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Fan Y, Zhao W, Tang X, Yang M, Yang Y, Zhang Z, Cheng B, Zhou E, He Z. Co-infection of Four Novel Mycoviruses from Three Lineages Confers Hypovirulence on Phytopathogenic Fungus Ustilaginoidea virens. RICE (NEW YORK, N.Y.) 2024; 17:44. [PMID: 39014281 PMCID: PMC11252108 DOI: 10.1186/s12284-024-00721-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 06/21/2024] [Indexed: 07/18/2024]
Abstract
Rice false smut caused by Ustilaginoidea virens has become one of the most important diseases of rice. Mycoviruses are viruses that can infect fungi with the potential to control fungal diseases. However, little is known about the biocontrol role of hypoviruses in U. virens. In this study, we revealed that the hypovirulence-associated U. virens strain Uv325 was co-infected by four novel mycoviruses from three lineages, designated Ustilaginoidea virens RNA virus 16 (UvRV16), Ustilaginoidea virens botourmiavirus virus 8 (UvBV8), Ustilaginoidea virens botourmiavirus virus 9 (UvBV9), and Ustilaginoidea virens narnavirus virus 13 (UvNV13), respectively. The U. virens strain co-infected by four mycoviruses showed slower growth rates, reduced conidial yield, and attenuated pigmentation. We demonstrated that UvRV16 was not only the major factor responsible for the hypovirulent phenotype in U. vriens, but also able to prevent U. virens to accumulate more mycotoxin, thereby weakening the inhibitory effects on rice seed germination and seedling growth. Additionally, we indicated that UvRV16 can disrupt the antiviral response of U. virens by suppressing the transcriptional expression of multiple genes involved in autophagy and RNA silencing. In conclusion, our study provided new insights into the biological control of rice false smut.
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Affiliation(s)
- Yu Fan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Wenhua Zhao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaolin Tang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Mei Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Yingqing Yang
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Zixuan Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Baoping Cheng
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection/Key Laboratory of Green Prevention and Control On Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong, 510642, China.
| | - Erxun Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China.
| | - Zhenrui He
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China.
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Ding H, Wang Y, Li C, Shuai S, An H, Fang S, Zhang S, Deng Q. Molecular characterization of a single-negative-stranded RNA virus from the rice blast fungus Magnaporthe oryzae isolate NJ39. Arch Virol 2024; 169:128. [PMID: 38802709 DOI: 10.1007/s00705-024-06054-y] [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: 12/23/2023] [Accepted: 02/29/2024] [Indexed: 05/29/2024]
Abstract
A novel negative-sense single-stranded RNA mycovirus, designated as "Magnaporthe oryzae mymonavirus 1" (MoMNV1), was identified in the rice blast fungus Magnaporthe oryzae isolate NJ39. MoMNV1 has a single genomic RNA segment consisting of 10,515 nucleotides, which contains six open reading frames. The largest open reading frame contains 5837 bases and encodes an RNA replicase. The six open reading frames have no overlap and are arranged linearly on the genome, but the spacing of the genes is small, with a maximum of 315 bases and a minimum of 80 bases. Genome comparison and phylogenetic analysis indicated that MoMNV1 is a new member of the genus Penicillimonavirus of the family Mymonaviridae.
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Affiliation(s)
- Hang Ding
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Yao Wang
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Cong Li
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Simin Shuai
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
| | - Hongliu An
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Jingzhou, China
| | - Shouguo Fang
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Jingzhou, China
| | - Songbai Zhang
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Jingzhou, China
| | - Qingchao Deng
- College of Agriculture, Yangtze University, Jingzhou, 434005, Hubei, China.
- Hubei Engineering Research Center for Pest Forewarning and Management, Jingzhou, China.
