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Mahillon M, Brodard J, Dubuis N, Gugerli P, Blouin AG, Schumpp O. Mixed infection of ITPase-encoding potyvirid and secovirid in Mercurialis perennis: evidences for a convergent euphorbia-specific viral counterstrike. Virol J 2024; 21:6. [PMID: 38178191 PMCID: PMC10768138 DOI: 10.1186/s12985-023-02257-y] [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: 09/26/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND In cellular organisms, inosine triphosphate pyrophosphatases (ITPases) prevent the incorporation of mutagenic deaminated purines into nucleic acids. These enzymes have also been detected in the genomes of several plant RNA viruses infecting two euphorbia species. In particular, two ipomoviruses produce replicase-associated ITPases to cope with high concentration of non-canonical nucleotides found in cassava tissues. METHOD Using high-throughput RNA sequencing on the wild euphorbia species Mercurialis perennis, two new members of the families Potyviridae and Secoviridae were identified. Both viruses encode for a putative ITPase, and were found in mixed infection with a new partitivirid. Following biological and genomic characterization of these viruses, the origin and function of the phytoviral ITPases were investigated. RESULTS While the potyvirid was shown to be pathogenic, the secovirid and partitivirid could not be transmitted. The secovirid was found belonging to a proposed new Comovirinae genus tentatively named "Mercomovirus", which also accommodates other viruses identified through transcriptome mining, and for which an asymptomatic pollen-associated lifestyle is suspected. Homology and phylogenetic analyses inferred that the ITPases encoded by the potyvirid and secovirid were likely acquired through independent horizontal gene transfer events, forming lineages distinct from the enzymes found in cassava ipomoviruses. Possible origins from cellular organisms are discussed for these proteins. In parallel, the endogenous ITPase of M. perennis was predicted to encode for a C-terminal nuclear localization signal, which appears to be conserved among the ITPases of euphorbias but absent in other plant families. This subcellular localization is in line with the idea that nucleic acids remain protected in the nucleus, while deaminated nucleotides accumulate in the cytoplasm where they act as antiviral molecules. CONCLUSION Three new RNA viruses infecting M. perennis are described, two of which encoding for ITPases. These enzymes have distinct origins, and are likely required by viruses to circumvent high level of cytoplasmic non-canonical nucleotides. This putative plant defense mechanism has emerged early in the evolution of euphorbias, and seems to specifically target certain groups of RNA viruses infecting perennial hosts.
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Affiliation(s)
- Mathieu Mahillon
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Justine Brodard
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Nathalie Dubuis
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Paul Gugerli
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Arnaud G Blouin
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland
| | - Olivier Schumpp
- Research Group Virology, Bacteriology and Phytoplasmology, Plant Protection Department, Agroscope, Nyon, Switzerland.
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Wang P, Pan S, Zheng Y, Pan X, Gao Z, Zhou X, Dai F, Li Z, Deng Q, Fang S, Wang H, Zhang S. Four closely related endornaviruses each with a low incidence in the phytopathogenic fungi Exserohilum turcicum or Bipolaris maydis. Virus Res 2024; 339:199256. [PMID: 37898320 PMCID: PMC10628355 DOI: 10.1016/j.virusres.2023.199256] [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: 09/24/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 10/30/2023]
Abstract
Endornaviruses are known to occur widely in plants, fungi, and oomycetes, but our understanding of their diversity and distribution is limited. In this study, we report the discovery of four endornaviruses tentatively named Setosphaeria turcica endornavirus 1 (StEV1), Setosphaeria turcica endornavirus 2 (StEV2), Bipolaris maydis endornavirus 1 (BmEV1), and Bipolaris maydis endornavirus 2 (BmEV2). StEV1 and StEV2 infect Exserohilum turcicum, while BmEV1 and BmEV2 infect Bipolaris maydis. The four viruses encode a polyprotein with less than 40 % amino acid sequence identity to other known endornaviruses, indicating that they are novel, previously undescribed endornaviruses. However, StEV1 and BmEV1 share a sequence identity of 78 % at the full-genome level and 87 % at the polyprotein level, suggesting that they may belong to the same species. Our study also found that each of the four endornaviruses has an incidence of approximately 3.5 % to 5.5 % in E. turcicum or B. maydis. Interestingly, BmEV1 and BmEV2 were found to be unable to transmit between hosts of different vegetative incompatibility groups, which may explain their low incidence.
