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Santos YS, Vidal AH, Abreu EFM, Nogueira I, Faleiro FG, Lacorte CC, Melo FL, de Araújo Campos M, de Rezende RR, Morgan T, Varsani A, Alfenas-Zerbini P, Ribeiro SG. Detection and molecular characterization of a novel mitovirus associated with Passiflora edulis Sims. Arch Virol 2024; 169:190. [PMID: 39222118 DOI: 10.1007/s00705-024-06115-2] [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: 04/18/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Mitoviruses are cryptic capsidless viruses belonging to the family Mitoviridae that replicate and are maintained in the mitochondria of fungi. Complete mitovirus-like sequences were recently assembled from plant transcriptome data and plant leaf tissue samples. Passion fruit (Passiflora spp.) is an economically important crop for numerous tropical and subtropical countries worldwide, and many virus-induced diseases impact its production. From a large-scale genomic study targeting viruses infecting Passiflora spp. in Brazil, we detected a de novo-assembled contig with similarity to other plant-associated mitoviruses. The contig is ∼2.6 kb long, with a single open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRP). This contig has been named "passion fruit mitovirus-like 1" (PfMv1). An alignment of the predicted amino acid sequence of the RdRP of PfMv1 and those of other plant-associated mitoviruses revealed the presence of the six conserved motifs of mitovirus RdRPs. PfMv1 has 79% coverage and 50.14% identity to Humulus lupulus mitovirus 1. Phylogenetic analysis showed that PfMV1 clustered with other plant-associated mitoviruses in the genus Duamitovirus. Using RT-PCR, we detected a PfMv1-derived fragment, but no corresponding DNA was identified, thus excluding the possibility that this is an endogenized viral-like sequence. This is the first evidence of a replicating mitovirus associated with Passiflora edulis, and it should be classified as a member of a new species, for which we propose the name "Duamitovirus passiflorae".
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Affiliation(s)
- Yam Sousa Santos
- Centro de Educação e Saúde, Universidade Federal de Campina Grande, Cuité, PB, 58175-000, Brazil
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-917, Brazil
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Andreza Henrique Vidal
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-917, Brazil
- Instituto de Ciências Biológicas-IB, PPG BIOMOL, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | | | - Isadora Nogueira
- Instituto de Ciências Biológicas-IB, PPG BIOMOL, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | | | | | - Fernando L Melo
- Instituto de Ciências Biológicas-IB, PPG BIOMOL, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | | | - Rafael Reis de Rezende
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Tulio Morgan
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil
| | - Arvind Varsani
- The Bio design Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa (UFV), Viçosa, MG, 36570-900, Brazil.
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Ahmed A, Khan HA, Jamal A, Virk N, Bhatti MF. Characterization of two novel fusariviruses co-infecting a single isolate of phytopathogenic fungus Botrytis cinerea. Virus Genes 2024; 60:402-411. [PMID: 38717669 DOI: 10.1007/s11262-024-02073-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/16/2024] [Indexed: 07/13/2024]
Abstract
A wide diversity of mycoviruses has been reported from Botrytis species, some with the potential to suppress the pathogenic abilities of this fungus. Considering their importance, this study was devised to find potential hypovirulence-associated mycoviruses found in Botrytis cinerea strains isolated from Pakistani strawberry fields. Here we report the complete genome characterization of two fusariviruses co-infecting a single isolate of phytopathogenic fungus B. cinerea (Kst14a). The viral genomes were sequenced by deep sequencing using total RNA fractions of the Kst14a isolate. The identified viruses were tentatively named Botrytis cinerea fusarivirus 9 (BcFV9) and Botrytis cinerea fusarivirus 3a (BcFV3a). Both viruses had a single-segmented (ssRNA) genome having a size of 6424 and 8370 nucleotides encoding two discontinuous open reading frames (ORFs). ORF-1 of both mycoviruses encodes for a polyprotein having a conserved domain of RNA-dependent RNA polymerase (RdRP) and a helicase domain (Hel) which function in RNA replication, while ORF2 encodes a hypothetical protein with an unknown function, respectively. Phylogenetic analysis indicated that BcFV9 made a clade with the genus Alphafusarivirus and BcFV3a fall in the genus Betafusarivirus in the family Fusariviridae. To our knowledge, this is the first report of two fusariviruses identified in isolates of B. cinerea from Pakistan. Both mycoviruses successfully transfected to a compatible strain of B. cinerea (Mst11). A comparison of virus-free (VF) and virus-infected (VI) isogenic lines showed the presence of these viruses was causing hypovirulence in infected strains. Virus-infected strains also had a small lesion size while testing the pathogenicity via apple assay.
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Affiliation(s)
- Aqeel Ahmed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Department of Biotechnology, University of Mianwali, Punjab, 42200, Pakistan
| | - Atif Jamal
- Crop Disease Research Institute (CDRI), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Nasar Virk
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- EBS Business School, EBS Universität für Wirtschaft und Recht, Rheingaustrasse 1, 65375, Oestrich-Winkel, Germany
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.
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Tian Z, Hu T, Holmes EC, Ji J, Shi W. Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system. Virus Evol 2024; 10:veae059. [PMID: 39119135 PMCID: PMC11306317 DOI: 10.1093/ve/veae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/21/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024] Open
Abstract
RNA viruses are characterized by a broad host range and high levels of genetic diversity. Despite a recent expansion in the known virosphere following metagenomic sequencing, our knowledge of the species rank genetic diversity of RNA viruses, and how often they are misassigned and misclassified, is limited. We performed a clustering analysis of 7801 RNA-directed RNA polymerase (RdRp) sequences representing 1897 established RNA virus species. From this, we identified substantial genetic divergence within some virus species and inconsistency in RNA virus assignment between the GenBank database and The International Committee on Taxonomy of Viruses (ICTV). In particular, 27.57% virus species comprised multiple virus operational taxonomic units (vOTUs), including Alphainfluenzavirus influenzae, Mammarenavirus lassaense, Apple stem pitting virus, and Rotavirus A, with each having over 100 vOTUs. In addition, the distribution of average amino acid identity between vOTUs within single assigned species showed a relatively low threshold: <90% and sometimes <50%. However, when only exemplar sequences from virus species were analyzed, 1889 of the ICTV-designated RNA virus species (99.58%) were clustered into a single vOTU. Clustering of the RdRp sequences from different virus species also revealed that 17 vOTUs contained two distinct virus species. These potential misassignments were confirmed by phylogenetic analysis. A further analysis of average nucleotide identity (ANI) values ranging from 70% to 97.5% revealed that at an ANI of 82.5%, 1559 (82.18%) of the 1897 virus species could be correctly clustered into one single vOTU. However, at ANI values >82.5%, an increasing number of species were clustered into two or more vOTUs. In sum, we have identified some inconsistency and misassignment of the RNA virus species based on the analysis of RdRp sequences alone, which has important implications for the development of an automated RNA virus classification system.
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Affiliation(s)
- Zhongshuai Tian
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 6699 Qingdao Road, Ji’nan 250117, China
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqingnanlu, Shanghai 200025, China
| | - Tao Hu
- Key Laboratory of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 6699 Qingdao Road, Ji’nan 250117, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia
- Laboratory of Data Discovery for Health Limited, 19 Science Park West Avenue, Hong Kong 999077, China
| | - Jingkai Ji
- School of Life Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, No. 619 Changcheng Road, Taian 271000, China
| | - Weifeng Shi
- Shanghai Institute of Virology, Shanghai Jiao Tong University School of Medicine, No. 227 Chongqingnanlu, Shanghai 200025, China
- Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijinerlu, Shanghai 200025, China
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Yu D, Wang Q, Song W, Kang Y, Lei Y, Wang Z, Chen Y, Huai D, Wang X, Liao B, Yan L. Characterization of Two Novel Single-Stranded RNA Viruses from Agroathelia rolfsii, the Causal Agent of Peanut Stem Rot. Viruses 2024; 16:854. [PMID: 38932147 PMCID: PMC11209298 DOI: 10.3390/v16060854] [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: 04/06/2024] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Peanut stem rot is a soil-borne disease caused by Agroathelia rolfsii. It occurs widely and seriously affects the peanut yield in most peanut-producing areas. The mycoviruses that induce the hypovirulence of some plant pathogenic fungi are potential resources for the biological control of fungal diseases in plants. Thus far, few mycoviruses have been found in A. rolfsii. In this study, two mitoviruses, namely, Agroathelia rolfsii mitovirus 1 (ArMV1) and Agroathelia rolfsii mitovirus 2 (ArMV2), were identified from the weakly virulent A. rolfsii strain GP3-1, and they were also found in other A. rolfsii isolates. High amounts of ArMV1 and ArMV2in the mycelium could reduce the virulence of A. rolfsii strains. This is the first report on the existence of mitoviruses in A. rolfsii. The results of this study may provide insights into the classification and evolution of mitoviruses in A. rolfsii and enable the exploration of the use of mycoviruses as biocontrol agents for the control of peanut stem rot.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Boshou Liao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural and Rural Affairs, Wuhan 430062, China; (D.Y.); (Q.W.); (W.S.); (Y.K.); (Y.L.); (Z.W.); (Y.C.); (D.H.); (X.W.)
| | - Liying Yan
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agricultural and Rural Affairs, Wuhan 430062, China; (D.Y.); (Q.W.); (W.S.); (Y.K.); (Y.L.); (Z.W.); (Y.C.); (D.H.); (X.W.)