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Li S, Ma Z, Zhang X, Cai Y, Han C, Wu X. Sixteen Novel Mycoviruses Containing Positive Single-Stranded RNA, Double-Stranded RNA, and Negative Single-Stranded RNA Genomes Co-Infect a Single Strain of Rhizoctonia zeae. J Fungi (Basel) 2023; 10:30. [PMID: 38248940 PMCID: PMC10817634 DOI: 10.3390/jof10010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
In the present study, sixteen novel RNA mycoviruses co-infecting a single strain of Rhizoctonia zeae (strain D40) were identified and molecularly characterized using metatranscriptome sequencing combined with a method for rapid amplification of cDNA ends. The fungal strain was isolated from diseased seedlings of sugar beet with damping-off symptoms. Based on genome analysis and phylogenetic analysis of amino acid sequences of RNA-dependent RNA polymerase, the sixteen mycoviruses associated with strain D40 contained three genome types with nine distinct lineages, including positive single-stranded RNA (Hypoviridae, Yadokariviridae, Botourmiaviridae, and Gammaflexiviridae), double-stranded RNA (Phlegiviridae, Megabirnaviridae, Megatotiviridae, and Yadonushiviridae), and negative single-stranded RNA (Tulasviridae), suggesting a complex composition of a mycoviral community in this single strain of R. zeae (strain D40). Full genome sequences of six novel mycoviruses and the nearly full-length sequences of the remaining ten novel mycoviruses were obtained. Furthermore, seven of these sixteen mycoviruses were confirmed to assemble virus particles present in the R. zeae strain D40. To the best of our knowledge, this is the first detailed study of mycoviruses infecting R. zeae.
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Affiliation(s)
| | | | | | | | | | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, China; (S.L.); (Z.M.); (X.Z.); (Y.C.); (C.H.)
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Reyes BMD, Fonseca PLC, Heming NM, Conceição LBDA, Nascimento KTDS, Gramacho KP, Arevalo-Gardini E, Pirovani CP, Aguiar ERGR. Characterization of the microbiota dynamics associated with Moniliophthora roreri, causal agent of cocoa frosty pod rot disease, reveals new viral species. Front Microbiol 2023; 13:1053562. [PMID: 36817107 PMCID: PMC9936985 DOI: 10.3389/fmicb.2022.1053562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/23/2022] [Indexed: 02/05/2023] Open
Abstract
Introduction Theobroma cacao, the cocoa tree, is a target for pathogens, such as fungi from the genera Phytophthora, Moniliophthora, Colletotrichum, Ceratocystis, among others. Some cacao pathogens are restricted to specific regions of the world, such as the Cacao swollen shoot virus (CSSV) in West African countries, while others are expanding geographically, such as Moniliophthora roreri in the Americas. M. roreri is one of the most threatening cacao pathogens since it directly attacks the cacao pods driving a significant reduction in production, and therefore economic losses. Despite its importance, the knowledge about the microenvironment of this pathogen and the cocoa pods is still poorly characterized. Methods Herein we performed RNA sequencing of spores in differential stages of culture in a medium supplemented with cacao pod extract and mycelium collected of the susceptible variety ICT 7121 naturally infected by the pathogen to evaluate the diversity and transcriptional activity of microorganisms associated with the in vitro sporulation of M. roreri. Results Our data revealed a great variety of fungi and bacteria associated with M. roreri, with an exceptional diversity of individuals from the genus Trichoderma sp. Interestingly, the dynamics of microorganisms from different kingdoms varied proportionally, suggesting they are somehow affected by M. roreri culture time. We also identified three sequences similar to viral genomes from the Narnaviridae family, posteriorly confirmed by phylogenetic analysis as members of the genus Narnavirus. Screening of M. roreri public datasets indicated the virus sequences circulating in samples from Ecuador, suggesting a wide spread of these elements. Of note, we did not identify traces of the viral sequences in the M. roreri genome or DNA sequencing, restricting the possibility of these sequences representing endogenized elements. Discussion To the best of our knowledge, this is the first report of viruses infecting the fungus of the genus Moniliophthora and only the third description of viruses that are able to parasite elements from the Marasmiaceae family.
