we describe a novel mycovirus, Auricularia heimuer fusarivirus 1 (AhFV1), isolated from the edible fungus Auricularia heimuer strain CCMJ1296. The virus has a single-stranded positive-sense [+ssRNA] genome of 7,127 nucleotides containing two overlapping open reading frames (ORFs) and a poly(A) tail. The large ORF1 encodes a polyprotein of 1,637 amino acids (aa) with conserved RNA-dependent RNA polymerase (RdRp) and DEAD-like helicase superfamily (DEXDc) domains. ORF2 encodes a putative 633-aa protein with unknown function. A BLAST search showed that the nucleotide sequence of the AhFV1 genome is 41.28% identical to that of Sclerotium rolfsii fusarivirus 2 and 40.49% identical to that of Sclerotium rolfsii fusarivirus 1. Phylogenetic analysis based on RdRp and helicase (Hel) sequences indicated that AhFV1 is related to unclassified mycoviruses and other fusariviruses. Our data suggest that AhFV1 should be classified as a member of the newly proposed family "Fusariviridae". This is the second virus and the first full genome sequence of a fusarivirus from A. heimuer.
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Affiliation(s)
- Xuefei Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin, China.,College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Kunpeng Sui
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin, China.,College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Du Hai
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Weiqi Yin
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin, China.,College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Frederick Leo Sossah
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Bing Song
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin, China.
| | - Yu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun, 130118, Jilin, China.
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Sahin E, Akata I, Keskin E. Novel and divergent bipartite mycoviruses associated with the ectomycorrhizal fungus Sarcosphaera coronaria. Virus Res 2020; 286:198071. [PMID: 32589898 DOI: 10.1016/j.virusres.2020.198071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023]
Abstract
Members of the family Partitiviridae are reported from a variety of fungal and plant taxa. After dsRNA-preparation, deep sequencing, and bioinformatics, we here reveal the existence of various divergent partitiviruses co-infecting the ectomycorrhizal fungus Sarcosphaera coronaria, symbiotically associated with the pine species Pinus brutia in Turkey. A total of 75 complete or nearly complete sequences related to the members of Alphapartitivirus and Betapartitivirus, were detected from the ascocarp sample of the fungal isolate. Two of the identified partitivirus genome segments encoding for partitiviral capsid protein represent evolutionarily distinct members of Alphapartitivirus, indicating that they may have diverged in the presence of long spatial isolation. In an attempt to match the two genome segments of the identified partitiviruses and distinguish individual species co-inhabiting a single host, nine possible genome segment pairs were identified.
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Affiliation(s)
- Ergin Sahin
- Ankara University Faculty of Science Department of Biology, 06100, Tandogan, Ankara, Turkey.
| | - Ilgaz Akata
- Ankara University Faculty of Science Department of Biology, 06100, Tandogan, Ankara, Turkey
| | - Emre Keskin
- Ankara University Faculty of Agriculture Department of Fisheries and Aquaculture, 06110 Dışkapı, Ankara, Turkey
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29
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Molecular characteristics of a novel ssRNA virus isolated from Auricularia heimuer in China. Arch Virol 2020; 165:1495-1499. [PMID: 32266549 DOI: 10.1007/s00705-020-04615-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/16/2020] [Indexed: 10/24/2022]
Abstract
A novel positive-sense single-stranded RNA virus was isolated from strain CCMJ1271 of the fungus Auricularia heimuer, and the complete genome sequence of the virus was determined. Database searching, sequence alignment, and phylogenetic analysis revealed that this fungal virus and some viruses of family Virgaviridae clustered into a single branch of a phylogenetic tree, and we thus tentatively named the virus "Auricularia heimuer mycovirgavirus 1" (AhMV1). The AhMV1 genome consists of 9,934 nucleotides and contains a short poly(A) tail and three open reading frames (ORFs). ORF1 encodes an RNA-dependent RNA polymerase (RdRp), ORF2 encodes a protein that is homologous to movement proteins of plant virgaviruses, and ORF3 encodes a coat protein (CP). AhMV1 is the first virus to be discovered in A. heimuer.
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30
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Petrzik K, Koloniuk I, Sehadová H, Sarkisova T. Chrysoviruses Inhabited Symbiotic Fungi of Lichens. Viruses 2019; 11:v11121120. [PMID: 31817044 PMCID: PMC6949994 DOI: 10.3390/v11121120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/26/2019] [Accepted: 11/30/2019] [Indexed: 12/28/2022] Open
Abstract
A lichen body is formed most often from green alga cells trapped in a net of ascomycetous fungi and accompanied by endolichenic or parasitic fungi, other algae, and symbiotic or free-living bacteria. The lichen’s microcosmos is inhabited by mites, insects, and other animals for which the lichen is a source of food or a place to live. Novel, four-segmented dsRNA viruses were detected in saxicolous Chrysothrixchlorina and Lepraria incana lichens. Comparison of encoded genome proteins revealed classification of the viruses to the genus Alphachrysovirus and a relationship to chrysoviruses from filamentous ascomycetous fungi. We propose the names Chrysothrix chrysovirus 1 (CcCV1) and Lepraria chrysovirus 1 (LiCV1) as acronyms for these viruses. Surprisingly, observation of Chrysothrix chlorina hybridization with fluorescent-labelled virus probe by confocal microscope revealed that the CcCV1 virus is not present in the lichen body-forming fungus but in accompanying endolichenic Penicilliumcitreosulfuratum fungus. These are the first descriptions of mycoviruses from a lichen environment.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic; (I.K.); (T.S.)