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Hua H, Zhang X, Yao Y, Wu X. Complete genome sequence of a novel mitovirus identified in the phytopathogenic fungus Fusarium oxysporum f. sp. melonis strain T-SD3. Arch Virol 2024; 169:126. [PMID: 38753067 DOI: 10.1007/s00705-024-06042-2] [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: 02/18/2024] [Accepted: 04/22/2024] [Indexed: 06/13/2024]
Abstract
A novel mitovirus was identified in Fusarium oxysporum f. sp. melonis strain T-SD3 and designated as "Fusarium oxysporum mitovirus 3" (FoMV3). The virus was isolated from diseased muskmelon plants with the typical symptom of fusarium wilt. The complete genome of FoMV3 is 2269 nt in length with a predicted AU content of 61.40% and contains a single open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF was predicted to encode a polypeptide of 679 amino acids (aa) containing a conserved RNA-dependent RNA polymerase (RdRp) domain with a molecular mass of 77.39 kDa, which contains six conserved motifs with the highly conserved GDD tripeptide in motif IV. The 5'-untranslated region (UTR) and 3'-UTR of FoMV3 were predicted to fold into stem-loop structures. BLASTp analysis revealed that the RdRp of FoMV3 shared the highest aa sequence identity (83.85%) with that of Fusarium asiaticum mitovirus 5 (FaMV5, a member of the family Mitoviridae) infecting F. asiaticum, the causal agent of wheat fusarium head blight. Phylogenetic analysis further suggested that FoMV3 is a new member of the genus Unuamitovirus within the family Mitoviridae. This is the first report of a new mitovirus associated with F. oxysporum f. sp. melonis.
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Affiliation(s)
- Huihui Hua
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Xinyi Zhang
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Yilin Yao
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China.
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Grybchuk D, Galan A, Klocek D, Macedo DH, Wolf YI, Votýpka J, Butenko A, Lukeš J, Neri U, Záhonová K, Kostygov AY, Koonin EV, Yurchenko V. Identification of diverse RNA viruses in Obscuromonas flagellates (Euglenozoa: Trypanosomatidae: Blastocrithidiinae). Virus Evol 2024; 10:veae037. [PMID: 38774311 PMCID: PMC11108086 DOI: 10.1093/ve/veae037] [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: 10/26/2023] [Revised: 04/03/2024] [Accepted: 04/29/2024] [Indexed: 05/24/2024] Open
Abstract
Trypanosomatids (Euglenozoa) are a diverse group of unicellular flagellates predominately infecting insects (monoxenous species) or circulating between insects and vertebrates or plants (dixenous species). Monoxenous trypanosomatids harbor a wide range of RNA viruses belonging to the families Narnaviridae, Totiviridae, Qinviridae, Leishbuviridae, and a putative group of tombus-like viruses. Here, we focus on the subfamily Blastocrithidiinae, a previously unexplored divergent group of monoxenous trypanosomatids comprising two related genera: Obscuromonas and Blastocrithidia. Members of the genus Blastocrithidia employ a unique genetic code, in which all three stop codons are repurposed to encode amino acids, with TAA also used to terminate translation. Obscuromonas isolates studied here bear viruses of three families: Narnaviridae, Qinviridae, and Mitoviridae. The latter viral group is documented in trypanosomatid flagellates for the first time. While other known mitoviruses replicate in the mitochondria, those of trypanosomatids appear to reside in the cytoplasm. Although no RNA viruses were detected in Blastocrithidia spp., we identified an endogenous viral element in the genome of B. triatomae indicating its past encounter(s) with tombus-like viruses.
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Affiliation(s)
- Danyil Grybchuk
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czechia
| | - Arnau Galan
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Donnamae Klocek
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Diego H Macedo
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
| | - Yuri I Wolf
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda 20894, USA
| | - Jan Votýpka
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Department of Parasitology, Faculty of Science, Charles University, Prague 128 00, Czechia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czechia
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 39040, Israel
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec 252 50, Czechia
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Alexei Yu Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
- Zoological Institute of the Ruian Academy of Sciences, St. Petersburg 199034, Russia
| | - Eugene V Koonin
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda 20894, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czechia
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Shamsi W, Mittelstrass J, Ulrich S, Kondo H, Rigling D, Prospero S. Possible Biological Control of Ash Dieback Using the Mycoparasite Hymenoscyphus Fraxineus Mitovirus 2. PHYTOPATHOLOGY 2024; 114:1020-1027. [PMID: 38114080 DOI: 10.1094/phyto-09-23-0346-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Invasive fungal diseases represent a major threat to forest ecosystems worldwide. As the application of fungicides is often unfeasible and not a sustainable solution, only a few other control options are available, including biological control. In this context, the use of parasitic mycoviruses as biocontrol agents of fungal pathogens has recently gained particular attention. Since the 1990s, the Asian fungus Hymenoscyphus fraxineus has been causing lethal ash dieback across Europe. In the present study, we investigated the biocontrol potential of the mitovirus Hymenoscyphus fraxineus mitovirus 2 (HfMV2) previously identified in Japanese populations of the pathogen. HfMV2 could be successfully introduced via co-culturing into 16 of 105 HfMV2-free isolates. Infection with HfMV2 had contrasting effects on fungal growth in vitro, from cryptic to detrimental or beneficial. Virus-infected H. fraxineus isolates whose growth was reduced by HfMV2 showed overall a lower virulence on ash (Fraxinus excelsior) saplings as compared with their isogenic HfMV2-free lines. The results suggest that mycoviruses exist in the native populations of H. fraxineus in Asia that have the potential for biological control of ash dieback in Europe. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Wajeeha Shamsi
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Jana Mittelstrass
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Sven Ulrich
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Daniel Rigling
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Simone Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland
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Comont G, Faure C, Candresse T, Laurens M, Valière S, Lluch J, Lefebvre M, Gambier S, Jolivet J, Corio-Costet MF, Marais A. Characterization of the RNA Mycovirome Associated with Grapevine Fungal Pathogens: Analysis of Mycovirus Distribution and Their Genetic Variability within a Collection of Botryosphaeriaceae Isolates. Viruses 2024; 16:392. [PMID: 38543758 PMCID: PMC10975779 DOI: 10.3390/v16030392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 05/23/2024] Open
Abstract
Botryosphaeriaceae are fungi involved in the decay of various woody species, including the grapevine, leading to significant production losses. This fungal family is largely ubiquitous, and seven species of Botryosphaeriaceae have been identified in French vineyards, with variable levels of aggressiveness, both in vitro and in planta. Mycoviruses can impact the life traits of their fungal hosts, including aggressiveness, and are one of the factors influencing fungal pathogenicity. In this study, the RNA mycovirome of fifteen Botryosphaeriaceae isolates was characterized through the high-throughput sequencing of double-stranded RNA preparations from the respective samples. Eight mycoviruses were detected, including three potential novel species in the Narnaviridae family, as well as in the proposed Mycobunyaviridae and Fusagraviridae families. A large collection of Botryosphaeriaceae isolates was screened using RT-PCR assays specific for 20 Botryosphaeriaceae-infecting mycoviruses. Among the mycoviruses detected, some appeared to be specialists within a single host species, while others infected isolates belonging to multiple Botryosphaeriaceae species. This screening allowed us to conclude that one-third of the Botryosphaeriaceae isolates were infected by at least one mycovirus, and a significant proportion of isolates (43.5%) were found to be coinfected by several viruses, with very complex RNA mycoviromes for some N. parvum isolates.
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Affiliation(s)
- Gwenaëlle Comont
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Chantal Faure
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
| | - Thierry Candresse
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
| | - Marie Laurens
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Sophie Valière
- INRAE, US 1426, GeT-PlaGe, GenoToul, 31320 Castanet-Tolosan, France; (S.V.); (J.L.)
| | - Jérôme Lluch
- INRAE, US 1426, GeT-PlaGe, GenoToul, 31320 Castanet-Tolosan, France; (S.V.); (J.L.)
| | - Marie Lefebvre
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
| | - Sébastien Gambier
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Jérôme Jolivet
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Marie-France Corio-Costet
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Armelle Marais
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
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9
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Ma K, Cai L, Wang R, Wang J, Zhan H, Ni H, Lu B, Zhang Y, Gao J. Complete genome sequence of a novel mitovirus isolated from the fungus Fusarium oxysporum f. sp. ginseng causing ginseng root rot. Arch Virol 2024; 169:53. [PMID: 38381240 DOI: 10.1007/s00705-024-05962-3] [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: 10/24/2023] [Accepted: 12/18/2023] [Indexed: 02/22/2024]
Abstract
A novel mitovirus, tentatively designated as "Fusarium oxysporum mitovirus 2" (FoMV2), was isolated from the pathogenic Fusarium oxysporum f. sp. ginseng strain 0414 infecting Panax ginseng. The complete genome of FoMV2 is 2388 nt in length with a GC content of 30.57%. It contains a large open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) of 713 amino acids with a molecular weight of 83.05 kDa. The sequence identity between FoMV2 and Botrytis cinerea mitovirus 8 and Fusarium verticillioides mitovirus 1 was 87.94% and 77.85%, respectively. Phylogenetic analysis showed that FoMV2 belongs to the genus Unuamitovirus in the family Mitoviridae. To the best of our knowledge, this is the first report of an unuamitovirus isolated from F. oxysporum f. sp. ginseng causing ginseng root rot.
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Affiliation(s)
- Kaige Ma
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Liping Cai
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Ruojin Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Jun Wang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Haoxin Zhan
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Hechi Ni
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Baohui Lu
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, 130118, China
| | - Yanjing Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, 130118, China.
| | - Jie Gao
- College of Plant Protection, Jilin Agricultural University, Changchun, 130118, Jilin Province, China.
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Changchun, 130118, China.