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Affiliation(s)
| | - Paula Luize Camargos Fonseca
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil,Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Neander Marcel Heming
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | | | | | - Karina Peres Gramacho
- Centro de Pesquisas do Cacau, Comissão Executivo do Plano da Lavoura Cacaueira, CEPEC/CEPLAC, Rodovia Ilhéus-Itabuna, Ilhéus, Brazil
| | - Enrique Arevalo-Gardini
- Instituto de Cultivos Tropicales, Tarapoto, Peru,Universidad Nacional Autónoma de Alto Amazonas, Yurimaguas, Peru
| | | | - Eric Roberto Guimarães Rocha Aguiar
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, Brazil,*Correspondence: Eric Roberto Guimarães Rocha Aguiar, ✉
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Characterization of a Fungal Virus Representing a Novel Genus in the Family Alphaflexiviridae. Viruses 2023; 15:v15020339. [PMID: 36851552 PMCID: PMC9967154 DOI: 10.3390/v15020339] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/15/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Sclerotinia sclerotiorum is an ascomycetous fungus and hosts various mycoviruses. In this study, a novel fungal alphaflexivirus with a special genomic structure, named Sclerotinia sclerotiorum alphaflexivirus 1 (SsAFV1), was cloned from a hypovirulent strain, AHS31. Strain AHS31 was also co-infected with two botourmiaviruses and two mitoviruses. The complete genome of SsAFV1 comprised 6939 bases with four open reading frames (ORFs), a conserved 5'-untranslated region (UTR), and a poly(A) tail in the 3' terminal; the ORF1 and ORF3 encoded a replicase and a coat protein (CP), respectively, while the function of the proteins encoded by ORF2 and ORF4 was unknown. The virion of SsAFV1 was flexuous filamentous 480-510 nm in length and 9-10 nm in diameter. The results of the alignment and the phylogenetic analysis showed that SsAFV1 is related to allexivirus and botrexvirus, such as Garlic virus X of the genus Allexivirus and Botrytis virus X of the genus Botrevirus, both with 44% amino-acid (aa) identity of replicase. Thus, SsAFV1 is a novel virus and a new genus, Sclerotexvirus, is proposed to accommodate this novel alphaflexivirus.
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Novel Mycoviruses Discovered from a Metatranscriptomics Survey of the Phytopathogenic Alternaria Fungus. Viruses 2022; 14:v14112552. [PMID: 36423161 PMCID: PMC9693364 DOI: 10.3390/v14112552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Alternaria fungus can cause notable diseases in cereals, ornamental plants, vegetables, and fruits around the world. To date, an increasing number of mycoviruses have been accurately and successfully identified in this fungus. In this study, we discovered mycoviruses from 78 strains in 6 species of the genus Alternaria, which were collected from 10 pear production areas using high-throughput sequencing technology. Using the total RNA-seq, we detected the RNA-dependent RNA polymerase of 19 potential viruses and the coat protein of two potential viruses. We successfully confirmed these viruses using reverse transcription polymerase chain reaction with RNA as the template. We identified 12 mycoviruses that were positive-sense single-stranded RNA (+ssRNA) viruses, 5 double-strand RNA (dsRNA) viruses, and 4 negative single-stranded RNA (-ssRNA) viruses. In these viruses, five +ssRNA and four -ssRNA viruses were novel mycoviruses classified into diverse the families Botourmiaviridae, Deltaflexivirus, Mymonaviridea, and Discoviridae. We identified a novel -ssRNA mycovirus isolated from an A. tenuissima strain HB-15 as Alternaria tenuissima negative-stranded RNA virus 2 (AtNSRV2). Additionally, we characterized a novel +ssRNA mycovirus isolated from an A. tenuissima strain SC-8 as Alternaria tenuissima deltaflexivirus 1 (AtDFV1). According to phylogenetic and sequence analyses, we determined that AtNSRV2 was related to the viruses of the genus Sclerotimonavirus in the family Mymonaviridae. We also found that AtDFV1 was related to the virus family Deltaflexivirus. This study is the first to use total RNA sequencing to characterize viruses in Alternaria spp. These results expand the number of Alternaria viruses and demonstrate the diversity of these mycoviruses.
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Metatranscriptomic Analysis Reveals Rich Mycoviral Diversity in Three Major Fungal Pathogens of Rice. Int J Mol Sci 2022; 23:ijms23169192. [PMID: 36012458 PMCID: PMC9409214 DOI: 10.3390/ijms23169192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022] Open
Abstract
In recent years, three major fungal diseases of rice, i.e., rice blast, rice false smut, and rice-sheath blight, have caused serious worldwide rice-yield reductions and are threatening global food security. Mycoviruses are ubiquitous in almost all major groups of filamentous fungi, oomycetes, and yeasts. To reveal the mycoviral diversity in three major fungal pathogens of rice, we performed a metatranscriptomic analysis of 343 strains, representing the three major fungal pathogens of rice, Pyricularia oryzae, Ustilaginoidea virens, and Rhizoctonia solani, sampled in southern China. The analysis identified 682 contigs representing the partial or complete genomes of 68 mycoviruses, with 42 described for the first time. These mycoviruses showed affinity with eight distinct lineages: Botourmiaviridae, Partitiviridae, Totiviridae, Chrysoviridae, Hypoviridae, Mitoviridae, Narnaviridae, and Polymycoviridae. More than half (36/68, 52.9%) of the viral sequences were predicted to be members of the families Narnaviridae and Botourmiaviridae. The members of the family Polymycoviridae were also identified for the first time in the three major fungal pathogens of rice. These findings are of great significance for understanding the diversity, origin, and evolution of, as well as the relationship between, genome structures and functions of mycoviruses in three major fungal pathogens of rice.
