1
|
Zhou J, Liu S, Xu Y, Yan J, Xie C, Zheng L, Chen D. Complete genome sequence of a novel botourmiavirus infecting the fungus Phomopsis asparagi. Arch Virol 2024; 169:161. [PMID: 38981885 DOI: 10.1007/s00705-024-06084-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 06/03/2024] [Indexed: 07/11/2024]
Abstract
Here, we report a novel ourmia-like mycovirus, named "Phomopsis asparagi magoulivirus 1" (PaMV1), derived from the phytopathogenic fungus Phomopsis asparagi. The genome of PaMV1 consists of a positive-sense single-stranded RNA (+ ssRNA) that is 2,639 nucleotides in length, with a GC content of 57.13%. It contains a single open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) consisting of 686 amino acids with a molecular mass of 78.57 kDa. Phylogenetic analysis based on RdRp sequences revealed that PaMV1 grouped together with Diaporthe gulyae magoulivirus 1 (DgMV1) in a distinct clade. Sequence comparisons and phylogenetic analysis suggest that PaMV1 is a novel member of the genus Magoulivirus, family Botourmiaviridae.
Collapse
Affiliation(s)
- Jingyi Zhou
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, School of Tropical Agriculture and Forestry, Ministry of Education, Hainan University, Haikou, Hainan, 570228, China
| | - Shuang Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, School of Tropical Agriculture and Forestry, Ministry of Education, Hainan University, Haikou, Hainan, 570228, China
| | - Yun Xu
- School of Life and Health, Hainan University, Haikou, Hainan, 570228, China
| | - Junhan Yan
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, School of Tropical Agriculture and Forestry, Ministry of Education, Hainan University, Haikou, Hainan, 570228, China
| | - Changping Xie
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, School of Tropical Agriculture and Forestry, Ministry of Education, Hainan University, Haikou, Hainan, 570228, China
| | - Li Zheng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, School of Tropical Agriculture and Forestry, Ministry of Education, Hainan University, Haikou, Hainan, 570228, China
| | - Daipeng Chen
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, School of Tropical Agriculture and Forestry, Ministry of Education, Hainan University, Haikou, Hainan, 570228, China.
| |
Collapse
|
2
|
Hua H, Zhang X, Liu L, Wu X. A Novel Strain of Fusarium oxysporum Alternavirus 1 Isolated from Fusarium oxysporum f. sp. melonis Strain T-BJ17 Confers Hypovirulence and Increases the Sensitivity of Its Host Fungus to Difenoconazole and Pydiflumetofen. Viruses 2024; 16:901. [PMID: 38932193 PMCID: PMC11209391 DOI: 10.3390/v16060901] [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: 03/17/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
In the current study, a novel strain of Fusarium oxysporum alternavirus 1 (FoAV1) was identified from the Fusarium oxysporum f. sp. melonis (FOM) strain T-BJ17 and was designated as Fusarium oxysporum alternavirus 1-FOM (FoAV1-FOM). Its genome consists of four dsRNA segments of 3515 bp (dsRNA1), 2663 bp (dsRNA2), 2368 bp (dsRNA3), and 1776 bp (dsRNA4) in length. Open reading frame 1 (ORF1) in dsRNA1 was found to encode a putative RNA-dependent RNA polymerase (RdRp), whose amino acid sequence was 99.02% identical to that of its counterpart in FoAV1; while ORF2 in dsRNA2, ORF3 in dsRNA3, and ORF4 in dsRNA4 were all found to encode hypothetical proteins. Strain T-BJ17-VF, which was verified to FoAV1-FOM-free, was obtained using single-hyphal-tip culture combined with high-temperature treatment to eliminate FoAV1-FOM from strain T-BJ17. The colony growth rate, ability to produce spores, and virulence of strain T-BJ17 were significantly lower than those of T-BJ17-VF, while the dry weight of the mycelial biomass and the sensitivity to difenoconazole and pydiflumetofen of strain T-BJ17 were greater than those of T-BJ17-VF. FoAV1-FOM was capable of 100% vertical transmission via spores. To our knowledge, this is the first time that an alternavirus has infected FOM, and this is the first report of hypovirulence and increased sensitivity to difenoconazole and pydiflumetofen induced by FoAV1-FOM infection in FOM.