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10
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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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11
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Contreras-Soto MB, Tovar-Pedraza JM. Viruses of plant-pathogenic fungi: a promising biocontrol strategy for Sclerotinia sclerotiorum. Arch Microbiol 2023; 206:38. [PMID: 38142438 DOI: 10.1007/s00203-023-03774-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/17/2023] [Accepted: 11/26/2023] [Indexed: 12/26/2023]
Abstract
Plant pathogenic fungi pose a significant and ongoing threat to agriculture and food security, causing economic losses and significantly reducing crop yields. Effectively managing these fungal diseases is crucial for sustaining agricultural productivity, and in this context, mycoviruses have emerged as a promising biocontrol option. These viruses alter the physiology of their fungal hosts and their interactions with the host plants. This review encompasses the extensive diversity of reported mycoviruses, including their taxonomic classification and range of fungal hosts. We highlight representative examples of mycoviruses that affect economically significant plant-pathogenic fungi and their distinctive characteristics, with a particular emphasis on mycoviruses impacting Sclerotinia sclerotiorum. These mycoviruses exhibit significant potential for biocontrol, supported by their specificity, efficacy, and environmental safety. This positions mycoviruses as valuable tools in crop protection against diseases caused by this pathogen, maintaining their study and application as promising research areas in agricultural biotechnology. The remarkable diversity of mycoviruses, coupled with their ability to infect a broad range of plant-pathogenic fungi, inspires optimism, and suggests that these viruses have the potential to serve as an effective management strategy against major fungi-causing plant diseases worldwide.
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Affiliation(s)
- María Belia Contreras-Soto
- Laboratorio de Fitopatología, Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, 80110, Culiacán, Sinaloa, Mexico
| | - Juan Manuel Tovar-Pedraza
- Laboratorio de Fitopatología, Centro de Investigación en Alimentación y Desarrollo, Coordinación Regional Culiacán, 80110, Culiacán, Sinaloa, Mexico.
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12
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Li W, Sun H, Cao S, Zhang A, Zhang H, Shu Y, Chen H. Extreme Diversity of Mycoviruses Present in Single Strains of Rhizoctonia cerealis, the Pathogen of Wheat Sharp Eyespot. Microbiol Spectr 2023; 11:e0052223. [PMID: 37436153 PMCID: PMC10433806 DOI: 10.1128/spectrum.00522-23] [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: 02/03/2023] [Accepted: 06/18/2023] [Indexed: 07/13/2023] Open
Abstract
Rhizoctonia cerealis is the pathogen of wheat sharp eyespot, which occurs throughout temperate wheat-growing regions of the world. In this project, the genomes of viruses from four strains of R. cerealis were analyzed based on Illumina high-throughput transcriptome sequencing (RNA-Seq) data. After filtering out reads that mapped to the fungal genome, viral genomes were assembled. In total, 131 virus-like sequences containing complete open reading frames (ORFs), belonging to 117 viruses, were obtained. Based on phylogenetic analysis, some of them were identified as novel members of the families Curvulaviridae, Endornaviridae, Hypoviridae, Mitoviridae, Mymonaviridae, and Phenuiviridae, while others were unclassified viruses. Most of these viruses from R. cerealis were significantly different from the viruses already reported. We propose the establishment of a new family, Rhizoctobunyaviridae, and two new genera, Rhizoctobunyavirus and Iotahypovirus. We further clarified the distribution and coinfection of these viruses in the four strains. Surprisingly, 39 viral genomes of up to 12 genera were found in strain R1084. Strain R0942, containing the fewest viruses, also contained 21 viral genomes belonging to 10 genera. Based on the RNA-Seq data, we estimated the accumulation level of some viruses in host cells and found that the mitoviruses in R. cerealis generally have very high accumulation. In conclusion, in the culturable phytopathogenic fungus R. cerealis, we discovered a considerable diversity of mycoviruses and a series of novel viruses. This study expands our understanding of the mycoviral diversity in R. cerealis and provides a rich resource for the further use of mycoviruses to control wheat sharp eyespot. IMPORTANCE Rhizoctonia cerealis is a binucleate fungus that is widely distributed worldwide and can cause sharp eyespot disease in cereal crops. In this study, 131 virus-like sequences belonging to 117 viruses were obtained based on analysis of high-throughput RNA-Seq data from four strains of R. cerealis. Many of these viruses were novel members of various virus families, while others were unclassified viruses. As a result, a new family named Rhizoctobunyaviridae and two new genera, Rhizoctobunyavirus and Iotahypovirus, were proposed. Moreover, the discovery of multiple viruses coinfecting a single host and the high accumulation levels of mitoviruses have shed light on the complex interactions between different viruses in a single host. In conclusion, a significant diversity of mycoviruses was discovered in the culturable phytopathogenic fungus R. cerealis. This study expands our understanding of mycoviral diversity, and provides a valuable resource for the further utilization of mycoviruses to control wheat diseases.
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Affiliation(s)
- Wei Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
| | - Haiyan Sun
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Shulin Cao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Aixiang Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Haotian Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Yan Shu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Huaigu Chen
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, Jiangsu, China
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13
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Khan HA, Nerva L, Bhatti MF. The good, the bad and the cryptic: The multifaceted roles of mycoviruses and their potential applications for a sustainable agriculture. Virology 2023; 585:259-269. [PMID: 37453341 DOI: 10.1016/j.virol.2023.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Mycoviruses are natural inhabitants of fungi and have been identified in almost all fungal taxonomic groups. Mycoviruses that infect phytopathogenic fungi are now becoming a hot research area due to their potential for the biocontrol of important plant pathogens. But, before considering a mycovirus for biocontrol, we should be fully aware of the effects it induces in a fungal host and its interactions with other viruses, fungal strains and even the host plants. Mycoviral infections are generally associated with different effects, ranging from hypovirulence to hypervirulence, but they can often be cryptic (latent infections). The cryptic lifestyle has been associated to many mycoviruses, but thanks to growing knowledge we are now aware that it is often associated to axenic conditions while the real effects can be observed only in nature. Other mycoviruses either promote (hypervirulence) or (hypovirulence) fungal pathogenicity by a strong impact on the fungal physiology or by blocking the production of toxins or effectors. Finally, indirect effects of mycoviral infections can also be provided to the plant that hosts the fungal isolate, highlighting not only their potential as direct biocontrol agents but also as priming agents for plant resilience to biotic and abiotic stresses. This review provides a broad overview of mycoviral interactions both with their hosts and with other mycoviruses, highlighting the most interesting examples. In contrast to what has been observed to date, we believe that the collective availability of these data will not only improve our understanding of mycoviruses, but also increase our confidence in considering them as alternative measures against fungal diseases to improve the sustainable production of food and feed commodities.
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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; Department of Biotechnology, University of Mianwali, Punjab, 42200, Pakistan
| | - Luca Nerva
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile, 31015, Conegliano, (TV), Italy.
| | - 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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14
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Zhang Y, Guo H, Zhou S, Chen D, Xu G, Kang Z, Zheng L. A Novel Mitovirus PsMV2 Facilitates the Virulence of Wheat Stripe Rust Fungus. Viruses 2023; 15:1265. [PMID: 37376565 DOI: 10.3390/v15061265] [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: 04/02/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Wheat stripe rust, caused by the obligate biotrophic fungus Puccinia striiformis f. sp. tritici (Pst), seriously affects wheat production. Here, we report the complete genome sequence and biological characterization of a new mitovirus from P. striiformis strain GS-1, which was designated as "Puccinia striiformis mitovirus 2" (PsMV2). Genome sequence analysis showed that PsMV2 is 2658 nt in length with an AU-rich of 52.3% and comprises a single ORF of 2348 nt encoding an RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that PsMV2 is a new member of the genus Unuamitovirus within the family Mitoviridae. In addition, PsMV2 multiplied highly during Pst infection and it suppresses programmed cell death (PCD) triggered by Bax. Silencing of PsMV2 in Pst by barley stripe mosaic virus (BSMV)-mediated Host Induced Gene Silencing (HIGS) reduced fungal growth and decreased pathogenicity of Pst. These results indicate PsMV2 promotes host pathogenicity in Pst. Interestingly, PsMV2 was detected among a wide range of field isolates of Pst and may have coevolved with Pst in earlier times. Taken together, our results characterized a novel mitovirus PsMV2 in wheat stripe rust fungus, which promotes the virulence of its fungal host and wide distribution in Pst which may offer new strategies for disease control.
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Affiliation(s)
- Yanhui Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Hualong Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Siyu Zhou
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
| | - Daipeng Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
| | - Gang Xu
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Li Zheng
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
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15
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Hough B, Steenkamp E, Wingfield B, Read D. Fungal Viruses Unveiled: A Comprehensive Review of Mycoviruses. Viruses 2023; 15:1202. [PMID: 37243288 PMCID: PMC10224137 DOI: 10.3390/v15051202] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/07/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Mycoviruses (viruses of fungi) are ubiquitous throughout the fungal kingdom and are currently classified into 23 viral families and the genus botybirnavirus by the International Committee on the Taxonomy of Viruses (ICTV). The primary focus of mycoviral research has been on mycoviruses that infect plant pathogenic fungi, due to the ability of some to reduce the virulence of their host and thus act as potential biocontrol against these fungi. However, mycoviruses lack extracellular transmission mechanisms and rely on intercellular transmission through the hyphal anastomosis, which impedes successful transmission between different fungal strains. This review provides a comprehensive overview of mycoviruses, including their origins, host range, taxonomic classification into families, effects on their fungal counterparts, and the techniques employed in their discovery. The application of mycoviruses as biocontrol agents of plant pathogenic fungi is also discussed.
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Affiliation(s)
| | | | - Brenda Wingfield
- Forestry & Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics & Microbiology, University of Pretoria, Pretoria 0002, South Africa; (B.H.); (E.S.); (D.R.)