- Correspondence: ; Tel.: +420-387-775-549
| | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic; (I.K.); (T.S.)
| | - Hana Sehadová
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic;
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Tatiana Sarkisova
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic; (I.K.); (T.S.)
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31
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Sahin E, Akata I. Complete genome sequence of a novel mitovirus from the ectomycorrhizal fungus Geopora sumneriana. Arch Virol 2019; 164:2853-2857. [PMID: 31377887 DOI: 10.1007/s00705-019-04367-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/09/2019] [Indexed: 01/01/2023]
Abstract
A double-stranded RNA (dsRNA) segment was extracted from the ectomycorrhizal fungus Geopora sumneriana (Cooke) M. Torre, and its full-length cDNA sequence, comprising 3146 nucleotides, was determined. Sequence analysis revealed the presence of a large open reading frame (ORF) on the positive strand of this dsRNA segment when the mold mitochondrial genetic code was applied. The ORF encodes a putative RNA-dependent RNA polymerase (RdRp), which shares the highest degree of similarity with Tuber excavatum mitovirus, with 37.52% identity. This dsRNA segment represents the genome replication intermediate of a novel mitovirus that was tentatively designated as "Geopora sumneriana mitovirus 1" (GsMV1). Phylogenetic analysis further suggested that GsMV1 is a member of the family Narnaviridae. This is the first study reporting on a mitovirus genome sequence in the ectomycorrhizal fungus G. sumneriana.
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Affiliation(s)
- Ergin Sahin
- Department of Biology, Faculty of Science, Ankara University, Tandogan, 06100, Ankara, Turkey.
| | - Ilgaz Akata
- Department of Biology, Faculty of Science, Ankara University, Tandogan, 06100, Ankara, Turkey
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32
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Petrzik K, Siddique AB. A mycoparasitic and opportunistic fungus is inhabited by a mycovirus. Arch Virol 2019; 164:2545-2549. [PMID: 31317260 DOI: 10.1007/s00705-019-04359-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/28/2019] [Indexed: 01/04/2023]
Abstract
A novel bisegmented double-stranded RNA virus was identified in the mycoparasitic and opportunistic fungus Hypomyces chrysospermus. The RNA1 genome segment comprises 1866 bp and encodes an RNA-dependent RNA polymerase (RdRp). The RNA2 segment comprises 1822 bp and encodes a capsid protein. Phylogenetic analysis of the RdRp protein indicated that this virus is a new member of genus Alphapartitivirus in the family Partitiviridae. We have designated this mycovirus as "Hypomyces chrysospermus partitivirus 1" (HcPV1). HcPV1 is highly transmissible with aleurioconidia and is present in large amounts within growing mycelium in comparison to the GAPDH reference gene.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic.
| | - Abu Bakar Siddique
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic
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33
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Kartali T, Nyilasi I, Szabó B, Kocsubé S, Patai R, Polgár TF, Nagy G, Vágvölgyi C, Papp T. Detection and Molecular Characterization of Novel dsRNA Viruses Related to the Totiviridae Family in Umbelopsis ramanniana. Front Cell Infect Microbiol 2019; 9:249. [PMID: 31380294 PMCID: PMC6644447 DOI: 10.3389/fcimb.2019.00249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/26/2019] [Indexed: 11/24/2022] Open
Abstract
Umbelopsis ramanniana is an oleaginous fungus belonging to the Mucoromycotina subphylum. Our group had previously detected four double-stranded RNA (dsRNA) bands in the U. ramanniana NRRL 1296 strain by gel electrophoresis. Here we describe the molecular characterization of its dsRNA elements as well as the discovery of four novel dsRNA viruses: Umbelopsis ramanniana virus 1 (UrV1), Umbelopsis ramanniana virus 2 (UrV2), Umbelopsis ramanniana virus 3 (UrV3), and Umbelopsis ramanniana virus 4 (UrV4). Full genomes of UrV1, UrV3, and UrV4 were determined using the full-length amplification of cDNAs (FLAC) technique; they contain two open reading frames (ORF), which putatively encode the coat protein (CP) and the RNA dependent RNA polymerase (RdRp), respectively. In case of UrV2, a partial ORF encoding a partial RdRp gene could be determined. Based on the phylogeny inferred from the RdRp sequences, UrV1 and UrV4 belong to the genus Totivirus, while UrV2 may belong to the genus Victorivirus. UrV3 nested to a novel, unclassified group of Totiviridae, which is related to the genus Totivirus. Hybridization analysis revealed that the dsRNA molecules of UrV1 and UrV4 correspond to the same 5.0-kbp electrophoretic band, whilst the probe for the UrV3 hybridized to the largest, 5.3-kbp and the 3.0-kbp bands of the dsRNA pattern of U. ramanniana. Interestingly, the probe for the UrV2 sequence did not hybridized to any dsRNA bands, but it could be amplified from the isolated 3.0-kbp fragment. By transmission electron microscopy, two different isometric virus particles with about 50 and 35 nm in diameter were detected in U. ramanniana NRRL 1296 indicating that this strain harbor multiple viruses. Beside U. ramanniana, dsRNA elements were also detected in other Umbelopsis isolates with different patterns consisting of 2 to 4 discrete and different sized (0.7–5.3-kbp) dsRNA molecules. Based on a hybridization analysis with UrV1 CP and RdRp probes, the bands with the size of around 5.0-kbp, which were present in all tested Umbelopsis strains, are presumed as possible full mycovirus genomes.