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Affiliation(s)
- Peng Wang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, China
| | - Shouhui Pan
- Anshun Branch of Guizhou Tobacco Company, Anshun 561000, China
| | - Yun Zheng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, China
| | - Xin Pan
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, China
| | - Zhongnan Gao
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, China
| | - Xuan Zhou
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, China
| | - Fei Dai
- Anshun Branch of Guizhou Tobacco Company, Anshun 561000, China
| | - Zhanbiao Li
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Qingchao Deng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, China
| | - Shouguo Fang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, China
| | - Haoran Wang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, China.
| | - Songbai Zhang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-construction by Ministry and Province), Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, China.
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3
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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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4
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Wang J, Ni Y, Liu X, Zhao H, Xiao Y, Xiao X, Li S, Liu H. Divergent RNA viruses in Macrophomina phaseolina exhibit potential as virocontrol agents. Virus Evol 2020; 7:veaa095. [PMID: 33505706 PMCID: PMC7816680 DOI: 10.1093/ve/veaa095] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Macrophomina phaseolina is an important necrotrophic phytopathogenic fungus and cause extensive damage in many oilseed crops. Twelve M.phaseolina isolates with diverse biological phenotypes were selected for a high-throughput sequencing-based metatranscriptomic and bioinformatics analysis to identify viruses infecting M.phaseolina. The analysis identified 40 partial or nearly complete viral genome segments, 31 of which were novel viruses. Among these viral sequences, 43% of the viral genomes were double-stranded RNA (dsRNA), 47% were positive single-stranded RNA (ssRNA+), and the remaining 10% were negative sense-stranded RNA (ssRNA−). The 40 viruses showed affinity to 13 distinct viral lineages, including Bunyavirales (four viruses), Totiviridae (three viruses), Chrysoviridae (five viruses), Partitiviridae (four viruses), Hypoviridae (one virus), Endornaviridae (two viruses), Tombusviridae (three viruses), Narnaviridae (one virus), Potyviridae (one virus), Bromoviridae (one virus), Virgaviridae (six viruses), ‘Fusagraviridae’ (five viruses), and Ourmiavirus (four viruses). Two viruses are closely related to two families, Potyviridae and Bromoviridae, which previously contained no mycovirus species. Moreover, nine novel viruses associated with M.phaseolina were identified in the family Totiviridae, Endornaviridae, and Partitiviridae. Coinfection with multiple viruses is prevalent in M.phaseolina, with each isolate harboring different numbers of viruses, ranging from three to eighteen. Furthermore, the effects of the viruses on the fungal host were analyzed according to the biological characteristics of each isolate. The results suggested that M.phaseolina hypovirus 2, M.phaseolina fusagravirus virus 1-5 (MpFV1-5), M.phaseolina endornavirus 1-2 (MpEV1-2), M.phaseolina ourmia-like virus 1-3 (MpOLV1-3), M.phaseolina mitovirus 4 (MpMV4), and M.phaseolina mycobunyavirus 1-4 (MpMBV1-4) were only detected in hypovirulent isolates. Those viruses associated with hypovirulence might be used as biological control agents as an environmentally friendly alternative to chemical fungicides. These findings considerably expand our understanding of mycoviruses in M.phaseolina and unvailed the presence of a huge difference among viruses in isolates from different hosts in distant geographical regions. Together, the present study provides new knowledge about viral evolution and fungus-virus coevolution.