Collapse
Affiliation(s)
| | | | | | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, China (X.Z.); (L.L.)
| |
Collapse
|
3
|
Hua H, Zhang X, Xia J, Wu X. A Novel Strain of Fusarium oxysporum Virus 1 Isolated from Fusarium oxysporum f. sp. niveum Strain X-GS16 Influences Phenotypes of F. oxysporum Strain HB-TS-YT-1 hyg. J Fungi (Basel) 2024; 10:252. [PMID: 38667923 PMCID: PMC11050907 DOI: 10.3390/jof10040252] [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: 03/04/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
A novel strain of Fusarium oxysporum virus 1 (FoV1) was identified from the Fusarium oxysporum f. sp. niveum strain X-GS16 and designated as Fusarium oxysporum virus 1-FON (FoV1-FON). The full genome of FoV1-FON is 2902 bp in length and contains two non-overlapping open reading frames (ORFs), ORF1 and ORF2, encoding a protein with an unknown function (containing a typical -1 slippery motif G_GAU_UUU at the 3'-end) and a putative RNA-dependent RNA polymerase (RdRp), respectively. BLASTx search against the National Center for the Biotechnology Information (NCBI) non-redundant database showed that FoV1-FON had the highest identity (97.46%) with FoV1. Phylogenetic analysis further confirmed that FoV1-FON clustered with FoV1 in the proposed genus Unirnavirus. FoV1-FON could vertically transmit via spores. Moreover, FoV1-FON was transmitted horizontally from the F. oxysporum f. sp. niveum strain X-GS16 to the F. oxysporum strain HB-TS-YT-1hyg. This resulted in the acquisition of the F. oxysporum strain HB-TS-YT-1hyg-V carrying FoV1-FON. No significant differences were observed in the sporulation and dry weight of mycelial biomass between HB-TS-YT-1hyg and HB-TS-YT-1hyg-V. FoV1-FON infection significantly increased the mycelial growth of HB-TS-YT-1hyg, but decreased its virulence to potato tubers and sensitivity to difenoconazole, prochloraz, and pydiflumetofen. To our knowledge, this is the first report of hypovirulence and reduced sensitivity to difenoconazole, prochloraz, and pydiflumetofen in F. oxysporum due to FoV1-FON infection.
Collapse
Affiliation(s)
| | | | | | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, China; (H.H.); (X.Z.); (J.X.)
| |
Collapse
|
4
|
Wang J, Ni Y, Zhao H, Liu X, Qiu R, Li S, Liu H. Complete genome sequence of a novel dsRNA virus from the phytopathogenic fungus Fusarium oxysporum. Arch Virol 2024; 169:75. [PMID: 38492088 DOI: 10.1007/s00705-024-05976-x] [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: 10/23/2023] [Accepted: 12/13/2023] [Indexed: 03/18/2024]
Abstract
Fusarium oxysporum is a widespread plant pathogen that causes fusarium wilt and fusarium root rot in many economically significant crops. Here, a novel dsRNA virus tentatively named "Fusarium oxysporum virus 1" (FoV1) was identified in F. oxysporum strain 3S-18. The genome of FoV1 is 2,944 nucleotides (nt) in length and contains two non-overlapping open reading frames (ORF1 and 2). The larger of these, ORF2, encodes an RNA-dependent RNA polymerase (RdRp) of 590 amino acids with a molecular mass of 67.52 kDa. ORF1 encodes a putative nucleocapsid protein consisting of 134 amino acids with a molecular mass of 34.25 kDa. The RdRp domain of FoV1 shares 60.00% to 84.24% sequence identity with non-segmented dsRNA viruses. Phylogenetic analysis further suggested that FoV1 is a new member of the proposed genus "Unirnavirus" accommodating unclassified monopartite dsRNA viruses.