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16
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Ye Y, Liu Y, Zhang Y, Wang X, Li H, Li P. Metatranscriptome-based strategy reveals the existence of novel mycoviruses in the plant pathogenic fungus Fusarium oxysporum f. sp. cubense. Front Microbiol 2023; 14:1193714. [PMID: 37275129 PMCID: PMC10234264 DOI: 10.3389/fmicb.2023.1193714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/28/2023] [Indexed: 06/07/2023] Open
Abstract
Fusarium oxysporum f. sp. cubense (Foc) is a devastating plant pathogen that caused a great financial loss in the banana's source area. Metatranscriptomic analysis was used to determine the diversity of mycoviruses in 246 isolates of F. oxysporum f. sp. cubense. Partial or nearly complete genomes of 20 mycoviruses were obtained by BLASTp analysis of RNA sequences using the NCBI database. These 20 viruses were grouped into five distinct lineages, namely Botourmiaviridae, Endornaviridae, Mitoviridae, Mymonaviridae, Partitiviridae, and two non-classified mycoviruses lineages. To date, there is no report of the presence of mycoviruses in this pathogen. In this study, we demonstrate the presence of mycoviruses isolated from Foc. These findings enhance our overall knowledge of viral diversity and taxonomy in Foc. Further characterization of these mycoviruses is warranted, especially in terms of exploring these novel mycoviruses for innovative biocontrol of banana Fusarium wilt disease.
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17
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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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18
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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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Viral cross-class transmission results in disease of a phytopathogenic fungus. THE ISME JOURNAL 2022; 16:2763-2774. [PMID: 36045287 PMCID: PMC9428384 DOI: 10.1038/s41396-022-01310-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 12/15/2022]
Abstract
Interspecies transmission of viruses is a well-known phenomenon in animals and plants whether via contacts or vectors. In fungi, interspecies transmission between distantly related fungi is often suspected but rarely experimentally documented and may have practical implications. A newly described double-strand RNA (dsRNA) virus found asymptomatic in the phytopathogenic fungus Leptosphaeria biglobosa of cruciferous crops was successfully transmitted to an evolutionarily distant, broad-host range pathogen Botrytis cinerea. Leptosphaeria biglobosa botybirnavirus 1 (LbBV1) was characterized in L. biglobosa strain GZJS-19. Its infection in L. biglobosa was asymptomatic, as no significant differences in radial mycelial growth and pathogenicity were observed between LbBV1-infected and LbBV1-free strains. However, cross-species transmission of LbBV1 from L. biglobosa to infection in B. cinerea resulted in the hypovirulence of the recipient B. cinerea strain t-459-V. The cross-species transmission was succeeded only by inoculation of mixed spores of L. biglobosa and B. cinerea on PDA or on stems of oilseed rape with the efficiency of 4.6% and 18.8%, respectively. To investigate viral cross-species transmission between L. biglobosa and B. cinerea in nature, RNA sequencing was carried out on L. biglobosa and B. cinerea isolates obtained from Brassica samples co-infected by these two pathogens and showed that at least two mycoviruses were detected in both fungal groups. These results indicate that cross-species transmission of mycoviruses may occur frequently in nature and result in the phenotypical changes of newly invaded phytopathogenic fungi. This study also provides new insights for using asymptomatic mycoviruses as biocontrol agent.
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20
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Shamsi W, Kondo H, Ulrich S, Rigling D, Prospero S. Novel RNA viruses from the native range of Hymenoscyphus fraxineus, the causal fungal agent of ash dieback. Virus Res 2022; 320:198901. [PMID: 36058013 DOI: 10.1016/j.virusres.2022.198901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022]
Abstract
The native Japanese population of the fungus Hymenoscyphus fraxineus, the causal agent of ash dieback in Europe, was screened for viruses using a high-throughput sequencing method. Five RNA viruses were detected in 116 fungal isolates sequenced via Illumina RNA-seq platform, with an overall virus prevalence of 11.2%. The viruses were completely sequenced by RNA ligase mediated rapid amplification of cDNA ends (RLM-RACE) followed by Sanger sequencing. The sequences appear to represent new species from three established families (Mito-, Endorna- and Partitiviridae), one recognized genus (Botybirnavirus) and a negative-sense single-stranded RNA virus in the order Bunyavirales from the proposed family "Mybuviridae". The highest prevalence was found for the mitovirus (7.8%), that had two genomic forms (linear and circular), while the other viruses were detected each in one isolate. Co-infection of a mitovirus and an endornavirus was also observed in one of the infected isolates. Here we describe the molecular characterization of the identified viruses. This study expands the diversity of viruses in H. fraxineus and provides the basis for investigating the virus-mediated control of ash dieback in Europe.
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Affiliation(s)
- Wajeeha Shamsi
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland.
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan
| | - Sven Ulrich
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
| | - Daniel Rigling
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
| | - Simone Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zuercherstrasse 111, Birmensdorf 8903, Switzerland
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Bocos-Asenjo IT, Niño-Sánchez J, Ginésy M, Diez JJ. New Insights on the Integrated Management of Plant Diseases by RNA Strategies: Mycoviruses and RNA Interference. Int J Mol Sci 2022; 23:9236. [PMID: 36012499 PMCID: PMC9409477 DOI: 10.3390/ijms23169236] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
RNA-based strategies for plant disease management offer an attractive alternative to agrochemicals that negatively impact human and ecosystem health and lead to pathogen resistance. There has been recent interest in using mycoviruses for fungal disease control after it was discovered that some cause hypovirulence in fungal pathogens, which refers to a decline in the ability of a pathogen to cause disease. Cryphonectria parasitica, the causal agent of chestnut blight, has set an ideal model of management through the release of hypovirulent strains. However, mycovirus-based management of plant diseases is still restricted by limited approaches to search for viruses causing hypovirulence and the lack of protocols allowing effective and systemic virus infection in pathogens. RNA interference (RNAi), the eukaryotic cell system that recognizes RNA sequences and specifically degrades them, represents a promising. RNA-based disease management method. The natural occurrence of cross-kingdom RNAi provides a basis for host-induced gene silencing, while the ability of most pathogens to uptake exogenous small RNAs enables the use of spray-induced gene silencing techniques. This review describes the mechanisms behind and the potential of two RNA-based strategies, mycoviruses and RNAi, for plant disease management. Successful applications are discussed, as well as the research gaps and limitations that remain to be addressed.
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Affiliation(s)
- Irene Teresa Bocos-Asenjo
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
| | - Jonatan Niño-Sánchez
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
| | - Mireille Ginésy
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
| | - Julio Javier Diez
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
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Vieira AC, Lopes ÍS, Fonseca PLC, Olmo RP, Bittencourt F, de Vasconcelos LM, Pirovani CP, Gaiotto FA, Aguiar ERGR. Expanding the environmental virome: Infection profile in a native rainforest tree species. Front Microbiol 2022; 13:874319. [PMID: 35992690 PMCID: PMC9387356 DOI: 10.3389/fmicb.2022.874319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 06/29/2022] [Indexed: 11/21/2022] Open
Abstract
Agroforestry systems (AFS) for cocoa production combine traditional land-use practices with local biodiversity conservation, resulting in both ecological and agricultural benefits. The cacao-cabruca AFS model is widely implemented in regions of the Brazilian Atlantic Forest. Carpotroche brasiliensis (Raddi) A. Gray (Achariaceae) is a tree found in cabruca landscapes that is often used for reforestation and biotechnological applications. Despite its importance, we still lack information about viruses circulating in C. brasiliensis, particularly considering the possibility of spillover that could affect cocoa production. In our study, we analyzed the Carpotroche brasiliensis virome from Atlantic Forest and cacao-cabruca AFS regions using metatranscriptomics from several vegetative and reproductive organs. Our results revealed a diverse virome detecting near-complete or partial coding sequences of single- and double-stranded DNA and RNA viruses classified into at least six families (Botourmiaviridae, Bromoviridae, Caulimoviridae, Genomoviridae, Mitoviridae, and Rhabdoviridae) plus unclassified elements. We described with high confidence the near-complete and the partial genomes of two tentative novel viruses: Carpotroche-associated ilarvirus and Carpotroche-associated genomovirus, respectively. Interestingly, we also described sequences likely derived from a rhabdovirus, which could represent a novel member of the genus Gammanucleorhabdovirus. We observed higher viral diversity in cacao-cabruca AFS and reproductive organs of C. brasiliensis with preferential tropism to fruits, which could directly affect production. Altogether, our results provide data to better understand the virome in this unexplored agroecological interface, such as cacao-cabruca AFS and forest ecosystem, providing information on the aspects of virus–plant interactions.
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Affiliation(s)
- Anderson Carvalho Vieira
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Ícaro Santos Lopes
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Paula Luize Camargos Fonseca
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
- Department of Genetics, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Flora Bittencourt
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | | | - Carlos Priminho Pirovani
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Fernanda Amato Gaiotto
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
- *Correspondence: Fernanda Amato Gaiotto,
| | - Eric Roberto Guimarães Rocha Aguiar
- Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
- Eric Roberto Guimarães Rocha Aguiar,
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Wang R, Liu C, Jiang X, Tan Z, Li H, Xu S, Zhang S, Shang Q, Deising HB, Behrens SE, Wu B. The Newly Identified Trichoderma harzianum Partitivirus (ThPV2) Does Not Diminish Spore Production and Biocontrol Activity of Its Host. Viruses 2022; 14:1532. [PMID: 35891512 PMCID: PMC9317543 DOI: 10.3390/v14071532] [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: 05/17/2022] [Revised: 06/27/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
A new partititvirus isolated from a Trichoderma harzianum strain (T673), collected in China, was characterized and annotated as Trichoderma harzianum partitivirus 2 (ThPV2). The genome of ThPV2 consists of a 1693 bp dsRNA1 encoding a putative RNA-dependent RNA polymerase (RdRp) and a 1458 bp dsRNA2 encoding a hypothetical protein. In comparative studies employing the ThPV2-infected strain (T673) and a strain cured by ribavirin treatment (virus-free strain T673-F), we investigated biological effects of ThPV2 infection. While the growth rate of the virus-infected fungus differed little from that of the cured variant, higher mycelial density, conidiospore, and chlamydospore production were observed in the virus-infected strain T673. Furthermore, both the ThPV2-infected and the cured strain showed growth- and development-promoting activities in cucumber plants. In vitro confrontation tests showed that strains T673 and T673-F inhibited several important fungal pathogens and an oomycete pathogen in a comparable manner. Interestingly, in experiments with cucumber seeds inoculated with Fusarium oxysporum f. sp. cucumerinum, the ThPV2-infected strain T673 showed moderately but statistically significantly improved biocontrol activity when compared with strain T673-F. Our data broaden the spectrum of known mycoviruses and provide relevant information for the development of mycoviruses for agronomic applications.