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Affiliation(s)
- Jing Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China.,Institute of Tobacco, Henan Academy of Agricultural Sciences, Key Laboratory for Green Preservation & Control of Tobacco Diseases and Pest in Huanghuai Growing Area, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Yunxia Ni
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Xintao Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Hui Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Yannong Xiao
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070 Hubei Province, PR China
| | - Xueqiong Xiao
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan, 430070 Hubei Province, PR 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, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
| | - Hongyan Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Key Laboratory of Crop Pest Control, No.116, Garden road, Jingshui District, Zhengzhou, 450002 Henan Province, PR China
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5
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Abstract
Mycoviruses, just as the fungal endophytes they infect, are ubiquitous biological entities on Earth. Mycoviruses constitute a diverse group of viruses, and metagenomic approaches have-through recent discoveries of been mycoviruses-only recently began to provide evidence of this astonishing diversity. The current review presents (1) various mycoviruses which infect fungal endophytes and forest pathogens, (2) their presumed origins and interactions with fungi, plants and the environment, (3) high-throughput sequencing techniques that can be used to explore the horizontal gene transfer of mycoviruses, and (4) how the hypo- and hypervirulence induced by mycoviral infection is relevant to the biological control of pathogenic fungi.
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Affiliation(s)
- Abu Bakar Siddique
- Department of Ecology and Environmental Sciences (EMG), Umeå University, Umeå, Sweden.
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6
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High-Throughput Sequencing Reveals Bell Pepper Endornavirus Infection in Pepper ( Capsicum annum) in Slovakia and Enables Its Further Molecular Characterization. PLANTS 2019; 9:plants9010041. [PMID: 31887986 PMCID: PMC7020154 DOI: 10.3390/plants9010041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/21/2019] [Accepted: 12/24/2019] [Indexed: 12/24/2022]
Abstract
Ribosomal RNA-depleted total RNAs from a sweet pepper plant (Capsicum annuum, labelled as N65) grown in western Slovakia and showing severe virus-like symptoms (chlorosis, mottling and deformation of leaf lamina) were subjected to high-throughput sequencing (HTS) on an Illumina MiSeq platform. The de novo assembly of ca. 5.5 million reads, followed by mapping to the reference sequences, revealed the coinfection of pepper by several viruses; i.e., cucumber mosaic virus (CMV), watermelon mosaic virus (WMV), pepper cryptic virus 2 (PCV2) and bell pepper endornavirus (BPEV). A complete polyprotein-coding genomic sequence (14.6 kb) of BPEV isolate N65 was determined. A comparison of BPEV-N65 sequences with BPEV genomes available in GenBank showed 86.1% to 98.6% identity at the nucleotide level. The close phylogenetic relationship with isolates from India and China resulted in their distinct grouping compared to the other BPEV isolates. Further analysis has revealed the presence of BPEV in sweet or chili peppers obtained from various sources and locations in Slovakia (plants grown in gardens, greenhouse or retail shop). Additionally, the partial sequencing of two genomic portions from 15 BPEV isolates revealed that the Slovak isolates segregated into two molecular clusters, indicating a genetically distinct population (mean inter-group nucleotide divergence reaching 12.7% and 14.5%, respectively, based on the genomic region targeted). Due to the mix infections of BPEV-positive peppers by potato virus Y (PVY) and/or CMV, the potential role of individual viruses in the observed symptomatology could not be determined. This is the first evidence and characterization of BPEV from the central European region.
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7
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Takahashi H, Fukuhara T, Kitazawa H, Kormelink R. Virus Latency and the Impact on Plants. Front Microbiol 2019; 10:2764. [PMID: 31866963 PMCID: PMC6908805 DOI: 10.3389/fmicb.2019.02764] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/12/2019] [Indexed: 11/15/2022] Open
Abstract
Plant viruses are thought to be essentially harmful to the lives of their cultivated crop hosts. In most cases studied, the interaction between viruses and cultivated crop plants negatively affects host morphology and physiology, thereby resulting in disease. Native wild/non-cultivated plants are often latently infected with viruses without any clear symptoms. Although seemingly non-harmful, these viruses pose a threat to cultivated crops because they can be transmitted by vectors and cause disease. Reports are accumulating on infections with latent plant viruses that do not cause disease but rather seem to be beneficial to the lives of wild host plants. In a few cases, viral latency involves the integration of full-length genome copies into the host genome that, in response to environmental stress or during certain developmental stages of host plants, can become activated to generate and replicate episomal copies, a transition from latency to reactivation and causation of disease development. The interaction between viruses and host plants may also lead to the integration of partial-length segments of viral DNA genomes or copy DNA of viral RNA genome sequences into the host genome. Transcripts derived from such integrated viral elements (EVEs) may be beneficial to host plants, for example, by conferring levels of virus resistance and/or causing persistence/latency of viral infections. Studies on viral latency in wild host plants might help us to understand and elucidate the underlying mechanisms of latency and provide insights into the raison d’être for viruses in the lives of plants.