Collapse
Affiliation(s)
- Jing Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Yunxia Ni
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Hui Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Xintao Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Rui Qiu
- Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Zhengzhou, 450002, Henan Province, People's Republic of China
| | - Shujun Li
- Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pest in Huanghuai Growing Area, Zhengzhou, 450002, Henan Province, People's Republic of China.
| | - Hongyan Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan Province, People's Republic of China.
| |
Collapse
|
5
|
Chen G, Jiang J, Sun Y. RNAVirHost: a machine learning-based method for predicting hosts of RNA viruses through viral genomes. Gigascience 2024; 13:giae059. [PMID: 39172545 PMCID: PMC11340644 DOI: 10.1093/gigascience/giae059] [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: 03/07/2024] [Revised: 05/29/2024] [Accepted: 07/23/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND The high-throughput sequencing technologies have revolutionized the identification of novel RNA viruses. Given that viruses are infectious agents, identifying hosts of these new viruses carries significant implications for public health and provides valuable insights into the dynamics of the microbiome. However, determining the hosts of these newly discovered viruses is not always straightforward, especially in the case of viruses detected in environmental samples. Even for host-associated samples, it is not always correct to assign the sample origin as the host of the identified viruses. The process of assigning hosts to RNA viruses remains challenging due to their high mutation rates and vast diversity. RESULTS In this study, we introduce RNAVirHost, a machine learning-based tool that predicts the hosts of RNA viruses solely based on viral genomes. RNAVirHost is a hierarchical classification framework that predicts hosts at different taxonomic levels. We demonstrate the superior accuracy of RNAVirHost in predicting hosts of RNA viruses through comprehensive comparisons with various state-of-the-art techniques. When applying to viruses from novel genera, RNAVirHost achieved the highest accuracy of 84.3%, outperforming the alignment-based strategy by 12.1%. CONCLUSIONS The application of machine learning models has proven beneficial in predicting hosts of RNA viruses. By integrating genomic traits and sequence homologies, RNAVirHost provides a cost-effective and efficient strategy for host prediction. We believe that RNAVirHost can greatly assist in RNA virus analyses and contribute to pandemic surveillance.
Collapse
Affiliation(s)
- Guowei Chen
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong (SAR), China
| | - Jingzhe Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong (SAR), China
| |
Collapse
|
6
|
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.
Collapse
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.)
| | | |
Collapse
|
7
|
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.
Collapse
|
8
|
Wei C, Wen C, Zhang Y, Du H, Zhong R, Guan Z, Wang M, Qin Y, Wang F, Song L, Zhao Y. The FomYjeF Protein Influences the Sporulation and Virulence of Fusarium oxysporum f. sp. momordicae. Int J Mol Sci 2023; 24:ijms24087260. [PMID: 37108422 PMCID: PMC10138616 DOI: 10.3390/ijms24087260] [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: 03/15/2023] [Revised: 04/06/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Fusarium oxysporum causes vascular wilt in more than 100 plant species, resulting in massive economic losses. A deep understanding of the mechanisms of pathogenicity and symptom induction by this fungus is necessary to control crop wilt. The YjeF protein has been proven to function in cellular metabolism damage-repair in Escherichia coli and to play an important role in Edc3 (enhancer of the mRNA decapping 3) function in Candida albicans, but no studies have been reported on related functions in plant pathogenic fungi. In this work, we report how the FomYjeF gene in F. oxysporum f. sp. momordicae contributes to conidia production and virulence. The deletion of the FomYjeF gene displayed a highly improved capacity for macroconidia production, and it was shown to be involved in carbendazim's associated stress pathway. Meanwhile, this gene caused a significant increase in virulence in bitter gourd plants with a higher disease severity index and enhanced the accumulation of glutathione peroxidase and the ability to degrade hydrogen peroxide in F. oxysporum. These findings reveal that FomYjeF affects virulence by influencing the amount of spore formation and the ROS (reactive oxygen species) pathway of F. oxysporum f. sp. momordicae. Taken together, our study shows that the FomYjeF gene affects sporulation, mycelial growth, pathogenicity, and ROS accumulation in F. oxysporum. The results of this study provide a novel insight into the function of FomYjeF participation in the pathogenicity of F. oxysporum f. sp. momordicae.