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Affiliation(s)
- Tünde Kartali
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Ildikó Nyilasi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Boglárka Szabó
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Sándor Kocsubé
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Roland Patai
- Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biophysics, Szeged, Hungary
| | - Tamás F Polgár
- Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biophysics, Szeged, Hungary
| | - Gábor Nagy
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Hungarian Academy of Sciences, Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Tamás Papp
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.,MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Department of Microbiology, University of Szeged, Hungarian Academy of Sciences, Szeged, Hungary
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34
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Complete genomic sequence and organization of a novel mycovirus from Phoma matteuccicola strain LG915. Arch Virol 2019; 164:2209-2213. [PMID: 31161389 DOI: 10.1007/s00705-019-04314-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/14/2019] [Indexed: 10/26/2022]
Abstract
The complete genome of a double-stranded RNA (dsRNA) mycovirus, Phoma matteuccicola partitivirus 1 (PmPV1) was sequenced. It consists of two dsRNA segments, 1664 bp (dsRNA-1) and 1383 bp (dsRNA-2) in length, each containing a single open reading frame (ORF) potentially encoding a 46.78-kDa protein and a 40.92-kDa protein, respectively. dsRNA-1 encodes a putative polypeptide with a conserved RNA-dependent RNA polymerase (RdRp) domain that shows sequence similarity to the corresponding proteins of partitiviruses. The protein encoded by dsRNA-2 has no significant similarity to the typical coat proteins (CPs) of partitiviruses, but structure analysis nevertheless suggested that it might function as a coat protein. Purified viral particles of PmPV1 were isometric and approximately 29 nm in diameter. Phylogenetic analysis showed that PmPV1 is closely related to members of the genus Gammapartitivirus within the family Partitiviridae but forms a separate branch with Colletotrichum acutatum RNA virus 1 and Ustilaginoidea virens partitivirus 2. This is the first report of the full-length nucleotide sequence of a novel virus of the genus Gammapartitivirus infecting P. matteuccicola strain LG915, the causal agent of leaf blight of Curcuma wenyujin.
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Characterization of a novel RNA virus from the phytopathogenic fungus Leptosphaeria biglobosa related to members of the genus Mitovirus. Arch Virol 2019; 164:913-916. [PMID: 30656466 DOI: 10.1007/s00705-018-04143-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/12/2018] [Indexed: 10/27/2022]
Abstract
Mycovirus infection is a universal phenomenon in the major fungus groups. So far, however, mycoviruses have not been described in the phytopathogenic fungus Leptosphaeria biglobosa, the causal agent of phoma stem canker (blackleg). Here, we report the complete genome sequence of a novel mitovirus, Leptosphaeria biglobosa mitovirus 1 (LbMV1), isolated from the strain H3-38 of L. biglobosa. The LbMV1 genome comprises 2568 nucleotides with a low G+C content of 30%. Using the mitochondrial genetic code, the genome of LbMV1 was found to contain a single large open reading frame that encodes a predicted protein of 756 amino acids. Multiple alignment of the predicted protein sequence showed the highest similarity (51% identity) to the putative RNA-dependent RNA polymerase of Ophiostoma mitovirus 4. In addition, phylogenetic analysis grouped LbMV1 within the genus Mitovirus of the family Narnaviridae. Our results suggest that the double-stranded RNA found in strain H3-38 is the replicating genome of the mitovirus LbMV1, its deletion represents the first evidence of a mycovirus infecting L. biglobosa.
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Molecular characterization of a new gammapartitivirus isolated from the citrus-pathogenic fungus Penicillium digitatum. Arch Virol 2018; 163:3185-3189. [PMID: 30076474 DOI: 10.1007/s00705-018-3951-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 07/02/2018] [Indexed: 10/28/2022]
Abstract
To date, partitiviruses, including gammapartitiviruses, have been extensively studied in various fungal hosts but have not been reported in Penicillium digitatum (also called green mold, the pathogenic fungus infecting citrus). In the present work, we isolated and molecularly characterized a double-stranded RNA (dsRNA) partitivirus from citrus green mold, which we have named "Penicillium digitatum gammapartitivirus 1" (PdGV1). The bisegmented genome of PdGV1 contains two dsRNA segments (dsRNA1 and dsRNA2) with a length of 1795 bp and 1622 bp, respectively. Each of the two genomic dsRNAs contains a single open reading frame encoding a putative RNA-dependent RNA polymerase (RdRp) and a coat protein (CP), respectively. Phylogenetic analysis based on RdRp and CP sequences showed that PdGV1 clustered with mycoviruses belonging to the genus Gammapartitivirus, family Partitiviridae, e.g., Penicillium stoloniferum virus S. The 5'- and 3'-untranslated regions (UTRs) of the PdGV1 genomic dsRNAs both contained unique conserved RNA motifs that have never been found in any other partitivirus. This is the first report of a new gammapartitivirus that infects the citrus-pathogenic fungus P. digitatum.