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Affiliation(s)
- Hideki Takahashi
- Laboratory of Plant Pathology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Plant Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences and Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University, Wageningen, Netherlands
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8
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Willemsen A, Carrasco JL, Elena SF, Zwart MP. Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses. Heredity (Edinb) 2018; 121:499-509. [PMID: 29743566 DOI: 10.1038/s41437-018-0086-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 11/09/2022] Open
Abstract
Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental research on a plant RNA virus, tobacco etch potyvirus (TEV), to identify the patterns underlying the stability of a range of homologous and heterologous insertions in the viral genome. We obtained a wide range of estimates for the recombination rate-the rate at which deletions removing the insertion occur-and these appeared to be independent of the type of insertion and its location. Of the factors we considered, recombination rate was the best predictor of insertion stability, although we could not identify the specific sequence characteristics that would help predict insertion instability. We also considered experimentally the possibility that functional insertions lead to higher mutational robustness through increased redundancy. However, our observations suggest that both functional and non-functional increases in genome size decreased the mutational robustness. Our results therefore demonstrate the importance of recombination rates for predicting the long-term stability and evolution of viral RNA genomes and suggest that there are unexpected drawbacks to increases in genome size for mutational robustness.
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Affiliation(s)
- Anouk Willemsen
- Laboratory MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center for Scientific Research (CNRS), Montpellier, France
| | - José L Carrasco
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, València, Spain.,Instituto de Biología Integrativa de Sistemas (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Paterna, Spain.,The Santa Fe Institute, Santa Fe, NM, 87501, USA
| | - Mark P Zwart
- Microbial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands. .,Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.
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9
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Moniruzzaman M, Wurch LL, Alexander H, Dyhrman ST, Gobler CJ, Wilhelm SW. Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics. Nat Commun 2017; 8:16054. [PMID: 28656958 PMCID: PMC5493757 DOI: 10.1038/ncomms16054] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/16/2017] [Indexed: 01/12/2023] Open
Abstract
Establishing virus–host relationships has historically relied on culture-dependent approaches. Here we report on the use of marine metatranscriptomics to probe virus–host relationships. Statistical co-occurrence analyses of dsDNA, ssRNA and dsRNA viral markers of polyadenylation-selected RNA sequences from microbial communities dominated by Aureococcus anophagefferens (Quantuck Bay, NY), and diatoms (Narragansett Bay, RI) show active infections by diverse giant viruses (NCLDVs) associated with algal and nonalgal hosts. Ongoing infections of A. anophagefferens by a known Mimiviridae (AaV) occur during bloom peak and decline. Bloom decline is also accompanied by increased activity of viruses other than AaV, including (+) ssRNA viruses. In Narragansett Bay, increased temporal resolution reveals active NCLDVs with both ‘boom-and-bust’ and ‘steady-state infection’-like ecologies that include known as well as novel virus–host interactions. Our approach offers a method for screening active viral infections and develops links between viruses and their potential hosts in situ. Our observations further demonstrate that previously unknown virus–host relationships in marine systems are abundant. Viruses are partners in ecosystem ecology, yet their study has been primarily limited to laboratory models virus-host or derived from metagenomics. Here, Moniruzzaman et al. use metatranscriptomics to resolve interactions between giant viruses and single-celled eukaryotic hosts.