Collapse
Affiliation(s)
- Chenxing Wei
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Caiyi Wen
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Yuanyuan Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Hongyan Du
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Rongrong Zhong
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhengzhe Guan
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Mengjiao Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanhong Qin
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Fei Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Luyang Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| | - Ying Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| |
Collapse
|
9
|
Huang H, Hua X, Pang X, Zhang Z, Ren J, Cheng J, Fu Y, Xiao X, Lin Y, Chen T, Li B, Liu H, Jiang D, Xie J. Discovery and Characterization of Putative Glycoprotein-Encoding Mycoviruses in the Bunyavirales. J Virol 2023; 97:e0138122. [PMID: 36625579 PMCID: PMC9888262 DOI: 10.1128/jvi.01381-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/16/2022] [Indexed: 01/11/2023] Open
Abstract
Although segmented negative-sense RNA viruses (SNSRVs) have been frequently discovered in various fungi, most SNSRVs reported only the large segments. In this study, we investigated the diversity of the mycoviruses in the phytopathogenic fungus Fusarium asiaticum using the metatranscriptomic technique. We identified 17 fungal single-stranded RNA (ssRNA) viruses including nine viruses within Mitoviridae, one each in Narnaviridae, Botourmiaviridae, Hypoviridae, Fusariviridae, and Narliviridae, two in Mymonaviridae, and one trisegmented virus temporarily named Fusarium asiaticum mycobunyavirus 1 (FaMBV1). The FaMBV1 genome comprises three RNA segments, large (L), medium (M), and small (S) with 6,468, 2,639, and 1,420 nucleotides, respectively. These L, M, and S segments putatively encode the L protein, glycoprotein, and nucleocapsid, respectively. Phylogenetic analysis based on the L protein showed that FaMBV1 is phylogenetically clustered with Alternaria tenuissima negative-stranded RNA virus 2 (AtNSRV2) and Sclerotinia sclerotiorum negative-stranded RNA virus 5 (SsNSRV5) but distantly related to the members of the family Phenuiviridae. FaMBV1 could be vertically transmitted by asexual spores with lower efficiency (16.7%, 2/42). Comparison between FaMBV1-free and -infected fungal strains revealed that FaMBV1 has little effect on hyphal growth, pathogenicity, and conidium production, and its M segment is dispensable for viral replication and lost during subculture and asexual conidiation. The M and S segments of AtNSRV2 and SsNSRV5 were found using bioinformatics methods, indicating that the two fungal NSRVs harbor trisegmented genomes. Our results provide a new example of the existence and evolution of the segmented negative-sense RNA viruses in fungi. IMPORTANCE Fungal segmented negative-sense RNA viruses (SNSRVs) have been frequently found. Only the large segment encoding RNA-dependent RNA polymerase (RdRp) has been reported in most fungal SNSRVs, except for a few fungal SNSRVs reported to encode nucleocapsids, nonstructural proteins, or movement proteins. Virome analysis of the Fusarium spp. that cause Fusarium head blight discovered a novel virus, Fusarium asiaticum mycobunyavirus 1 (FaMBV1), representing a novel lineage of the family Phenuiviridae. FaMBV1 harbors a trisegmented genome that putatively encodes RdRp, glycoproteins, and nucleocapsids. The putative glycoprotein was first described in fungal SNSRVs and shared homology with glycoprotein of animal phenuivirus but was dispensable for its replication in F. asiaticum. Two other trisegmented fungal SNSRVs that also encode glycoproteins were discovered, implying that three-segment bunyavirus infections may be common in fungi. These findings provide new insights into the ecology and evolution of SNSRVs, particularly those infecting fungi.
Collapse
Affiliation(s)
- Huang Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Xiangmin Hua
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Xidan Pang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Zhongmei Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Jingyi Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU-Purdue Joint Research Center, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xueqiong Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU-Purdue Joint Research Center, College of Plant Protection, Northwest A&F University, Xianyang, Shaanxi, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, Hubei, China
| |
Collapse
|
10
|
Zhao Y, Du H, Liu Y, Zhong R, Guan Z, Wang G, Zhang Y, Wei C, Wang M, Wan X, Zang R, Wen C, Meng H. Molecular characterization of a novel victorivirus isolated from the phytopathogenic fungus Phaeobotryon rhois. Arch Virol 2023; 168:15. [PMID: 36593368 DOI: 10.1007/s00705-022-05678-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/22/2022] [Indexed: 01/03/2023]
Abstract
Phaeobotryon rhois is an important pathogenic fungus that causes dieback and canker disease of woody hosts. A novel mycovirus, tentatively named "Phaeobotryon rhois victorivirus 1" (PrVV1), was identified in P. rhois strain SX8-4. The PrVV1 has a double-stranded RNA (dsRNA) genome that is 5,224 base pairs long and contains two open reading frames (ORF1 and ORF2), which overlap at a AUGA sequence. ORF1 encodes a polypeptide of 786 amino acids (aa) that contains the conserved coat protein (CP) domain of victoriviruses, while ORF2, encodes a large polypeptide of 826 aa that contains the conserved RNA-dependent RNA polymerase (RdRp) domain of victoriviruses. Our analysis of genomic structure, homology, and phylogeny indicated that PrVV1 is a novel member of the genus Victorivirus in the family Totiviridae. This is the first report of the complete genome sequence of a victorivirus that infects P. rhois.