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Saxena A, Biswas SK, Chand K, Naskar J, Chauhan A, Mohd G, Tewari N, Kurat-ul-Ain, Ramakrishnan MA, Pandey AB. Genetic and phylogenetic analysis of the outer capsid protein genes of Indian isolates of bluetongue virus serotype-16. Vet World 2018; 11:1025-1029. [PMID: 30250358 PMCID: PMC6141295 DOI: 10.14202/vetworld.2018.1025-1029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 06/13/2018] [Indexed: 11/24/2022] Open
Abstract
AIM The aim of the study was to characterize bluetongue virus serotype 16 (BTV-16), recently isolated from different states of India. The evolutionary relationship of newly isolated BTV-16 and previously reported Indian and global BTV-16 isolates were compared using molecular analysis. MATERIALS AND METHODS In the present study, five (n=5) BTV-16 isolates were used to amplify gene segment-2 and segment-6 encoding the outer capsid proteins VP2 and VP5, respectively. The amplified products were purified and sequenced by the Sanger sequencing method. The phylogenetic relationship and nucleotide identity of all five BTV-16 isolates were compared with previously reported Indian and global BTV-16 isolates. Nucleotide sequence data were aligned using the CLUSTAL W algorithm implemented in the MegAlign of DNASTAR program package (MegAlign 5.00, DNASTAR Inc., Madison, USA). Phylogenetic analyses were carried out using MEGA version 6.0 software with the best nucleotide substitution model. RESULTS Phylogenetic analysis based on the VP2 and VP5 encoding genes, segregates Indian BTV-16 isolates in a distinct cluster with proximity to the Eastern topotype. Indian isolates make a monophyletic cluster with Eastern topotypes with Western topotype BTV-16 (BTV-16/NIG/AJ586694) occupying a separate cluster. Indian isolates were found to share 91.5%-97.5% and 96.5%-98.9% identity at the nucleotide and deduced amino acid (aa) level, respectively, to the global BTV-16 isolates. There is a high degree of variation with the Nigerian isolate with 27.0-27.7% and 26.0-26.9% at the nucleotide and aa sequence level, respectively. These data suggest that Indian BTV-16 isolates might have evolved separately within the Eastern BTV topotype. CONCLUSION Phylogenetic analyses and nucleotide identity of BTV-16 isolates at the VP2 and VP5 gene encoded level indicate that isolates used in the present study might have evolved from a common Eastern topotype ancestor. The data presented in this study will be helpful for future selection of reference strains in a serological and molecular epidemiology study.
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Affiliation(s)
- Arpit Saxena
- Division of Virology, Indian Veterinary Research Institute (IVRI) Mukteswar, Nainital - 263 138, Uttarakhand, India
- Department of Molecular and Cellular Engineering, Sam Higginbottom University of Agriculture Technology and Sciences (SHUATS), Allahabad - 211 007, Uttar Pradesh, India
| | - Sanchay K. Biswas
- Division of Virology, Indian Veterinary Research Institute (IVRI) Mukteswar, Nainital - 263 138, Uttarakhand, India
| | - Karam Chand
- Division of Virology, Indian Veterinary Research Institute (IVRI) Mukteswar, Nainital - 263 138, Uttarakhand, India
| | - Jishnu Naskar
- Department of Molecular and Cellular Engineering, Sam Higginbottom University of Agriculture Technology and Sciences (SHUATS), Allahabad - 211 007, Uttar Pradesh, India
| | - Ankita Chauhan
- Division of Virology, Indian Veterinary Research Institute (IVRI) Mukteswar, Nainital - 263 138, Uttarakhand, India
| | - Gulam Mohd
- Division of Biological Standardization, Indian Veterinary Research Institute (IVRI) Izatnagar, Bareilly - 243 122, Uttar Pradesh, India
| | - Neha Tewari
- Division of Virology, Indian Veterinary Research Institute (IVRI) Mukteswar, Nainital - 263 138, Uttarakhand, India
| | - Kurat-ul-Ain
- Division of Virology, Indian Veterinary Research Institute (IVRI) Mukteswar, Nainital - 263 138, Uttarakhand, India
| | - Muthannan A. Ramakrishnan
- Division of Virology, Indian Veterinary Research Institute (IVRI) Mukteswar, Nainital - 263 138, Uttarakhand, India
| | - Awadh Bihari Pandey
- Division of Biological Standardization, Indian Veterinary Research Institute (IVRI) Izatnagar, Bareilly - 243 122, Uttar Pradesh, India
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A Novel Deltaflexivirus that Infects the Plant Fungal Pathogen, Sclerotinia sclerotiorum, Can Be Transmitted Among Host Vegetative Incompatible Strains. Viruses 2018; 10:v10060295. [PMID: 29857477 PMCID: PMC6024712 DOI: 10.3390/v10060295] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/25/2018] [Accepted: 05/29/2018] [Indexed: 11/17/2022] Open
Abstract
Various mycoviruses have been isolated from Sclerotinia sclerotiorum. Here, we identified a viral RNA sequence contig, representing a novel virus, Sclerotinia sclerotiorum deltaflexivirus 2 (SsDFV2), from an RNA_Seq database. We found that SsDFV2 was harbored in the hypovirulent strain, 228, which grew slowly on potato dextrose agar, produced a few sclerotia, and could not induce typical lesions on detached rapeseed (Brassica napus) leaves. Strain 228 was also infected by Botrytis porri RNA Virus 1 (BpRV1), a virus originally isolated from Botrytis porri. The genome of SsDFV2 comprised 6711 nucleotides, excluding the poly (A) tail, and contained a single large predicted open reading frame encoding a putative viral RNA replicase. Phylogenetic analysis demonstrated that SsDFV2 is closely related to viruses in the family Deltaflexiviridae; however, it also differs significantly from members of this family, suggesting that it may represent a new species. Further we determined that SsDFV2 could be efficiently transmitted to host vegetative incompatible individuals by dual culture. To our best knowledge, this is the first report that a (+) ssRNA mycovirus can overcome the transmission limitations of the vegetative incompatibility system, a phenomenon that may facilitate the potential use of mycoviruses for the control of crop fungal diseases.