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Affiliation(s)
- Mohammad Moniruzzaman
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Louie L Wurch
- Department of Biology, James Madison University, Harrisonburg, Virginia 22807, USA
| | - Harriet Alexander
- Department of Earth and Environmental Science and Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York 10964, USA
| | - Sonya T Dyhrman
- Department of Earth and Environmental Science and Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York 10964, USA
| | - Christopher J Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York 11794, USA
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Tennessee 37996, USA
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10
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Sabanadzovic S, Wintermantel WM, Valverde RA, McCreight JD, Aboughanem-Sabanadzovic N. Cucumis melo endornavirus: Genome organization, host range and co-divergence with the host. Virus Res 2016; 214:49-58. [DOI: 10.1016/j.virusres.2016.01.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/30/2015] [Accepted: 01/03/2016] [Indexed: 01/30/2023]
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11
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Multiple Barriers to the Evolution of Alternative Gene Orders in a Positive-Strand RNA Virus. Genetics 2016; 202:1503-21. [PMID: 26868766 DOI: 10.1534/genetics.115.185017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/07/2016] [Indexed: 01/06/2023] Open
Abstract
The order in which genes are organized within a genome is generally not conserved between distantly related species. However, within virus orders and families, strong conservation of gene order is observed. The factors that constrain or promote gene-order diversity are largely unknown, although the regulation of gene expression is one important constraint for viruses. Here we investigate why gene order is conserved for a positive-strand RNA virus encoding a single polyprotein in the context of its authentic multicellular host. Initially, we identified the most plausible trajectory by which alternative gene orders could evolve. Subsequently, we studied the accessibility of key steps along this evolutionary trajectory by constructing two virus intermediates: (1) duplication of a gene followed by (2) loss of the ancestral gene. We identified five barriers to the evolution of alternative gene orders. First, the number of viable positions for reordering is limited. Second, the within-host fitness of viruses with gene duplications is low compared to the wild-type virus. Third, after duplication, the ancestral gene copy is always maintained and never the duplicated one. Fourth, viruses with an alternative gene order have even lower fitness than viruses with gene duplications. Fifth, after more than half a year of evolution in isolation, viruses with an alternative gene order are still vastly inferior to the wild-type virus. Our results show that all steps along plausible evolutionary trajectories to alternative gene orders are highly unlikely. Hence, the inaccessibility of these trajectories probably contributes to the conservation of gene order in present-day viruses.
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12
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Complete Genome Sequence of a Bell Pepper Endornavirus Isolate from Canada. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00905-15. [PMID: 26294624 PMCID: PMC4543502 DOI: 10.1128/genomea.00905-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bell pepper endornavirus (BPEV) is a double-stranded RNA virus infecting economically important crops, such as peppers. Next-generation sequencing of small RNAs extracted from the leaves of a pepper plant showing mild viral symptoms, along with subsequent analysis, identified BPEV. The complete genome of this isolate was cloned and sequenced.
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Morozov SY, Solovyev AG. Phylogenetic relationship of some "accessory" helicases of plant positive-stranded RNA viruses: toward understanding the evolution of triple gene block. Front Microbiol 2015; 6:508. [PMID: 26042118 PMCID: PMC4436898 DOI: 10.3389/fmicb.2015.00508] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/08/2015] [Indexed: 12/16/2022] Open
Abstract
Recently, we hypothesized that silencing suppression activity gained by a viral replicative helicase led to the emergence of the second helicase possessing activity of the viral silencing suppressor and/or movement protein (MP). Our hypothesis accounted for the evolutionary origin of the specialized ‘triple gene block’ (TGB) in plant virus genomes encoding the MPs TGB1, TGB2, and TGB3 required for viral cell-to-cell transport through plasmodesmata. Here, we used public transcriptome databases to identify previously unrecognized viruses. The analysis of novel viral genomes further supported the previously proposed scenario of TGB origin and evolution, which included the following steps. First, the accessory helicase gene could have been acquired by horizontal gene transfer (HGT) presumably occured independently in different virus groups. Second, the TGB2 gene evolved by HGT or autonomization of the C-terminal transmembrane domain found in at least one TGB1 helicase. Third, the TGB3 gene has most likely emerged in the genomic block consisting of the TGB1 and TGB2 genes.