Collapse
Affiliation(s)
- Ying Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hongyan Du
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yuanyuan Liu
- Yinchuan City Center for Disease Control and Prevention, Yinchuan, China
| | - Rongrong Zhong
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Zhengzhe Guan
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Ganlin Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yuanyuan Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Chenxing Wei
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Mengjiao Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Xinru Wan
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Rui Zang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Caiyi Wen
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Haoguang Meng
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China.
| |
Collapse
|
11
|
Zhang X, Wu C, Hua H, Cai Q, Wu X. Characterization of the First Alternavirus Identified in Fusarium avenaceum, the Causal Agent of Potato Dry Rot. Viruses 2023; 15:145. [PMID: 36680185 PMCID: PMC9864086 DOI: 10.3390/v15010145] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
A novel virus with a double-stranded RNA (dsRNA) genome was isolated from Fusarium avenaceum strain GS-WW-224, the causal agent of potato dry rot. The virus has been designated as Fusarium avenaceum alternavirus 1 (FaAV1). Its genome consists of two dsRNA segments, 3538 bp (dsRNA1) and 2477 bp (dsRNA2) in length, encoding RNA-dependent RNA polymerase (RdRp) and a hypothetical protein (HP), respectively. The virions of FaAV1 are isometric spherical and approximately 30 nm in diameter. Multiple sequence alignments and phylogenetic analyses based on the amino acid sequences of RdRp and HP indicated that FaAV1 appears to be a new member of the proposed family Alternaviridae. No significant differences in colony morphology and spore production were observed between strains GS-WW-224 and GS-WW-224-VF, the latter strain being one in which FaAV1 was eliminated from strain GS-WW-224. Notably, however, the dry weight of mycelial biomass of GS-WW-224 was higher than that of mycelial biomass of GS-WW-224-VF. The depth and the width of lesions on potato tubers caused by GS-WW-224 were significantly greater, relative to GS-WW-224-VF, suggesting that FaAV1 confers hypervirulence to its host, F. avenaceum. Moreover, FaAV1 was successfully transmitted horizontally from GS-WW-224 to ten other species of Fusarium, and purified virions of FaAV1 were capable of transfecting wounded hyphae of the ten species of Fusarium. This is the first report of an alternavirus infecting F. avenaceum and conferring hypervirulence.
Collapse
Affiliation(s)
| | | | | | | | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Haidian District, Beijing 100193, China
| |
Collapse
|
12
|
Kinsella CM, Deijs M, Gittelbauer HM, van der Hoek L, van Dijk K. Human Clinical Isolates of Pathogenic Fungi Are Host to Diverse Mycoviruses. Microbiol Spectr 2022; 10:e0161022. [PMID: 35993766 PMCID: PMC9603141 DOI: 10.1128/spectrum.01610-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/08/2022] [Indexed: 12/31/2022] Open
Abstract
Fungi host viruses from many families, and next-generation sequencing can be used to discover previously unknown genomes. Some fungus-infecting viruses (mycoviruses) confer hypovirulence on their pathogenic hosts, raising the possibility of therapeutic application in the treatment of fungal diseases. Though all fungi probably host mycoviruses, many human pathogens have none documented, implying the mycoviral catalogue remains at an early stage. Here, we carried out virus discovery on 61 cultures of pathogenic fungi covering 27 genera and at least 56 species. Using next-generation sequencing of total nucleic acids, we found no DNA viruses but did find a surprising RNA virus diversity of 11 genomes from six classified families and two unclassified lineages, including eight genomes likely representing new species. Among these was the first jivivirus detected in a fungal host (Aspergillus lentulus). We separately utilized rolling circle amplification and next-generation sequencing to identify ssDNA viruses specifically. We identified 13 new cressdnaviruses across all libraries, but unlike the RNA viruses, they could not be confirmed by PCR in either the original unamplified samples or freshly amplified nucleic acids. Their distributions among sequencing libraries and inconsistent detection suggest low-level contamination of reagents. This highlights both the importance of validation assays and the risks of viral host prediction on the basis of highly amplified sequencing libraries. Meanwhile, the detected RNA viruses provide a basis for experimentation to characterize possible hypovirulent effects, and hint at a wealth of uncharted viral diversity currently frozen in biobanks. IMPORTANCE Fungal pathogens of humans are a growing global health burden. Viruses of fungi may represent future therapeutic tools, but for many fungal pathogens there are no known viruses. Our study examined the viral content of diverse human-pathogenic fungi in a clinical biobank, identifying numerous viral genomes, including one lineage previously not known to infect fungi.