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Laufer M, Mohammad H, Maiss E, Richert-Pöggeler K, Dall'Ara M, Ratti C, Gilmer D, Liebe S, Varrelmann M. Biological properties of Beet soil-borne mosaic virus and Beet necrotic yellow vein virus cDNA clones produced by isothermal in vitro recombination: Insights for reassortant appearance. Virology 2018; 518:25-33. [PMID: 29453056 DOI: 10.1016/j.virol.2018.01.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/15/2022]
Abstract
Two members of the Benyviridae family and genus Benyvirus, Beet soil-borne mosaic virus (BSBMV) and Beet necrotic yellow vein virus (BNYVV), possess identical genome organization, host range and high sequence similarity; they infect Beta vulgaris with variable symptom expression. In the US, mixed infections are described with limited information about viral interactions. Vectors suitable for agroinoculation of all genome components of both viruses were constructed by isothermal in vitro recombination. All 35S promoter-driven cDNA clones allowed production of recombinant viruses competent for Nicotiana benthamiana and Beta macrocarpa systemic infection and Polymyxa betae transmission and were compared to available BNYVV B-type clone. BNYVV and BSBMV RNA1 + 2 reassortants were viable and spread long-distance in N. benthamiana with symptoms dependent on the BNYVV type. Small genomic RNAs were exchangeable and systemically infected B. macrocarpa. These infectious clones represent a powerful tool for the identification of specific molecular host-pathogen determinants.
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Affiliation(s)
- Marlene Laufer
- Institute of Sugar Beet Research, Dept. of Phytopathology, 37079 Göttingen, Germany
| | - Hamza Mohammad
- Institute of Horticultural Production Systems, Dept. Phytomedicine, Plant Virology, Leibniz University, 30419 Hannover, Germany
| | - Edgar Maiss
- Institute of Horticultural Production Systems, Dept. Phytomedicine, Plant Virology, Leibniz University, 30419 Hannover, Germany
| | - Katja Richert-Pöggeler
- Julius-Kühn-Institute, Institute for Epidemiology and Pathogen Diagnostics, 38104 Braunschweig, Germany
| | - Mattia Dall'Ara
- DipSA-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy; Institut de biologie moléculaire des plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, France
| | - Claudio Ratti
- DipSA-Plant pathology, University of Bologna, Viale G. Fanin, 40, 40127 Bologna, Italy.
| | - David Gilmer
- Institut de biologie moléculaire des plantes, CNRS UPR2357, Université de Strasbourg, Strasbourg, France.
| | - Sebastian Liebe
- Institute of Sugar Beet Research, Dept. of Phytopathology, 37079 Göttingen, Germany
| | - Mark Varrelmann
- Institute of Sugar Beet Research, Dept. of Phytopathology, 37079 Göttingen, Germany.
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Zhang M, Zheng L, Liu C, Shu C, Zhou E. Characterization of a novel dsRNA mycovirus isolated from strain A105 of Rhizoctonia solani AG-1 IA. Arch Virol 2017; 163:427-430. [PMID: 29116463 DOI: 10.1007/s00705-017-3624-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/28/2017] [Indexed: 11/27/2022]
Abstract
Rhizoctonia solani dsRNA virus 3 (RsRV3), a novel mycovirus, was isolated from the rice sheath blight pathogen Rhizoctonia solani AG-1 IA strain A105. The RsRV3 genome consists of two segments of dsRNA (dsRNA1, 1,890 bp and dsRNA2, 1,811 bp). DsRNA1 has a single open reading frame (ORF) with a putative conserved RNA-dependent RNA polymerase (RdRp) domain, and dsRNA2 comprises a single ORF, predicted to encode a coat protein. Purified viral particles of RsRV3 were isometric and measured approximately 20 nm in diameter by negative-stain transmission electron microscope (TEM). Phylogenetic analyses indicated that RsRV3 is highly similar to viruses taxonomically classified in the genus Alphapartitivirus, family Partitiviridae. Taken together, the integrative analyses of viral genomic organization, amino acid sequence alignments and phylogenetic analyses clearly demonstrate that the RsRV3 virus isolated from R. solani AG-1 IA strain A105 is classifiable as a new member of the genus Alphapartitivirus, family Partitiviridae.
