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Aboughanem-Sabanadzovic N, Valverde RA, Sabanadzovic S. Complete genome sequence of lima bean endornavirus 1: a putative new member of the genus Alphaendornavirus (family Endornaviridae). Arch Virol 2024; 169:206. [PMID: 39305367 DOI: 10.1007/s00705-024-06135-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 09/04/2024] [Indexed: 09/25/2024]
Abstract
In this study, we completely sequenced the genome of a new member of the genus Alphaendornavirus, family Endornaviridae, from lima bean (Phaseolus lunatus), for which we propose the name "lima bean endornavirus 1" (LbEV1). The complete genome of LbEV1 consists of 15,265 nucleotides, including a stretch of 12 cytosine residues at its 3' end, and contains a long single open reading frame (ORF) coding for a 4980-aa-long polyprotein. Analysis of the polyprotein sequence revealed the presence of four conserved functional domains (in order from the N- to C-terminus): viral helicase 1, peptidase _C97, glycosyltransferase_GTB-type, and viral RNA-dependent RNA polymerase (RdRP). The LbEV1 polyprotein showed the highest amino acid sequence similarity (63% identity and 98% coverage) to Phaseolus vulgaris endornavirus 3 (PvEV3) and also showed 42% identity (95% coverage) to Geranium carolinianum endornavirus. Phylogenetic analysis based on the viral RdRp domain showed that LbEV1 belongs to a subclade within the genus Alphaendornavirus that includes three other viruses infecting plants of the genus Phaseolus.
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Affiliation(s)
| | - Rodrigo A Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University, Baton Rouge, USA
| | - Sead Sabanadzovic
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, USA
- Department of Agricultural Science and Plant Protection, Mississippi State University, Mississippi State, USA
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2
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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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Brine TJ, Crawshaw S, Murphy AM, Pate AE, Carr JP, Wamonje FO. Identification and characterization of Phaseolus vulgaris endornavirus 1, 2 and 3 in common bean cultivars of East Africa. Virus Genes 2023; 59:741-751. [PMID: 37563541 PMCID: PMC10500008 DOI: 10.1007/s11262-023-02026-7] [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: 03/15/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Persistent viruses include members of the family Endornavirus that cause no apparent disease and are transmitted exclusively via seed or pollen. It is speculated that these RNA viruses may be mutualists that enhance plant resilience to biotic and abiotic stresses. Using reverse transcription coupled polymerase chain reactions, we investigated if common bean (Phaseolus vulgaris L.) varieties popular in east Africa were hosts for Phaseolus vulgaris endornavirus (PvEV) 1, 2 or 3. Out of 26 bean varieties examined, four were infected with PvEV1, three were infected with both PvEV1 and PvEV2 and three had infections of all three (PvEV) 1, 2 and 3. Notably, this was the first identification of PvEV3 in common bean from Africa. Using high-throughput sequencing of two east African bean varieties (KK022 and KK072), we confirmed the presence of these viruses and generated their genomes. Intra- and inter-species sequence comparisons of these genomes with comparator sequences from GenBank revealed clear species demarcation. In addition, phylogenetic analyses based on sequences generated from the helicase domains showed that geographical distribution does not correlate to genetic relatedness or the occurrence of endornaviruses. These findings are an important first step towards future investigations to determine if these viruses engender positive effects in common bean, a vital crop in east Africa.
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Affiliation(s)
- Thomas J Brine
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Sam Crawshaw
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Alex M Murphy
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Adrienne E Pate
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - John P Carr
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Francis O Wamonje
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
- Pest and Pathogen Ecology, National Institute of Agricultural Botany, East Malling, ME19 6BJ, UK.