Collapse
Affiliation(s)
- Cormac M. Kinsella
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Martin Deijs
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - H. M. Gittelbauer
- Amsterdam UMC, Laboratory of Mycology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
| | - Lia van der Hoek
- Amsterdam UMC, Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
| | - Karin van Dijk
- Amsterdam UMC, Laboratory of Mycology, Department of Medical Microbiology and Infection Prevention, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
13
|
A Botybirnavirus Isolated from Alternaria tenuissima Confers Hypervirulence and Decreased Sensitivity of Its Host Fungus to Difenoconazole. Viruses 2022; 14:v14102093. [DOI: 10.3390/v14102093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022] Open
Abstract
Alternaria alternata botybirnavirus 1 (AaBRV1) was isolated from a strain of Alternaria alternata, causing watermelon leaf blight in our previous research. The effect of AaBRV1 on the phenotype of its host fungus, however, was not determined. In the present study, a novel strain of AaBRV1 was identified in A. tenuissima strain TJ-NH-51S-4, the causal agent of cotton Alternaria leaf spot, and designated as AaBRV1-AT1. A mycovirus AaBRV1-AT1-free strain TJ-NH-51S-4-VF was obtained by protoplast regeneration, which eliminated AaBRV1-AT1 from the mycovirus AaBRV1-AT1-infected strain TJ-NH-51S-4. Colony growth rate, spore production, and virulence of strain TJ-NH-51S-4 were greater than they were in TJ-NH-51S-4-VF, while the sensitivity of strain TJ-NH-51S-4 to difenoconazole, as measured by the EC50, was lower. AaBRV1-AT1 was capable of vertical transmission via asexual spores and horizontal transmission from strain TJ-NH-51S-4 to strain XJ-BZ-5-1hyg (another strain of A. tenuissima) through hyphal contact in pairing cultures. A total of 613 differentially expressed genes (DEGs) were identified in a comparative transcriptome analysis between TJ-NH-51S-4 and TJ-NH-51S-4-VF. Relative to strain TJ-NH-51S-4-VF, the number of up-regulated and down-regulated DEGs in strain TJ-NH-51S-4 was 286 and 327, respectively. Notably, the expression level of one DEG-encoding cytochrome P450 sterol 14α-demethylase and four DEGs encoding siderophore iron transporters were significantly up-regulated. To our knowledge, this is the first documentation of hypervirulence and reduced sensitivity to difenoconazole induced by AaBRV1-AT1 infection in A. tenuissima.
Collapse
|
14
|
Hypovirulence of Colletotrichum gloesporioides Associated with dsRNA Mycovirus Isolated from a Mango Orchard in Thailand. Viruses 2022; 14:v14091921. [PMID: 36146727 PMCID: PMC9504431 DOI: 10.3390/v14091921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/23/2022] Open
Abstract
The pathogenic fungus Colletotrichum gloeosporioides causes anthracnose disease, which is an important fungal disease affecting the production of numerous crops around the world. The presence of mycoviruses, however, may have an impact on the pathogenicity of the fungal host. Here, we describe a double-stranded RNA (dsRNA) mycovirus, which was isolated from a field strain of C. gloeosporioides, Ssa-44.1. The 2939 bp genome sequence comprises two open reading frames (ORFs) that encode for a putative protein and RNA-dependent RNA polymerase (RdRp). The Ssa-44.1 mycovirus is a member of the unclassified mycovirus family named Colletotrichum gloeosporioides RNA virus 1 strain Ssa-44.1 (CgRV1-Ssa-44.1), which has a phylogenetic similarity to Colletotrichum gleosporioides RNA virus 1 (CgRV1), which was isolated from citrus leaves in China. In C. gloeosporioides, CgRV1-Ssa-44.1 was shown to be linked to hypovirulence. CgRV1-Ssa-44.1 has a low spore transfer efficiency but can successfully spread horizontally to isogenic virus-free isolates. Furthermore, CgRV1-Ssa-44.1 had a strong biological control impact on C. gloeosporioides on mango plants. This study is the first to describe a hypovirulence-associated mycovirus infecting C. gloeosporioides, which has the potential to assist with anthracnose disease biological management.