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Affiliation(s)
- Meiling Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Li Zheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Chen Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Canwei Shu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Erxun Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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Zhang J, Zhao Z, Hu R, Guo L, Zheng L, Du Z, Wu Z, Fang S, Zhang S, Liu Y. The genome sequence of Brassica campestris chrysovirus 1, a novel putative plant-infecting tripartite chrysovirus. Arch Virol 2016; 162:1107-1111. [PMID: 28004250 DOI: 10.1007/s00705-016-3196-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 12/07/2016] [Indexed: 11/25/2022]
Abstract
A putative chrysovirus recovered from Brassica campestris var. purpurea and provisionally named "Brassica campestris chrysovirus 1" (BrcCV1) was sequenced. The genome of the putative BrcCV1 consists of three double-stranded RNAs (dsRNAs) comprising 3,639 (dsRNA 1), 3,567 (dsRNA 2) and 3,337 (dsRNA 3) base pairs, respectively, each containing a single open reading frame (ORF 1-3). The putative proteins encoded by ORF 1-3 show homologies to RdRp, CP and chryso-P3 of approved or tentative chrysoviruses. In addition, the three dsRNAs of BrcCV1 contain highly conserved 5' and 3' untranslated regions (UTRs) in a way similar to known chrysoviruses. In a phylogenetic tree based on the conserved amino acid sequences of the RdRps of chrysoviruses, totiviruses and partitiviruses, the putative BrcCV1 formed a separate clade with Raphanus sativus chrysovirus 1 (RasCV1), a putative trisegmented, plant-infecting chrysovirus, in the family Chrysoviridae.
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Affiliation(s)
- Jun Zhang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Zhonghao Zhao
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
- Hunan Plant Protection Institute, Changsha, 410125, Hunan, China
| | - Rong Hu
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Lingfang Guo
- College of Chemistry and environmental Engineering, Yangtze University, Jingzhou, 434023, Hubei, China
| | - Limin Zheng
- Hunan Plant Protection Institute, Changsha, 410125, Hunan, China
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhenguo Du
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zujian Wu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shouguo Fang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Songbai Zhang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China.
- Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Yong Liu
- Hunan Plant Protection Institute, Changsha, 410125, Hunan, China.
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Sasaki M, Orba Y, Sasaki S, Gonzalez G, Ishii A, Hang'ombe BM, Mweene AS, Ito K, Sawa H. Multi-reassortant G3P[3] group A rotavirus in a horseshoe bat in Zambia. J Gen Virol 2016; 97:2488-2493. [PMID: 27574104 DOI: 10.1099/jgv.0.000591] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Group A rotavirus is a major cause of diarrhoea in humans, especially in young children. Bats also harbour group A rotaviruses, but the genetic backgrounds of bat rotavirus strains are usually distinct from those of human rotavirus strains. We identified a new strain of group A rotavirus in the intestinal contents of a horseshoe bat in Zambia. Whole genome sequencing revealed that the identified virus, named RVA/Bat-wt/ZMB/LUS12-14/2012/G3P[3], possessed the genotype constellation G3-P[3]-I3-R2-C2-M3-A9-N2-T3-E2-H3. Several genome segments of LUS12-14 were highly similar to those of group A rotaviruses identified from humans, cows and antelopes, indicating interspecies transmission of rotaviruses between bats and other mammals with possible multiple genomic reassortment events.
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Affiliation(s)
- Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Satoko Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Gabriel Gonzalez
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Akihiro Ishii
- Hokudai Center for Zoonosis Control in Zambia, PO Box 32379, Lusaka, Zambia
| | - Bernard M Hang'ombe
- Department of Paraclinical Studies, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Aaron S Mweene
- Department of Disease Control, School of Veterinary and Medicine, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Global Virus Network, Baltimore, MD 21201, USA.,Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
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Novel mitoviruses in Rhizoctonia solani AG-3PT infecting potato. Fungal Biol 2016; 120:338-50. [DOI: 10.1016/j.funbio.2015.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 10/28/2015] [Accepted: 11/04/2015] [Indexed: 11/23/2022]
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Urayama SI, Takaki Y, Nunoura T. FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance. Microbes Environ 2016; 31:33-40. [PMID: 26877136 PMCID: PMC4791113 DOI: 10.1264/jsme2.me15171] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Knowledge of the distribution and diversity of RNA viruses is still limited in spite of their possible environmental and epidemiological impacts because RNA virus-specific metagenomic methods have not yet been developed. We herein constructed an effective metagenomic method for RNA viruses by targeting long double-stranded (ds)RNA in cellular organisms, which is a hallmark of infection, or the replication of dsRNA and single-stranded (ss)RNA viruses, except for retroviruses. This novel dsRNA targeting metagenomic method is characterized by an extremely high recovery rate of viral RNA sequences, the retrieval of terminal sequences, and uniform read coverage, which has not previously been reported in other metagenomic methods targeting RNA viruses. This method revealed a previously unidentified viral RNA diversity of more than 20 complete RNA viral genomes including dsRNA and ssRNA viruses associated with an environmental diatom colony. Our approach will be a powerful tool for cataloging RNA viruses associated with organisms of interest.