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8
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Mycoviromic Analysis Unveils Complex Virus Composition in a Hypovirulent Strain of Sclerotinia sclerotiorum. J Fungi (Basel) 2022; 8:jof8070649. [PMID: 35887405 PMCID: PMC9317179 DOI: 10.3390/jof8070649] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
Mycoviruses are ubiquitous in pathogenic fungi including Sclerotinia sclerotiorum. Using RNA sequencing, more mycoviruses have been identified in individual strains, which were previously reported to be infected by a single mycovirus. A hypovirulent strain of S. sclerotiorum, HC025, was previously thought to harbor a single mitovirus, Sclerotinia sclerotiorum mitovirus 1 (SsMV1), based on the analysis of the conventional dsRNA extraction method. We found HC025 to be co-infected by five mycoviruses. In addition to SsMV1, four mycoviruses were identified: Sclerotinia sclerotiorum narnavirus 4 (SsNV4), Sclerotinia sclerotiorum negative-stranded RNA virus 1 (SsNSRV1), Sclerotinia sclerotiorum ourmia-like virus 14 (SsOLV14), and SsOLV22. Three mycoviruses including SsNV4, SsNSRV1, and SsOLV14 share high replicase identities (more than 95%) with the previously reported corresponding mycoviruses, and SsOLV22 shows lower identity to the known viruses. The complete genome of SsOLV22 is 3987 nt long and contains a single ORF-encoded RdRp, which shares 24.84% identity with the RNA-dependent RNA polymerase (RdRp) of Hubei narna-like virus 10 (query coverage: 26%; e-value: 8 × 10−19). The phylogenetic tree of RdRp suggests that SsOLV22 is a new member within the family Botourmiaviridae. All of the mycoviruses except for SsNSRV1 could horizontally co-transfer from HC025 to the virulent strain Ep-1PNA367 with hypovirulent phenotypes, and converted a later strain into a hypovirulent strain. In summary, we molecularly characterized the hypovirulent strain HC025 and identified five RNA mycoviruses including a new member within Botourmiaviridae.
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De Miccolis Angelini RM, Raguseo C, Rotolo C, Gerin D, Faretra F, Pollastro S. The Mycovirome in a Worldwide Collection of the Brown Rot Fungus Monilinia fructicola. J Fungi (Basel) 2022; 8:jof8050481. [PMID: 35628739 PMCID: PMC9147972 DOI: 10.3390/jof8050481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
The fungus Monilinia fructicola is responsible for brown rot on stone and pome fruit and causes heavy yield losses both pre- and post-harvest. Several mycoviruses are known to infect fungal plant pathogens. In this study, a metagenomic approach was applied to obtain a comprehensive characterization of the mycovirome in a worldwide collection of 58 M. fructicola strains. Deep sequencing of double-stranded (ds)RNA extracts revealed a great abundance and variety of mycoviruses. A total of 32 phylogenetically distinct positive-sense (+) single-stranded (ss)RNA viruses were identified. They included twelve mitoviruses, one in the proposed family Splipalmiviridae, and twelve botourmiaviruses (phylum Lenarviricota), eleven of which were novel viral species; two hypoviruses, three in the proposed family Fusariviridae, and one barnavirus (phylum Pisuviricota); as well as one novel beny-like virus (phylum Kitrinoviricota), the first one identified in Ascomycetes. A partial sequence of a new putative ssDNA mycovirus related to viruses within the Parvoviridae family was detected in a M. fructicola isolate from Serbia. The availability of genomic sequences of mycoviruses will serve as a solid basis for further research aimed at deepening the knowledge on virus–host and virus–virus interactions and to explore their potential as biocontrol agents against brown rot disease.