Collapse
|
15
|
Li B, Cao Y, Ji Z, Zhang J, Meng X, Dai P, Hu T, Wang S, Cao K, Wang Y. Coinfection of Two Mycoviruses Confers Hypovirulence and Reduces the Production of Mycotoxin Alternariol in Alternaria alternata f. sp. mali. Front Microbiol 2022; 13:910712. [PMID: 35756001 PMCID: PMC9218907 DOI: 10.3389/fmicb.2022.910712] [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: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 11/22/2022] Open
Abstract
Alternaria leaf blotch caused by Alternaria alternata apple pathotype (Alternaria mali) is an important fungal disease that affects the production of apples worldwide. Mycoviruses harbored in plant pathogenic fungi can confer hypovirulence in their hosts and have attracted widespread attention as potential biocontrol tools. In this study, the coinfection of two mycoviruses, named A. alternata chrysovirus 1 strain QY2 (AaCV1-QY2) and A. alternata magoulivirus 1 (AaMV1), respectively, were isolated from A. alternata f. sp. mali strain QY21. Sequence analyses revealed that AaCV1-QY2 virus belonged to the genus Betachrysovirus and AaMV1 virus belonged to the genus Magoulvirus. These two mycoviruses were found to be associated with hypovirulence in A. alternata, among which AaCV1-QY2 might play a relatively leading role. Because the elimination of AaMV1 from the strain QY21 does not affect the hypovirulence trait, which indicates that the virus AaCV1-QY2 can independently induce slow growth and reduce host virulence. Moreover, the presence of viruses decreased the accumulation of the mycotoxin alternariol (AOH) in A. alternata strains. Intriguingly, AaCV1-QY2/AaMV1 mycoviruses can be horizontally transmitted to other A. alternata strains, and this coinfection can promote the interspecific transmission efficiency of AaCV1-QY2. To our knowledge, this study reports the first description of the member of Chrysovirus is related to hypovirulence in Alternaria spp. that facilitates the development of biocontrol measures of A. mali Roberts.
Collapse
Affiliation(s)
- Bo Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Yuhan Cao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Zixuan Ji
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Jingyi Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Xianglong Meng
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Pengbo Dai
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Tongle Hu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Shutong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Keqiang Cao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Yanan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| |
Collapse
|
16
|
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.
Collapse
|
17
|
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.
Collapse
|
18
|
Wang J, Li C, Song P, Qiu R, Song R, Li X, Ni Y, Zhao H, Liu H, Li S. Molecular and Biological Characterization of the First Mymonavirus Identified in Fusarium oxysporum. Front Microbiol 2022; 13:870204. [PMID: 35531277 PMCID: PMC9069137 DOI: 10.3389/fmicb.2022.870204] [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: 02/06/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022] Open
Abstract
We characterized a negative sense single-stranded RNA mycovirus, Fusarium oxysporum mymonavirus 1 (FoMyV1), isolated from the phytopathogenic fungus Fusarium oxysporum. The genome of FoMyV1 is 10,114 nt, including five open reading frames (ORFs1–5) that are non-overlapping and linearly arranged. The largest, ORF5, encodes a large polypeptide L containing a conserved regions corresponding to Mononegavirales RNA-dependent RNA polymerase and mRNA-capping enzyme region V; the putative functions of the remaining four ORFs are unknown. The L protein encoded by ORF5 shared a high amino acid identity of 65% with that of Hubei rhabdo-like virus 4, a mymonavirus that associated with arthropods. However, the L protein of FoMyV1 also showed amino acid similarity (27–36%) with proteins of mynonaviruses that infect the phytopathogenic fungi Sclerotinia sclerotiorum and Botrytis cineaea. Phylogenetic analysis based on L protein showed that FoMyV1 is clustered with the members of the genus Hubramonavirus in the family Mymonaviridae. Moreover, we found that FoMyV1 could successfully transfer by hyphal anastomosis to a virus-free strain. FoMyV1 reduced the vegetative growth and conidium production of its fungal host but did not alter its virulence. To the best of our knowledge, this is not only the first mymonavirus described in the species F. oxysporum, but also the first Hubramonavirus species found to infect a fungus. However, the incidence of FoMyV1 infections in the tested F. oxysporum strains was only 1%.