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Affiliation(s)
- Syun-Ichi Urayama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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Li K, Zheng D, Cheng J, Chen T, Fu Y, Jiang D, Xie J. Characterization of a novel Sclerotinia sclerotiorum RNA virus as the prototype of a new proposed family within the order Tymovirales. Virus Res 2015; 219:92-99. [PMID: 26603216 DOI: 10.1016/j.virusres.2015.11.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/12/2015] [Accepted: 11/14/2015] [Indexed: 11/18/2022]
Abstract
Recent studies have shown that Sclerotinia sclerotiorum, an important plant pathogen fungus, harbors diverse mycoviruses. A new mycovirus, tentatively named as Sclerotinia sclerotiorum deltaflexivirus 1 (SsDFV1), was isolated from a S. sclerotiorum strain AX19 containing multiple dsRNA elements. The complete genome of SsDFV1 was shown to be 8178 nucleotides long excluding the poly (A) tail. SsDFV1 has a large putative open reading frame (ORF1) and three smaller ORFs (2-4). ORF1 encodes a putative methyltransferase-helicase-RdRp polyprotein of 2075 amino acids. ORFs (2-4) encode three putative small hypothetical proteins (<40kDa) with unknown biological functions. No evidence for a coat protein encoded by SsDFV1 was obtained. Multiple alignment suggested that three conserved domains, RdRp, methyltransferase, and helicase, from SsDFV1 have lower identity (approximately 25%) with all the reported viruses of four approved families, Alphaflexiviridae, Betaflexiviridae, Gammaflexiviridae and Tymoviridae in the order Tymovirales. Moreover, a phylogenetic tree also suggested that the SsDFV1 could not be phylogenetically placed in any of the approved families, and forms a separated cluster distinct from other known viruses. Therefore, these combined results suggest that SsDFV1 could represent a new positive-sense single-stranded RNA virus with some unique molecular features, and we propose to create a tentative family Deltaflexiviridae that accommodates SsDFV1.
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Affiliation(s)
- Kunfei Li
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Dan Zheng
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Jiasen Cheng
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Tao Chen
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Yanping Fu
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Daohong Jiang
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Jiatao Xie
- State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China.
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46
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Complete genome sequence of a novel dsRNA mycovirus isolated from the phytopathogenic fungus Fusarium oxysporum f. sp. dianthi. Arch Virol 2015; 160:2375-9. [PMID: 26138558 DOI: 10.1007/s00705-015-2509-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/21/2015] [Indexed: 10/23/2022]
Abstract
A novel double-stranded RNA (dsRNA) mycovirus, designated Fusarium oxysporum f. sp. dianthi mycovirus 1 (FodV1), was isolated from a strain of the phytopathogenic fungus F. oxysporum f. sp. dianthi. The FodV1 genome had four dsRNA segments, designated, from the largest to the smallest one, dsRNA 1, 2 3, and 4. Each one of these segments contained a single open reading frame (ORF). dsRNA 1 (3555 bp) and dsRNA 3 (2794 bp) encoded a putative RNA-dependent RNA polymerase (RdRp) and a putative coat protein (CP), respectively. dsRNA 2 (2809 bp) and dsRNA 4 (2646 bp) contained ORFs encoding hypothetical proteins (named P2 and P4, respectively) with unknown functions. Analysis of its genomic structure, homology searches of the deduced amino acid sequences, and phylogenetic analysis all indicated that FodV1 is a new member of the family Chrysoviridae. This is the first report of the complete genomic characterization of a mycovirus identified in the plant pathogen Fusarium oxysporum.
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Li Y, Xu P, Zhang L, Xia Z, Qin X, Yang G, Mo X. Molecular characterization of a novel mycovirus from Rhizoctonia fumigata AG-Ba isolate C-314 Baishi. Arch Virol 2015; 160:2371-4. [PMID: 26133296 DOI: 10.1007/s00705-015-2483-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 06/03/2015] [Indexed: 11/25/2022]
Abstract
The complete genome sequence of a novel dsRNA virus isolated from Rhizoctonia fumigata AG-Ba isolate C-314 Baishi (designated as Rhizoctonia fumigata virus 1, RfV1) was determined. The RfV1 genome was 9,907 bp in length and contained two open reading frames (ORFs). ORF1 potentially coded for a 198.10-kDa protein (P1). P1 shared low but significant amino acid sequence similarity to the putative protein encoded by Lentinula edodes mycovirus (LeV) ORF1. P1 contained a NUDIX domain, which was also present in the putative proteins encoded by the ORF1s of LeV and Phlebiopsis gigantea large virus 1 (PgLV-1). ORF2 potentially coded for a 146.72-kDa protein (P2) that contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). ORF1 and ORF2 were overlapping, and it was predicted that ORF2 could be translated as a fusion with ORF1 via a ribosomal -1 frameshifting mechanism. Phylogenetic analysis indicated that RfV1 clustered with PgLV-1, LeV and Rosellinia necatrix megabirnavirus 1 (RnMBV1) in a separate clade independent of other virus genera. We propose that RfV1, along with PgLV-1 and LeV, should be grouped into a new viral genus related to the family Megabirnaviridae. This is the first report of the full-length genome sequence of a novel mycovirus isolated from R. fumigata.