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Affiliation(s)
- Sergey Y Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University Moscow, Russia
| | - Andrey G Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University Moscow, Russia
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De novo assembly of a bell pepper endornavirus genome sequence using RNA sequencing data. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00061-15. [PMID: 25792042 PMCID: PMC4395069 DOI: 10.1128/genomea.00061-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The genus Endornavirus is a double-stranded RNA virus that infects a wide range of hosts. In this study, we report on the de novo assembly of a bell pepper endornavirus genome sequence by RNA sequencing (RNA-Seq). Our result demonstrates the successful application of RNA-Seq to obtain a complete viral genome sequence from the transcriptome data.
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15
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Two endornaviruses show differential infection patterns between gene pools of Phaseolus vulgaris. Arch Virol 2015; 160:1131-7. [PMID: 25623050 DOI: 10.1007/s00705-015-2335-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/08/2015] [Indexed: 01/24/2023]
Abstract
We investigated the occurrence of two plant endornaviruses, Phaseolus vulgaris endornavirus 1 and Phaseolus vulgaris endornavirus 2, in breeding lines, cultivars, landraces, and wild genotypes of common bean (Phaseolus vulgaris) collected from the two centers of common bean domestication: Mesoamerica and the Andes. The two endornaviruses were detected in many genotypes of Mesoamerican origin but rarely in genotypes of Andean origin. The results suggest that these two endornaviruses were introduced into the Mesoamerican modern genotypes during common bean domestication and provide more evidence for the existence of two divergent gene pools of common bean.
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Ahn SJ, Dermauw W, Wybouw N, Heckel DG, Van Leeuwen T. Bacterial origin of a diverse family of UDP-glycosyltransferase genes in the Tetranychus urticae genome. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 50:43-57. [PMID: 24727020 DOI: 10.1016/j.ibmb.2014.04.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/28/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
UDP-glycosyltransferases (UGTs) catalyze the conjugation of a variety of small lipophilic molecules with uridine diphosphate (UDP) sugars, altering them into more water-soluble metabolites. Thereby, UGTs play an important role in the detoxification of xenobiotics and in the regulation of endobiotics. Recently, the genome sequence was reported for the two-spotted spider mite, Tetranychus urticae, a polyphagous herbivore damaging a number of agricultural crops. Although various gene families implicated in xenobiotic metabolism have been documented in T. urticae, UGTs so far have not. We identified 80 UGT genes in the T. urticae genome, the largest number of UGT genes in a metazoan species reported so far. Phylogenetic analysis revealed that lineage-specific gene expansions increased the diversity of the T. urticae UGT repertoire. Genomic distribution, intron-exon structure and structural motifs in the T. urticae UGTs were also described. In addition, expression profiling after host-plant shifts and in acaricide resistant lines supported an important role for UGT genes in xenobiotic metabolism. Expanded searches of UGTs in other arachnid species (Subphylum Chelicerata), including a spider, a scorpion, two ticks and two predatory mites, unexpectedly revealed the complete absence of UGT genes. However, a centipede (Subphylum Myriapoda) and a water flea and a crayfish (Subphylum Crustacea) contain UGT genes in their genomes similar to insect UGTs, suggesting that the UGT gene family might have been lost early in the Chelicerata lineage and subsequently re-gained in the tetranychid mites. Sequence similarity of T. urticae UGTs and bacterial UGTs and their phylogenetic reconstruction suggest that spider mites acquired UGT genes from bacteria by horizontal gene transfer. Our findings show a unique evolutionary history of the T. urticae UGT gene family among other arthropods and provide important clues to its functions in relation to detoxification and thereby host adaptation.
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Affiliation(s)
- Seung-Joon Ahn
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; National Institute of Horticultural and Herbal Science, Rural Development Administration, 441-440 Suwon, Korea.
| | - Wannes Dermauw
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Nicky Wybouw
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Thomas Van Leeuwen
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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The complete genome of a putative endornavirus identified in yerba mate (Ilex paraguariensis St. Hil.). Virus Genes 2014; 49:348-50. [DOI: 10.1007/s11262-014-1096-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/07/2014] [Indexed: 10/25/2022]
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