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Affiliation(s)
- Rongqun Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Rd., Haidian District, Beijing 100193, China; (R.W.); (C.L.); (X.J.); (Z.T.); (H.L.); (S.X.); (S.Z.)
| | - Chenchen Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Rd., Haidian District, Beijing 100193, China; (R.W.); (C.L.); (X.J.); (Z.T.); (H.L.); (S.X.); (S.Z.)
| | - Xiliang Jiang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Rd., Haidian District, Beijing 100193, China; (R.W.); (C.L.); (X.J.); (Z.T.); (H.L.); (S.X.); (S.Z.)
| | - Zhaoyan Tan
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Rd., Haidian District, Beijing 100193, China; (R.W.); (C.L.); (X.J.); (Z.T.); (H.L.); (S.X.); (S.Z.)
| | - Hongrui Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Rd., Haidian District, Beijing 100193, China; (R.W.); (C.L.); (X.J.); (Z.T.); (H.L.); (S.X.); (S.Z.)
- College of Horticulture and Landscapes, Tianjin Agricultural University, Tianjin 300392, China
| | - Shujin Xu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Rd., Haidian District, Beijing 100193, China; (R.W.); (C.L.); (X.J.); (Z.T.); (H.L.); (S.X.); (S.Z.)
- College of Horticulture and Landscapes, Tianjin Agricultural University, Tianjin 300392, China
| | - Shuaihu Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Rd., Haidian District, Beijing 100193, China; (R.W.); (C.L.); (X.J.); (Z.T.); (H.L.); (S.X.); (S.Z.)
| | - Qiaoxia Shang
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing 102206, China;
| | - Holger B. Deising
- Institute for Agricultural and Nutritional Sciences, Section Phytopathology and Plant Protection, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany;
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany;
| | - Beilei Wu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Rd., Haidian District, Beijing 100193, China; (R.W.); (C.L.); (X.J.); (Z.T.); (H.L.); (S.X.); (S.Z.)
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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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Li Y, Li S, Liang Z, Cai Q, Zhou T, Zhao C, Wu X. RNA-seq Analysis of Rhizoctonia solani AG-4HGI Strain BJ-1H Infected by a New Viral Strain of Rhizoctonia solani Partitivirus 2 Reveals a Potential Mechanism for Hypovirulence. PHYTOPATHOLOGY 2022; 112:1373-1385. [PMID: 34965159 DOI: 10.1094/phyto-08-21-0349-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rhizoctonia solani partitivirus 2 (RsPV2), in the genus Alphapartitivirus, confers hypovirulence on R. solani AG-1-IA, the causal agent of rice sheath blight. In this study, a new strain of RsPV2 obtained from R. solani AG-4HGI strain BJ-1H, the causal agent of black scurf on potato, wasidentified and designated as Rhizoctonia solani partitivirus 2 strain BJ-1H (RsPV2-BJ). An RNA sequencing analysis of strain BJ-1H and the virus RsPV2-BJ-free strain BJ-1H-VF derived from strain BJ-1H was conducted to investigate the potential molecular mechanism of hypovirulence induced by RsPV2-BJ. In total, 14,319 unigenes were obtained, and 1,341 unigenes were identified as differentially expressed genes (DEGs), with 570 DEGs being down-regulated and 771 being up-regulated. Notably, several up-regulated DEGs were annotated to cell wall degrading enzymes, including β-1,3-glucanases. Strain BJ-1H exhibited increased expression of β-1,3-glucanase after RsPV2-BJ infection, suggesting that cell wall autolysis activity in R. solani AG-4HGI strain BJ-1H might be promoted by RsPV2-BJ, inducing hypovirulence in its host fungus R. solani AG-4HGI. To the best of our knowledge, this is the first report on the potential mechanism of hypovirulence induced by a mycovirus in R. solani.
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Affiliation(s)
- Yuting Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Siwei Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Zhijian Liang
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Qingnian Cai
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Tao Zhou
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Can Zhao
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
- College of Horticulture, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, People's Republic of China
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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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Córdoba L, Ruiz-Padilla A, Rodríguez-Romero J, Ayllón MA. Construction and Characterization of a Botrytis Virus F Infectious Clone. J Fungi (Basel) 2022; 8:jof8050459. [PMID: 35628716 PMCID: PMC9146958 DOI: 10.3390/jof8050459] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/15/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022] Open
Abstract
Botrytis virus F (BVF) is a positive-sense, single-stranded RNA (+ssRNA) virus within the Gammaflexiviridae family of the plant-pathogenic fungus Botrytis cinerea. In this study, the complete sequence of a BVF strain isolated from B. cinerea collected from grapevine fields in Spain was analyzed. This virus, in this work BVF-V448, has a genome of 6827 nt in length, excluding the poly(A) tail, with two open reading frames encoding an RNA dependent RNA polymerase (RdRP) and a coat protein (CP). The 5′- and 3′-terminal regions of the genome were determined by rapid amplification of cDNA ends (RACE). Furthermore, a yet undetected subgenomic RNA species in BVF-V448 was identified, indicating that the CP is expressed via 3′ coterminal subgenomic RNAs (sgRNAs). We also report the successful construction of the first BVF full-length cDNA clone and synthesized in vitro RNA transcripts using the T7 polymerase, which could efficiently transfect two different strains of B. cinerea, B05.10 and Pi258.9. The levels of growth in culture and virulence on plants of BVF-V448 transfected strains were comparable to BVF-free strains. The infectious clones generated in this work provide a useful tool for the future development of an efficient BVF foreign gene expression vector and a virus-induced gene silencing (VIGS) vector as a biological agent for the control of B. cinerea.
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Affiliation(s)
- Laura Córdoba
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (L.C.); (A.R.-P.); (J.R.-R.)
| | - Ana Ruiz-Padilla
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (L.C.); (A.R.-P.); (J.R.-R.)
| | - Julio Rodríguez-Romero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (L.C.); (A.R.-P.); (J.R.-R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - María A. Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (L.C.); (A.R.-P.); (J.R.-R.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
- Correspondence:
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Kashif M, Jurvansuu J, Hyder R, Vainio EJ, Hantula J. Phenotypic Recovery of a Heterobasidion Isolate Infected by a Debilitation-Associated Virus Is Related to Altered Host Gene Expression and Reduced Virus Titer. Front Microbiol 2022; 12:661554. [PMID: 35310390 PMCID: PMC8930199 DOI: 10.3389/fmicb.2021.661554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
The fungal genus Heterobasidion includes forest pathogenic species hosting a diverse group of partitiviruses. They include the host debilitating Heterobasidion partitivirus 13 strain an1 (HetPV13-an1), which was originally observed in a slowly growing H. annosum strain 94233. In this study, a relatively fast-growing sector strain 94233-RC3 was isolated from a highly debilitated mycelial culture of 94233, and its gene expression and virus transcript quantities as well as the genomic sequence of HetPV13-an1 were examined. The sequence of HetPV13-an1 genome in 94233-RC3 was identical to that in the original 94233, and thus not the reason for the partial phenotypic recovery. According to RNA-seq analysis, the HetPV13-an1 infected 94233-RC3 transcribed eight genes differently from the partitivirus-free 94233-32D. Three of these genes were downregulated and five upregulated. The number of differentially expressed genes was considerably lower and the changes in their expression were small compared to those of the highly debilitated original strain 94233 with the exception of the most highly upregulated ones, and therefore viral effects on the host transcriptome correlated with the degree of the virus-caused debilitation. The amounts of RdRp and CP transcripts of HetPV13-an1 were considerably lower in 94233-RC3 and also in 94233 strain infected by a closely related mildly debilitating virus HetPV13-an2, suggesting that the virus titer would have a role in determining the effect of HetPV13 viruses on their hosts.