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Luo X, Jiang D, Xie J, Jia J, Duan J, Cheng J, Fu Y, Chen T, Yu X, Li B, Lin Y. Genome Characterization and Phylogenetic Analysis of a Novel Endornavirus That Infects Fungal Pathogen Sclerotinia sclerotiorum. Viruses 2022; 14:v14030456. [PMID: 35336865 PMCID: PMC8953294 DOI: 10.3390/v14030456] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Endornaviruses are capsidless linear (+) ssRNA viruses in the family Endornaviridae. In this study, Scelrotinia sclerotiorum endornavirus 11 (SsEV11), a novel endornavirus infecting hypovirulent Sclerotinia sclerotiorum strain XY79, was identified and cloned using virome sequencing analysis and rapid amplification of cDNA ends (RACE) techniques. The full-length genome of SsEV11 is 11906 nt in length with a large ORF, which encodes a large polyprotein of 3928 amino acid residues, containing a viral methyltransferase domain, a cysteine-rich region, a putative DEADc, a viral helicase domain, and an RNA-dependent RNA polymerase (RdRp) 2 domain. The 5’ and 3’ untranslated regions (UTR) are 31 nt and 90 nt, respectively. According to the BLAST result of the nucleotide sequence, SsEV11 shows the highest identity (45%) with Sclerotinia minor endornavirus 1 (SmEV1). Phylogenetic analysis based on amino acid sequence of RdRp demonstrated that SsEV11 clusters to endornavirus and has a close relationship with Betaendornavirus. Phylogenetic analysis based on the sequence of endornaviral RdRp domain indicated that there were three large clusters in the phylogenetic tree. Combining the results of alignment analysis, Cluster I at least has five subclusters including typical members of Alphaendornavirus and many unclassified endornaviruses that isolated from fungi, oomycetes, algae, and insects; Cluster II also has five subclusters including typical members of Betaendornavirus, SsEV11, and other unclassified viruses that infected fungi; Cluster III includes many endorna-like viruses that infect nematodes, mites, and insects. Viruses in Cluster I and Cluster II are close to each other and relatively distant to those in Cluster III. Our study characterized a novel betaendornavirus, SsEV11, infected fungal pathogen S. sclerotiorum, and suggested that notable phylogenetic diverse exists in endornaviruses. In addition, at least, one novel genus, Gammaendornavirus, should be established to accommodate those endorna-like viruses in Cluster III.
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Affiliation(s)
- Xin Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Jichun Jia
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
| | - Jie Duan
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Jiasen Cheng
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (D.J.); (J.X.); (J.J.); (T.C.)
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Xiao Yu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Bo Li
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
| | - Yang Lin
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (J.D.); (J.C.); (Y.F.); (X.Y.); (B.L.)
- Correspondence:
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Wang Q, Zou Q, Dai Z, Hong N, Wang G, Wang L. Four Novel Mycoviruses from the Hypovirulent Botrytis cinerea SZ-2-3y Isolate from Paris polyphylla: Molecular Characterisation and Mitoviral Sequence Transboundary Entry into Plants. Viruses 2022; 14:v14010151. [PMID: 35062353 PMCID: PMC8777694 DOI: 10.3390/v14010151] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
A hypovirulent SZ-2-3y strain isolated from diseased Paris polyphylla was identified as Botrytis cinerea. Interestingly, SZ-2-3y was coinfected with a mitovirus, two botouliviruses, and a 3074 nt fusarivirus, designated Botrytis cinerea fusarivirus 8 (BcFV8); it shares an 87.2% sequence identity with the previously identified Botrytis cinerea fusarivirus 6 (BcFV6). The full-length 2945 nt genome sequence of the mitovirus, termed Botrytis cinerea mitovirus 10 (BcMV10), shares a 54% sequence identity with Fusarium boothii mitovirus 1 (FbMV1), and clusters with fungus mitoviruses, plant mitoviruses and plant mitochondria; hence BcMV10 is a new Mitoviridae member. The full-length 2759 nt and 2812 nt genome sequences of the other two botouliviruses, named Botrytis cinerea botoulivirus 18 and 19 (BcBoV18 and 19), share a 40% amino acid sequence identity with RNA-dependent RNA polymerase protein (RdRp), and these are new members of the Botoulivirus genus of Botourmiaviridae. Horizontal transmission analysis showed that BcBoV18, BcBoV19 and BcFV8 are not related to hypovirulence, suggesting that BcMV10 may induce hypovirulence. Intriguingly, a partial BcMV10 sequence was detected in cucumber plants inoculated with SZ-2-3y mycelium or pXT1/BcMV10 agrobacterium. In conclusion, we identified a hypovirulent SZ-2-3y fungal strain from P. polyphylla, coinfected with four novel mycoviruses that could serve as potential biocontrol agents. Our findings provide evidence of cross-kingdom mycoviral sequence transmission.