Collapse
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, Zhengzhou, 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, Zhengzhou, China
| | - Pengyu Song
- College of Biological Sciences, China Agricultural University, Beijing, 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, Zhengzhou, China
| | - Ruifang Song
- Tobacco Company of Henan Province, Zhengzhou, 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, Zhengzhou, China
| | - Yunxia Ni
- Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hui Zhao
- Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hongyan Liu
- Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
- *Correspondence: Hongyan Liu,
| | - 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, Zhengzhou, China
- Shujun Li,
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Molecular Characterization of the First Alternavirus Identified in Fusarium oxysporum. Viruses 2021; 13:v13102026. [PMID: 34696456 PMCID: PMC8538667 DOI: 10.3390/v13102026] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/30/2021] [Accepted: 10/05/2021] [Indexed: 01/25/2023] Open
Abstract
A novel mycovirus named Fusarium oxysporum alternavirus 1(FoAV1) was identified as infecting Fusarium oxysporum strain BH19, which was isolated from a fusarium wilt diseased stem of Lilium brownii. The genome of FoAV1 contains four double-stranded RNA (dsRNA) segments (dsRNA1, dsRNA 2, dsRNA 3 and dsRNA 4, with lengths of 3.3, 2.6, 2.3 and 1.8 kbp, respectively). Additionally, dsRNA1 encodes RNA-dependent RNA polymerase (RdRp), and dsRNA2- dsRNA3- and dsRNA4-encoded hypothetical proteins (ORF2, ORF3 and ORF4), respectively. A homology BLAST search, along with multiple alignments based on RdRp, ORF2 and ORF3 sequences, identified FoAV1 as a novel member of the proposed family "Alternaviridae". Evolutionary relation analyses indicated that FoAV1 may be related to alternaviruses, thus dividing the family "Alternaviridae" members into four clades. In addition, we determined that dsRNA4 was dispensable for replication and may be a satellite-like RNA of FoAV1-and could perhaps play a role in the evolution of alternaviruses. Our results provided evidence for potential genera establishment within the proposed family "Alternaviridae". Additionally, FoAV1 exhibited biological control of Fusarium wilt. Our results also laid the foundations for the further study of mycoviruses within the family "Alternaviridae", and provide a potential agent for the biocontrol of diseases caused by F. oxysporum.
Collapse
|
21
|
Characterization of the Mycovirome from the Plant-Pathogenic Fungus Cercospora beticola. Viruses 2021; 13:v13101915. [PMID: 34696345 PMCID: PMC8537984 DOI: 10.3390/v13101915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 12/25/2022] Open
Abstract
Cercospora leaf spot (CLS) caused by Cercospora beticola is a devastating foliar disease of sugar beet (Beta vulgaris), resulting in high yield losses worldwide. Mycoviruses are widespread fungi viruses and can be used as a potential biocontrol agent for fugal disease management. To determine the presence of mycoviruses in C. beticola, high-throughput sequencing analysis was used to determine the diversity of mycoviruses in 139 C. beticola isolates collected from major sugar beet production areas in China. The high-throughput sequencing reads were assembled and searched against the NCBI database using BLASTn and BLASTx. The results showed that the obtained 93 contigs were derived from eight novel mycoviruses, which were grouped into 3 distinct lineages, belonging to the families Hypoviridae, Narnaviridae and Botourmiaviridae, as well as some unclassified (−)ssRNA viruses in the order Bunyavirales and Mononegavirales. To the best of our knowledge, this is the first identification of highly diverse mycoviruses in C. beticola. The novel mycoviruses explored in this study will provide new viral materials to biocontrol Cercospora diseases. Future studies of these mycoviruses will aim to assess the roles of each mycovirus in biological function of C. beticola in the future.
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|