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Affiliation(s)
- Yanqiong Li
- Yunnan Agricultural University, Kunming, 650201, Yunnan, China
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48
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Koloniuk I, Hrabáková L, Petrzik K. Molecular characterization of a novel amalgavirus from the entomopathogenic fungus Beauveria bassiana. Arch Virol 2015; 160:1585-8. [DOI: 10.1007/s00705-015-2416-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/30/2015] [Indexed: 11/30/2022]
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Xu Z, Wu S, Liu L, Cheng J, Fu Y, Jiang D, Xie J. A mitovirus related to plant mitochondrial gene confers hypovirulence on the phytopathogenic fungus Sclerotinia sclerotiorum. Virus Res 2014; 197:127-36. [PMID: 25550075 DOI: 10.1016/j.virusres.2014.12.023] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 12/15/2014] [Accepted: 12/18/2014] [Indexed: 11/17/2022]
Abstract
A double-stranded RNA (dsRNA) segment was isolated from a hypovirulent strain, HC025, of Sclerotinia sclerotiorum. The complete nucleotide sequence of the dsRNA was determined to be 2530 bp in length. Using the fungal mitochondrial genetic code, the positive strand of the dsRNA was found to contain a single large open reading frame (ORF) with the characteristic conserved motifs of the RNA-dependent RNA polymerase (RdRp). BLAST analysis revealed that RdRp shares 74% sequence identity with Sclerotinia sclerotiorum mitovirus 1 (SsMV1/KL-1). The positive strand of the dsRNA could be folded into potentially stable stem-loop structures at both the 5' and 3' terminal sequences. Moreover, the 5' and 3' terminal sequences were inverted complementary sequences and formed a panhandle structure. These results reveal that this dsRNA segment represents the replicative form of a mitovirus that is a strain of SsMV1 from the genus Mitovirus in the family Narnaviridae and was tentatively designated as Sclerotinia sclerotiorum mitovirus 1 (SsMV1/HC025). Sequence comparison and phylogenetic analysis suggest that mitovirus RdRp gene was evolutionarily related to plant mitochondrial genome. Our results demonstrate that SsMV1/HC025 infection exerted obvious effects on host biological properties. Hypovirulence feature and SsMV1/HC025 could be co-transmitted from hypovirulent strains to other virulent strains via hyphal contact. Thus, SsMV1/HC025 related to plant mitochondrial gene confers hypovirulence on S. sclerotiorum.
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Affiliation(s)
- Zhiyong Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Songsong Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Lijiang Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Jiasen Cheng
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Yanping Fu
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China; Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China
| | - Jiatao Xie
- Provincial Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei Province, People's Republic of China.
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Das S, Falloon RE, Stewart A, Pitman AR. Molecular characterisation of an endornavirus from Rhizoctonia solani AG-3PT infecting potato. Fungal Biol 2014; 118:924-34. [PMID: 25442295 DOI: 10.1016/j.funbio.2014.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/20/2014] [Accepted: 08/18/2014] [Indexed: 10/24/2022]
Abstract
Rhizoctonia solani (teleomorph: Thanatephorus cucumeris) is a soil-borne plant pathogenic fungus that has a broad host range, including potato. In this study, the double-stranded RNA (dsRNA) profiles were defined for 39 Rhizoctonia solani isolates representative of two different anastomosis groups (AGs) associated with black scurf of potato in New Zealand. A large dsRNA of c. 12 kb-18 kb was detected in each of the isolates, regardless of AG or virulence on potato. Characterisation of the large dsRNA from R. solani AG-3PT isolate RS002, using random amplification of total dsRNA and analyses of overlapping cDNA sequences, resulted in the assembly of a consensus sequence of 14 694 nt. A single, large open reading frame was identified on the positive strand of the assembled sequence encoding a putative polypeptide of at least 4893 amino acids, with a predicted molecular mass of 555.6 kDa. Conserved domains within this polypeptide included those for a viral methyltransferase, a viral RNA helicase 1 and an RNA-dependent RNA polymerase. The domains and their sequential organisation revealed the polyprotein was very similar to those encoded by dsRNA viruses of the genus Endornavirus, in the family Endornaviridae. This is the first report of an endornavirus in R. solani, and thus the putative virus is herein named Rhizoctonia solani endornavirus - RS002 (RsEV-RS002). Partial characterisation of the large dsRNAs in five additional AG-3PT isolates of R. solani also identified them as probable endornaviruses, suggesting this family of viruses is widespread in R. solani infecting potato. The ubiquitous nature of endornaviruses in this plant pathogen implies they may have an important, but yet uncharacterised, role in R. solani.
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Affiliation(s)
- Subha Das
- Bio-Protection Research Centre, PO Box 85084, Lincoln University 7647, Canterbury, New Zealand; The New Zealand Institute for Plant & Food Research Limited, PB 4704, Christchurch, New Zealand.
| | - Richard E Falloon
- Bio-Protection Research Centre, PO Box 85084, Lincoln University 7647, Canterbury, New Zealand; The New Zealand Institute for Plant & Food Research Limited, PB 4704, Christchurch, New Zealand.
| | - Alison Stewart
- Bio-Protection Research Centre, PO Box 85084, Lincoln University 7647, Canterbury, New Zealand; Marrone Bio Innovations, Inc., 2121 Second St, Suite 107B Davis, CA 95618, USA.
| | - Andrew R Pitman
- Bio-Protection Research Centre, PO Box 85084, Lincoln University 7647, Canterbury, New Zealand; The New Zealand Institute for Plant & Food Research Limited, PB 4704, Christchurch, New Zealand.
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