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Affiliation(s)
| | | | - Rafiqul Hyder
- Natural Resources Institute Finland, Helsinki, Finland
| | - Eeva J Vainio
- Natural Resources Institute Finland, Helsinki, Finland
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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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Molecular characterization of a novel fusagravirus in the phytopathogenic fungus Streptobotrys caulophylli. Arch Virol 2022; 167:619-623. [DOI: 10.1007/s00705-021-05328-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/27/2021] [Indexed: 11/02/2022]
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31
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Fournier P, Pellan L, Barroso-Bergadà D, Bohan DA, Candresse T, Delmotte F, Dufour MC, Lauvergeat V, Le Marrec C, Marais A, Martins G, Masneuf-Pomarède I, Rey P, Sherman D, This P, Frioux C, Labarthe S, Vacher C. The functional microbiome of grapevine throughout plant evolutionary history and lifetime. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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32
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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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Kamaruzzaman M, Islam MS, Hasan MA, Sultana R, Faruque MO, Jiang C. Characterization of a hypovirulent strain of Botrytis cinerea from apple and quantification of the ICs related gene expression. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01737-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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34
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Casas LL, Azevedo JL, Almeida LN, Costa-Neto PQ, Bianco RA, Pereira JO. Mycoviruses infecting Colletotrichum spp.: A comprehensive review. BRAZ J BIOL 2021; 83:e248975. [PMID: 34550289 DOI: 10.1590/1519-6984.248975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/07/2021] [Indexed: 06/01/2024] Open
Abstract
Colletotrichum is one of the most economically important fungal genera, which affects a wide range of hosts, specifically tropical and subtropical crops. Thus far, there have been several records of mycovirus infection in Colletotrichum spp., primarily by viruses of the Partitiviridae family. There have also been records of infections by mycoviruses of the Chrysoviridae family. Mycoviruses are (+)ssRNA and dsRNA genome viruses, which may or may not be enveloped. To date, no mycovirus with a DNA genome has been isolated from Colletotrichum spp. Typically, mycoviruses cause latent infections, although hypo- and hypervirulence have also been reported in Colletotrichum spp. In addition to its effects on pathogenic behavior, mycovirus infection can lead to important physiological changes, such as altered morphological characteristics, reduced vegetative growth, and suppressed conidia production. Therefore, research on mycoviruses infecting phytopathogenic fungi can help develop alternative methods to chemical control, which can cause irreversible damage to humans and the environment. From an agricultural perspective, mycoviruses can contribute to sustainable agriculture as biological control agents via changes in fungal physiology, ultimately resulting in the total loss of or reduction in the virulence of these pathogens.
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Affiliation(s)
- L L Casas
- Universidade do Estado do Amazonas - UEA, Programa de Pós-graduação em Biodiversidade e Biotecnologia - Bionorte, Manaus, AM, Brasil
| | - J L Azevedo
- Universidade de São Paulo - USP, Escola Superior de Agricultura Luiz de Queiroz, Piracicaba, SP, Brasil
| | - L N Almeida
- Universidade Federal do Amazonas - UFAM, Faculdade de Ciências Agrárias, Manaus, AM, Brasil
| | - P Q Costa-Neto
- Universidade Federal do Amazonas - UFAM, Faculdade de Ciências Agrárias, Manaus, AM, Brasil
| | - R A Bianco
- Centro Universitário do Norte - Uninorte, Manaus, AM, Brasil
| | - J O Pereira
- Universidade Federal do Amazonas - UFAM, Faculdade de Ciências Agrárias, Manaus, AM, Brasil
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35
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Wang J, Li C, Qiu R, Li X, Zhao J, Bai J, Chen Y, Li S. Complete genome sequence of a novel mitovirus from the phytopathogenic fungus Fusarium oxysporum. Arch Virol 2021; 166:3211-3216. [PMID: 34495411 DOI: 10.1007/s00705-021-05210-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/02/2021] [Indexed: 11/26/2022]
Abstract
Fusarium oxysporum is a cosmopolitan plant pathogen that causes fusarium wilt and fusarium root rot in many economically important crops. There is still limited information about mycoviruses that infect F. oxysporum. Here, a novel mitovirus tentatively named "Fusarium oxysporum mitovirus 1" (FoMV1) was identified in F. oxysporum strain B2-10. The genome of FoMV1 is 2,453 nt in length with a predicted AU content of 71.6% and contains one large open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF putatively encodes an RNA-dependent RNA polymerase (RdRp) of 723 aa with a molecular mass of 84.98 kDa. The RdRp domain of FoMV1 shares 29.01% to 68.43% sequence identity with the members of the family Mitoviridae. Phylogenetic analysis further suggested that FoMV1 is a new member of a distinct species in the genus Mitovirus.
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Affiliation(s)
- Jing Wang
- Key Laboratory for Green Preservation and Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Institute of Tobacco, Henan Academy of Agricultural Sciences, No. 116, Garden road, Jingshui District, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Chengjun Li
- Key Laboratory for Green Preservation and Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Institute of Tobacco, Henan Academy of Agricultural Sciences, No. 116, Garden road, Jingshui District, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Rui Qiu
- Key Laboratory for Green Preservation and Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Institute of Tobacco, Henan Academy of Agricultural Sciences, No. 116, Garden road, Jingshui District, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Xiaojie Li
- Key Laboratory for Green Preservation and Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Institute of Tobacco, Henan Academy of Agricultural Sciences, No. 116, Garden road, Jingshui District, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Jun Zhao
- Key Laboratory for Green Preservation and Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Institute of Tobacco, Henan Academy of Agricultural Sciences, No. 116, Garden road, Jingshui District, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Jingke Bai
- Key Laboratory for Green Preservation and Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Institute of Tobacco, Henan Academy of Agricultural Sciences, No. 116, Garden road, Jingshui District, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Yuguo Chen
- Key Laboratory for Green Preservation and Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Institute of Tobacco, Henan Academy of Agricultural Sciences, No. 116, Garden road, Jingshui District, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Shujun Li
- Key Laboratory for Green Preservation and Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Institute of Tobacco, Henan Academy of Agricultural Sciences, No. 116, Garden road, Jingshui District, Zhengzhou, 450002, Henan Province, People's Republic of China.
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Yang R, Li N, Zhou Z, Li G. Characterization of the Populations of Botrytis cinerea Infecting Plastic Tunnel-Grown Strawberry and Tomato in the Hubei Province of China. PLANT DISEASE 2021; 105:1890-1897. [PMID: 33054622 DOI: 10.1094/pdis-01-20-0164-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A total of 707 isolates of Botrytis were collected from plastic tunnel-grown strawberry and tomato in the Hubei province of China. They were identified based on the specific molecular markers. Diversity of the B. cinerea (Bc) isolates was evaluated by typing the transposable elements (Boty, Flipper) and the mating types (MAT1-1, MAT1-2), as well as by determining virulence on tobacco (Nicotiana benthamiana) and fenhexamid sensitivity in agar medium. The results showed that 706 isolates (99.9%) were Bc and 1 isolate (0.1%) was B. pseudocinerea. The Bc isolates (n = 706) were classified into four transposable element types, Vacuma (3.1%), Boty (9.6%), Flipper (18.4%), and Transposa (68.8%). The strawberry and tomato subpopulations of Bc had significantly different (P < 0.05) compositions of the four transposable element types. The overall ratio of MAT1-1 to MAT1-2 deviated from 1:1 (n = 706; P = 0.0002), and MAT1-2 (56.9%) predominated over MAT1-1 (43.1%). In 7 of 12 geographic subpopulations, the ratio of MAT1-1 to MAT1-2 matched 1:1; however, in the remaining five geographic subpopulations, the ratio of MAT1-1 to MAT1-2 did not match 1:1. Results of the biological characterizations showed that most Bc isolates were highly sensitive or sensitive to fenhexamid, and the majority of Bc isolates were highly virulent or virulent on tobacco. Moreover, the relationship between genetic diversity and biological characteristics was analyzed. The results achieved during this study are helpful for understanding of the populations of B. cinerea.
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Affiliation(s)
- Rui Yang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
- College of Resources and Environmental Science, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Na Li
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziliang Zhou
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
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Abstract
Botrytis cinerea is one of the most important plant-pathogenic fungus. Products based on microorganisms can be used in biocontrol strategies alternative to chemical control, and mycoviruses have been explored as putative biological agents in such approaches. Here, we have explored the mycovirome of B. cinerea isolates from grapevine of Italy and Spain to increase the knowledge about mycoviral diversity and evolution, and to search for new widely distributed mycoviruses that could be active ingredients in biological products to control this hazardous fungus. A total of 248 B. cinerea field isolates were used for our metatranscriptomic study. Ninety-two mycoviruses were identified: 62 new mycoviral species constituting putative novel viral genera and families. Of these mycoviruses, 57 had a positive-sense single-stranded RNA (ssRNA) genome, 19 contained a double-stranded RNA (dsRNA) genome, 15 had a negative-sense ssRNA genome, and 1 contained a single-stranded DNA (ssDNA) genome. In general, ssRNA mycoviruses were widely distributed in all sampled regions, the ssDNA mycovirus was more frequently found in Spain, and dsRNA mycoviruses were scattered in some pools of both countries. Some of the identified mycoviruses belong to clades that have never been found associated with Botrytis species: Botrytis-infecting narnaviruses; alpha-like, umbra-like, and tymo-like ssRNA+ mycoviruses; trisegmented ssRNA- mycovirus; bisegmented and tetrasegmented dsRNA mycoviruses; and finally, an ssDNA mycovirus. Among the results obtained in this massive mycovirus screening, the discovery of novel bisegmented viruses, phylogenetically related to narnaviruses, is remarkable.IMPORTANCE The results obtained here have expanded our knowledge of mycoviral diversity, horizontal transfers, and putative cross-kingdom events. To date, this study presents the most extensive and wide diversity collection of mycoviruses infecting the necrotrophic fungus B. cinerea The collection included all types of mycoviruses, with dsRNA, ssRNA+, ssRNA-, and ssDNA genomes, most of which were discovered here, and some of which were previously reported as infecting B. cinerea or other plant-pathogenic fungi. Some of these mycoviruses are reported for the first time here associated with B. cinerea, as a trisegmented ssRNA- mycovirus and as an ssDNA mycovirus, but even more remarkablly, we also describe here four novel bisegmented viruses (binarnaviruses) not previously described in nature. The present findings significantly contribute to general knowledge in virology and more particularly in the field of mycovirology.