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Affiliation(s)
- Qiong Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Zou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhaoji Dai
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, College of Plant Protection, Hainan University, Ministry of Education, Haikou 570100, China;
| | - Ni Hong
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Liping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (Q.Z.); (N.H.); (G.W.)
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: ; Tel.: +86-27-8728-2130; Fax: +86-27-8738-4670
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Khan HA, Shamsi W, Jamal A, Javaied M, Sadiq M, Fatma T, Ahmed A, Arshad M, Waseem M, Babar S, Dogar MM, Virk N, Janjua HA, Kondo H, Suzuki N, Bhatti MF. Assessment of mycoviral diversity in Pakistani fungal isolates revealed infection by 11 novel viruses of a single strain of Fusarium mangiferae isolate SP1. J Gen Virol 2021; 102. [PMID: 34850675 DOI: 10.1099/jgv.0.001690] [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] [Indexed: 11/18/2022] Open
Abstract
An extensive screening survey was conducted on Pakistani filamentous fungal isolates for the identification of viral infections. A total of 396 fungal samples were screened, of which 36 isolates were found double-stranded (ds) RNA positive with an overall frequency of 9% when analysed by a classical dsRNA isolation method. One of 36 dsRNA-positive strains, strain SP1 of a plant pathogenic fungus Fusarium mangiferae, was subjected to virome analysis. Next-generation sequencing and subsequent completion of the entire genome sequencing by a classical Sanger sequencing method showed the SP1 strain to be co-infected by 11 distinct viruses, at least seven of which should be described as new taxa at the species level according to the ICTV (International Committee on Taxonomy of Viruses) species demarcation criteria. The newly identified F. mangiferae viruses (FmVs) include two partitivirids, one betapartitivirus (FmPV1) and one gammapartitivirus (FmPV2); six mitovirids, three unuamitovirus (FmMV2, FmMV4, FmMV6), one duamitovirus (FmMV5), and two unclassified mitovirids (FmMV1, FmMV3); and three botourmiavirids, two magoulivirus (FmBOV1, FmBOV3) and one scleroulivirus (FmBOV2). The number of coinfecting viruses is among the largest ones of fungal coinfections. Their molecular features are thoroughly described here. This represents the first large virus survey in the Indian sub-continent.
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Affiliation(s)
- Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Wajeeha Shamsi
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Present address: Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland
| | - Atif Jamal
- Crop Diseases Research Institute, National Agricultural Research Centre, Islamabad, Pakistan
| | - Memoona Javaied
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Mashal Sadiq
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Aqeel Ahmed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Maleeha Arshad
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Mubashra Waseem
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Samra Babar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Midhat Mustafa Dogar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Nasar Virk
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan.,Present address: EBS Universität für Wirtschaft und Recht, EBS Business School, Rheingaustrasse 1, 65375, Oestrich-Winkel, Germany
| | - Hussnain Ahmed Janjua
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), H-12, 44000, Islamabad, Pakistan
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13
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Characterization of the Mycovirome from the Plant-Pathogenic Fungus Cercospora beticola. Viruses 2021; 13:v13101915. [PMID: 34696345 PMCID: PMC8537984 DOI: 10.3390/v13101915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 12/25/2022] Open
Abstract
Cercospora leaf spot (CLS) caused by Cercospora beticola is a devastating foliar disease of sugar beet (Beta vulgaris), resulting in high yield losses worldwide. Mycoviruses are widespread fungi viruses and can be used as a potential biocontrol agent for fugal disease management. To determine the presence of mycoviruses in C. beticola, high-throughput sequencing analysis was used to determine the diversity of mycoviruses in 139 C. beticola isolates collected from major sugar beet production areas in China. The high-throughput sequencing reads were assembled and searched against the NCBI database using BLASTn and BLASTx. The results showed that the obtained 93 contigs were derived from eight novel mycoviruses, which were grouped into 3 distinct lineages, belonging to the families Hypoviridae, Narnaviridae and Botourmiaviridae, as well as some unclassified (−)ssRNA viruses in the order Bunyavirales and Mononegavirales. To the best of our knowledge, this is the first identification of highly diverse mycoviruses in C. beticola. The novel mycoviruses explored in this study will provide new viral materials to biocontrol Cercospora diseases. Future studies of these mycoviruses will aim to assess the roles of each mycovirus in biological function of C. beticola in the future.
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