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Wang H, Liu H, Zhou Q. The complete genome sequence of a new mitovirus from the phytopathogenic fungus Colletotrichum higginsianum. Arch Virol 2021; 166:1481-1484. [PMID: 33616726 DOI: 10.1007/s00705-021-04996-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/27/2020] [Indexed: 02/07/2023]
Abstract
In this study, a novel mitovirus designed "Colletotrichum higginsianum mitovirus 1" (ChMV1) was isolated from the phytopathogenic fungus Colletotrichum higginsianum. The genome of this mitovirus is 2,893 nt in length with an A + U content of 61% and contains a large open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRp). A BLASTp analysis revealed that the RdRp domain of ChMV1 had 30.25% to 61.72% sequence identity to those of members of the genus Mitovirus and showed the highest degree of similarity (61.72% identity) to Botrytis cinerea mitovirus 3 (BcMV3). Phylogenetic analysis further indicated that ChMV1 is a member in the genus Mitovirus of the family Mitoviridae. To the best of our knowledge, this is the first report of a mitovirus in C. higginsianum.
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Affiliation(s)
- Hui Wang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Hong Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Qian Zhou
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China.
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39
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Kamaruzzaman M, Wang Z, Wu M, Yang L, Han Y, Li G, Zhang J. Promotion of tomato growth by the volatiles produced by the hypovirulent strain QT5-19 of the plant gray mold fungus Botrytis cinerea. Microbiol Res 2021; 247:126731. [PMID: 33676312 DOI: 10.1016/j.micres.2021.126731] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/05/2021] [Accepted: 02/17/2021] [Indexed: 10/22/2022]
Abstract
Our previous study identified a hypovirulent strain QT5-19 of Botrytis cinerea, the causal agent of the plant gray mold disease, and found that QT5-19 can produce volatile organic compounds (VOCs) with high antifungal activity and high control efficacy against B. cinerea. However, impact of the QT5-19 VOCs on plant growth remains unknown. This study was conducted to investigate the impact of the QT5-19 VOCs on tomato growth, and to elucidate the mechanisms for the plant growth-promoting (PGP) activity of the QT5-19 VOCs. Results showed that compared to the control treatment, the QT5-19 VOCs significantly (P < 0.05) promoted tomato growth, and the PGP activity of the QT5-19 VOCs acted in dose- and time-dependent manners. Results also showed that the values of photosynthetic assimilation, stomatal conductance and transpiration, water use efficiency and chlorophyll content in the treatments of the QT5-19 VOCs were significantly (P < 0.05) higher than the corresponding values in the control treatment. The QT5-19 VOCs up-regulated expression of the genes for expansins (EXP2, EXP9 and EXP18), IAA (SlIAA1, SlIAA3 and SlIAA9), cytokinins (SlCKX1) and gibberellins in leaves and/or roots, whereas down-regulated expression of the gene ACO1 for ethylene in both organs. Moreover, enhanced accumulation of auxins and decreased accumulation of ethylene were observed in tomato roots in the treatment of the QT5-19 VOCs, compared to the control treatment. These results suggest that the QT5-19 VOCs probably promote tomato growth through improving photosynthesis and biosynthesis of expansins and IAA, and reducing ethylene biosynthesis. This study suggests that QT5-19 is a versatile biocontrol control agent.
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Affiliation(s)
- Md Kamaruzzaman
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ze Wang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mingde Wu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Long Yang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yongchao Han
- Institute of Industrial Crops, Hubei Academy of Agricultural Science, Wuhan, 430070, Hubei, China
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jing Zhang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Liu H, Liu M, Zhu H, Zhong J, Liao X, Zhou Q. Molecular characterization of a novel mitovirus from the plant‑pathogenic fungus Botryosphaeria dothidea. Arch Virol 2021; 166:633-637. [PMID: 33222011 DOI: 10.1007/s00705-020-04886-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/02/2020] [Indexed: 02/03/2023]
Abstract
Here, a novel mycovirus, Botryosphaeria dothidea mitovirus 1 (BdMV1), was isolated from a phytopathogenic fungus, Botryosphaeria dothidea, and its molecular characteristics were determined. BdMV1 has a genome of 2,667 nt that contains a single large open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF encodes an RNA-dependent RNA polymerase (RdRp) of 727 amino acids with a molecular mass of 81.64 kDa. BLASTp analysis revealed that the RdRp domain of BdMV1 has 39.59% and 39.18% sequence identity to Plasmopara viticola associated mitovirus 43 and Setosphaeria turcica mitovirus 1, respectively. Phylogenetic analysis further suggested that BdMV1 is a new member of the genus Mitovirus within the family Mitoviridae. To the best of our knowledge, this is the first report of a mitovirus in B. dothidea.
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Affiliation(s)
- Hong Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Miao Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Hongjian Zhu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Jie Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China
| | - Xiaolan Liao
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China.
| | - Qian Zhou
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Nongda Road 1, Furong District, Changsha, 410128, Hunan, People's Republic of China.
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Hao F, Wu M, Li G. Characterization of a novel genomovirus in the phytopathogenic fungus Botrytis cinerea. Virology 2020; 553:111-116. [PMID: 33264653 DOI: 10.1016/j.virol.2020.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/31/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022]
Abstract
This study characterized a single-stranded circular DNA virus in Botrytis cinerea-namely, Botrytis cinerea genomovirus 1 (BcGV1). The genome of BcGV1 was 1710 nucleotides (nts) long, possessing two ORFs, encoding a putative replication initiation protein (Rep) and a hypothetical protein. The Rep contained seven conserved motifs. The two ORFs were separated by two intergenic regions; the large intergenic region (LIR) contained 259 nts while the small intergenic region (SIR) contained 95 nts. A nonanucleotide, TAACAGTAC, in the LIR was predicted to be associated with the initiation of viral replication. Based on the phylogenetic tree constructed by Reps, BcGV1 belongs to the family Genomoviridae, forming an independent branch, indicating that BcGV1 may belong to a new genus. BcGV1 could be detected in 6.7% of tested B. cinerea strains, suggesting that BcGV1 may be widely distributed in the Chinese B. cinerea population.
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Affiliation(s)
- Fangmin Hao
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; Institute of Vegetables and the Key Lab of Cucurbitaceous Vegetables Breeding in Ningbo City, Ningbo Academy of Agricultural Sciences, Ningbo, 315040, PR China
| | - Mingde Wu
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Guoqing Li
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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42
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Jacquat AG, Theumer MG, Cañizares MC, Debat HJ, Iglesias J, García Pedrajas MD, Dambolena JS. A Survey of Mycoviral Infection in Fusarium spp. Isolated from Maize and Sorghum in Argentina Identifies the First Mycovirus from Fusarium verticillioides. Viruses 2020; 12:v12101161. [PMID: 33066620 PMCID: PMC7602464 DOI: 10.3390/v12101161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022] Open
Abstract
Mycoviruses appear to be widespread in Fusarium species worldwide. The aim of this work was to identify mycoviral infections in Fusarium spp., isolated from maize and sorghum grown in Argentina, and to estimate their potential effects on the pathogenicity and toxigenesis of the host fungus towards maize. Mycoviruses were identified in 2 out of 105 isolates analyzed; Fusarium verticillioides strain Sec505 and Fusarium andiyazi strain 162. They were characterized as members of the genus Mitovirus by high-throughput sequencing and sequence analysis. The F. verticillioides mitovirus was a novel mycovirus whereas the F. andiyazi mitovirus was found to be a new strain of a previously identified mitovirus. We have named these mitoviruses, Fusarium verticillioides mitovirus 1 (FvMV1) and Fusarium andiyazi mitovirus 1 strain 162 (FaMV1-162). To our knowledge, FvMV1 is the first mycovirus reported as naturally infecting F. verticillioides, the major causal agent of ear rot and fumonisin producer in corn. Both mitoviruses exhibited 100% vertical transmission rate to microconidia. The Fa162 strain infected with FaMV1-162 did not show phenotypic alterations. In contract, F. verticillioides Sec505 infected with FvMV1 showed increased virulence as well as microconidia and fumonisin-B1 production, compared with two uninfected strains. These results suggest that FvMV1 could have a role in modulating F. verticillioides pathogenicity and toxin production worth further exploring.
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Affiliation(s)
- Andrés Gustavo Jacquat
- Facultad de Ciencias Exactas Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Vélez Sarsfield 1611, Córdoba X5016GCA, Argentina
| | - Martín Gustavo Theumer
- Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas (FCQ), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Centro de Investigaciones en Bioquímica Clínica e Inmunología (CIBICI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Haya de la Torre y Medina Allende—Ciudad Universitaria, Córdoba X5000HUA, Argentina
| | - María Carmen Cañizares
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM—UMA—CSIC), Estación Experimental “La Mayora”, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
| | - Humberto Julio Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5.5, Córdoba X5020ICA, Argentina;
| | - Juliana Iglesias
- Estación Experimental Pergamino, (EEA) INTA Pergamino, Universidad Nacional Noroeste (UNNOBA), Pergamino (Buenos Aires) B2700, Argentina;
| | - María Dolores García Pedrajas
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM—UMA—CSIC), Estación Experimental “La Mayora”, Avenida Dr. Wienberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
- Correspondence: (M.D.G.P.); (J.S.D.)
| | - José Sebastián Dambolena
- Facultad de Ciencias Exactas Físicas y Naturales (FCEFyN), Universidad Nacional de Córdoba (UNC), Córdoba 5000, Argentina;
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Vélez Sarsfield 1611, Córdoba X5016GCA, Argentina
- Correspondence: (M.D.G.P.); (J.S.D.)
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43
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Li S, Li Y, Hu C, Han C, Zhou T, Zhao C, Wu X. Full genome sequence of a new mitovirus from the phytopathogenic fungus Rhizoctonia solani. Arch Virol 2020; 165:1719-1723. [PMID: 32424446 DOI: 10.1007/s00705-020-04664-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/05/2020] [Indexed: 12/14/2022]
Abstract
A double-stranded RNA (dsRNA) segment was identified in Rhizoctonia solani anastomosis group (AG)-2-2IIIB, the primary causal agent of Rhizoctonia crown and root rot of sugar beet. The dsRNA segment represented the genome replication intermediate of a new mitovirus that was tentatively designated as "Rhizoctonia solani mitovirus 39" (RsMV-39). The complete sequence of the dsRNA was 2805 bp in length with 61.9% A+U content. Using either the fungal mitochondrial or universal genetic code, a protein of 840 amino acids containing an RNA-dependent RNA polymerase (RdRp) domain was predicted with a molecular mass of 94.46 kDa. BLASTp analysis revealed that the RdRp domain of RsMV-39 had 43.55% to 72.96% sequence identity to viruses in the genus Mitovirus, and was the most similar (72.96% identical) to that of Ceratobasidium mitovirus A (CbMV-A). Phylogenetic analysis based on RdRp domains clearly showed that RsMV-39 is a member of a distinct species in the genus Mitovirus of the family Mitoviridae. This is the first full genome sequence of a mycovirus associated with R. solani AG-2-2IIIB.
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Affiliation(s)
- Siwei Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Yuting Li
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Chenghui Hu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Chenggui Han
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Tao Zhou
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China
| | - Can Zhao
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China.
- College of Horticulture, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China.
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing, 100193, People's Republic of China.
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Torres-Trenas A, Pérez-Artés E. Characterization and Incidence of the First Member of the Genus Mitovirus Identified in the Phytopathogenic Species Fusarium oxysporum. Viruses 2020; 12:v12030279. [PMID: 32138251 PMCID: PMC7150889 DOI: 10.3390/v12030279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 02/26/2020] [Accepted: 03/02/2020] [Indexed: 02/06/2023] Open
Abstract
A novel mycovirus named Fusarium oxysporum f. sp. dianthi mitovirus 1 (FodMV1) has been identified infecting a strain of Fusarium oxysporum f. sp. dianthi from Colombia. The genome of FodMV1 is 2313 nt long, and comprises a 172-nt 5’-UTR, a 2025-nt single ORF encoding an RdRp of 675 amino acid residues, and a 113-nt 3´-UTR. Homology BlastX searches identifies FodMV1 as a novel member of the genus Mitovirus in the family Narnaviridae. As the rest of mitoviruses, the genome of FodMV1 presents a high percentage of A+U (58.8%) and contains a number of UGA codons that encode the amino acid tryptophan rather than acting as stop codons as in the universal genetic code. Another common feature with other mitoviruses is that the 5′- and 3′-UTR regions of FodMV1 can be folded into potentially stable stem-loop structures. Result from phylogenetic analysis place FodMV1 in a different clade than the rest of mitoviruses described in other Fusarium spp. Incidence of FodMV1-infections in the collection of F. oxysporum f. sp. dianthi isolates analyzed is relatively high. Of particular interest is the fact that FodMV1 has been detected infecting isolates from two geographical areas as distant as Spain and Colombia.
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45
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Liang N, Yang D, Wu M, Zhang J, Li G, Yang L. Molecular characterization of a novel botoulivirus from the phytopathogenic fungus Sclerotinia minor. Arch Virol 2020; 165:785-788. [PMID: 31980938 DOI: 10.1007/s00705-020-04530-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/17/2019] [Indexed: 11/26/2022]
Abstract
In this study, the complete genomic sequence of a novel botoulivirus (Sclerotinia minor botoulivirus 1, SmBV1) from the phytopathogenic fungus Sclerotinia minor strain LC45 was determined. The genome of SmBV1 is 2,882 nucleotides in length and contains a single large open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis showed that SmBV1 clustered with the botoulivirus clade within the family Botourmiaviridae. This is the first report of a botoulivirus in S. minor.
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Affiliation(s)
- Na Liang
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dan Yang
- Hubei Biopesticide Engineering Research Center, Wuhan, 430064, China
| | - Mingde Wu
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing Zhang
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guoqing Li
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Long Yang
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan, 430070, China.
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46
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Starr EP, Nuccio EE, Pett-Ridge J, Banfield JF, Firestone MK. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. Proc Natl Acad Sci U S A 2019; 116:25900-25908. [PMID: 31772013 PMCID: PMC6926006 DOI: 10.1073/pnas.1908291116] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was Narnaviridae that may parasitize fungi or Leviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.
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Affiliation(s)
- Evan P Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA 94720;
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
- Innovative Genomics Institute, Berkeley, CA 94720
| | - Mary K Firestone
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720;
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
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47
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You J, Zhou K, Liu X, Wu M, Yang L, Zhang J, Chen W, Li G. Defective RNA of a Novel Mycovirus with High Transmissibility Detrimental to Biocontrol Properties of Trichoderma spp. Microorganisms 2019; 7:microorganisms7110507. [PMID: 31671828 PMCID: PMC6920978 DOI: 10.3390/microorganisms7110507] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 10/20/2019] [Accepted: 10/25/2019] [Indexed: 01/07/2023] Open
Abstract
Trichoderma species are a group of fungi which is widely distributed in major terrestrial ecosystems; they are also commonly used as biocontrol agents for many plant diseases. A virus, namely Trichoderma harzianum hypovirus 1 (ThHV1), was identified in T. harzianum isolate T-70, and also infected isolate T-70D, together with its defective RNA (ThHV1-S). The ThHV1 genome possessed two Open Reading Frames (ORFs), namely ORF1 and ORF2. The start codon of ORF2 overlapped with the stop codon of ORF1 in a 43 nt long region. The polypeptide encoded by ORF2 of ThHV1 shared sequence similarities with those of betahypoviruses, indicating that ThHV1 is a novel member of Hypoviridea. Isolate T-70D, carrying both ThHV1 and ThHV1-S, showed abnormal biological properties, notably a decreased mycoparasitism ability when compared with isolate T-70. Both ThHV1 and ThHV1-S could be vertically transmitted to conidia and horizontally transmitted to T. harzianum isolate T-68 and T. koningiopsis T-51. The derivative strains carrying both ThHV1 and ThHV1-S showed decreased mycoparasitism ability, whereas strains carrying ThHV1 alone were normal, indicating that ThHV1-S is closely associated with the decreased mycoparasitism ability of T. harzianum isolate T-70D. ThHV1 was widely detected in isolates of T. harzianum, T. koningiopsis and T. atroviride originating from soil of China. Therefore, viruses in fungal biocontrol agents may also be a factor associated with the stability of their application.
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Affiliation(s)
- Jiaqi You
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
- Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
| | - Kang Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaolin Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Mingde Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Long Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jing Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Weidong Chen
- U.S. Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, WA 99164, USA.
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
- The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
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48
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Vainio EJ. Mitoviruses in the conifer root rot pathogens Heterobasidion annosum and H. parviporum. Virus Res 2019; 271:197681. [PMID: 31394105 DOI: 10.1016/j.virusres.2019.197681] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 10/26/2022]
Abstract
Mitoviral infections are highly common among fungi, but so far only one mitovirus has been described in Heterobasidion spp. conifer pathogens. Here, the occurrence of further mitoviruses was investigated using a previously published RNA-Seq dataset for de novo contig assembly. This allowed the identification of two additional mitovirus strains designated as Heterobasidion mitovirus 2 (HetMV2) and HetMV3 with genome lengths of ca. 2.9 and 5.0 kb. Furthermore, the occurrence of similar viruses was screened among a collection of Heterobasidion isolates using RT-PCR. Mitoviruses were detected in six more fungal isolates and two different host species, H. annosum and H. parviporum.
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Affiliation(s)
- Eeva J Vainio
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790 Helsinki, Finland.
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49
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Zhang T, Li N, Yuan Y, Cao Q, Chen Y, Tan B, Li G, Liu D. Blue-White Colony Selection of Virus-Infected Isogenic Recipients Based on a Chrysovirus Isolated from Penicillium italicum. Virol Sin 2019; 34:688-700. [PMID: 31376081 DOI: 10.1007/s12250-019-00150-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 05/14/2019] [Indexed: 11/29/2022] Open
Abstract
Mycoviruses have been found to infect more than 12 species of Penicillium, but have not been isolated from Penicillium italicum (P. italicum). In this study, we isolated and characterized a new double-stranded RNA (dsRNA) virus, designated Penicillium italicum chrysovirus 1 (PiCV1), from the citrus pathogen P. italicum HSPi-YN1. Viral genome sequencing and molecular characterization indicated that PiCV1 was highly homologous to the previously described Penicillium chrysogenum virus. We further constructed the mutant HSPi-YN1ΔpksP defective in the polyketide synthase gene (pksP), which is involved in pigment biosynthesis, and these mutants formed albino (white) colonies. Then we applied hyphal anastomosis method to horizontally transmit PiCV1 from the white virus-donors (i.e., HSPi-YN1 mutants) to wild-type recipients (i.e., P. italicum strains HSPi-CQ54, HSPi-HB4, and HSPi-HN1), and the desirable PiCV1-infected isogenic recipients, a certain part of blue wild-type strains, can be eventually selected and confirmed by viral genomic dsRNA profile analysis. This blue-white colony screening would be an easier method to select virus-infected P. italicum recipients, according to distinguishable color phenotypes between blue virus-recipients and white virus-donors. In summary, the current work newly isolated and characterized PiCV1, verified its horizontal transmission among dually cultured P. italicum isolates, and based on these, established an effective and simplified approach to screen PiCV1-infected isogenic recipients.
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Affiliation(s)
- Tingfu Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Na Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.,Yunnan Higher Education Institutions, College of Life Science and Technology, Honghe University, Mengzi, 661199, China
| | - Yongze Yuan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Qianwen Cao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Yanfen Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Binglan Tan
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Guoqi Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Deli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
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50
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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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