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4
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Dahan J, Orellana GE, Lee J, Karasev AV. Grapevine Endophyte Endornavirus and Two New Endornaviruses Found Associated with Grapevines ( Vitis vinifera L.) in Idaho, USA. Viruses 2023; 15:1347. [PMID: 37376645 DOI: 10.3390/v15061347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Five virus genomes, ranging between 12.0 and 12.3 kb in length and identified as endornaviruses, were discovered through a high-throughput sequencing (HTS) analysis of the total RNA samples extracted from two wine grape cultivars collected in the State of Idaho. One was found in a declining Chardonnay vine and was determined to be a local isolate of grapevine endophyte endornavirus (GEEV), and four others represented two novel endornaviruses named grapevine endornavirus 1 (GEV1) and grapevine endornavirus 2 (GEV2). All three virus genomes span a large, single open reading frame encoding polyproteins with easily identifiable helicase (HEL) and RNA-dependent RNA polymerase (RdRP) domains, while the GEV2 polyprotein also contains a glycosyltransferase domain. The GEV1 genome found in an asymptomatic Cabernet franc vine was related to, but distinct from, GEEV: the 5'-proximal, 4.7 kb segment of the GEV1 genome had a 72% identical nucleotide sequence to that of GEEV, while the rest of the genome displayed no significant similarity to the GEEV nucleotide sequence. Nevertheless, the amino acid sequence of the RdRP domain of GEV1 exhibited the closest affinity to the RdRP of GEEV. GEV2 was found in declining Chardonnay and asymptomatic Cabernet franc vines as three genetic variants exhibiting a 91.9-99.8% nucleotide sequence identity among each other; its RdRP had the closest affinity to the Shahe endorna-like virus 1 found in termites. In phylogenetic analyses, the RdRP and HEL domains of the GEV1 and GEV2 polyproteins were placed in two separate clades inside the large lineage of alphaendornaviruses, showing an affinity to GEEV and Phaseolus vulgaris endornavirus 1, respectively.
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Affiliation(s)
- Jennifer Dahan
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844, USA
| | - Gardenia E Orellana
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844, USA
| | - Jungmin Lee
- Horticultural Crops Production and Genetic Improvement Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR 97330, USA
| | - Alexander V Karasev
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844, USA
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5
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Alcalá Briseño RI, Batuman O, Brawner J, Cuellar WJ, Delaquis E, Etherton BA, French-Monar RD, Kreuze JF, Navarrete I, Ogero K, Plex Sulá AI, Yilmaz S, Garrett KA. Translating virome analyses to support biosecurity, on-farm management, and crop breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1056603. [PMID: 36998684 PMCID: PMC10043385 DOI: 10.3389/fpls.2023.1056603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/14/2023] [Indexed: 06/19/2023]
Abstract
Virome analysis via high-throughput sequencing (HTS) allows rapid and massive virus identification and diagnoses, expanding our focus from individual samples to the ecological distribution of viruses in agroecological landscapes. Decreases in sequencing costs combined with technological advances, such as automation and robotics, allow for efficient processing and analysis of numerous samples in plant disease clinics, tissue culture laboratories, and breeding programs. There are many opportunities for translating virome analysis to support plant health. For example, virome analysis can be employed in the development of biosecurity strategies and policies, including the implementation of virome risk assessments to support regulation and reduce the movement of infected plant material. A challenge is to identify which new viruses discovered through HTS require regulation and which can be allowed to move in germplasm and trade. On-farm management strategies can incorporate information from high-throughput surveillance, monitoring for new and known viruses across scales, to rapidly identify important agricultural viruses and understand their abundance and spread. Virome indexing programs can be used to generate clean germplasm and seed, crucial for the maintenance of seed system production and health, particularly in vegetatively propagated crops such as roots, tubers, and bananas. Virome analysis in breeding programs can provide insight into virus expression levels by generating relative abundance data, aiding in breeding cultivars resistant, or at least tolerant, to viruses. The integration of network analysis and machine learning techniques can facilitate designing and implementing management strategies, using novel forms of information to provide a scalable, replicable, and practical approach to developing management strategies for viromes. In the long run, these management strategies will be designed by generating sequence databases and building on the foundation of pre-existing knowledge about virus taxonomy, distribution, and host range. In conclusion, virome analysis will support the early adoption and implementation of integrated control strategies, impacting global markets, reducing the risk of introducing novel viruses, and limiting virus spread. The effective translation of virome analysis depends on capacity building to make benefits available globally.
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Affiliation(s)
- Ricardo I. Alcalá Briseño
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Plant Pathology Department, Oregon State University, Corvallis, OR, United States
| | - Ozgur Batuman
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Southwest Florida Research and Education Center (SWFREC), Immokalee, FL, United States
| | - Jeremy Brawner
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
| | - Wilmer J. Cuellar
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Erik Delaquis
- International Center for Tropical Agriculture (CIAT), Vientiane, Laos
| | - Berea A. Etherton
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | | | - Jan F. Kreuze
- Crop and System Sciences Division, International Potato Center (CIP), Lima, Peru
| | - Israel Navarrete
- Crop and System Sciences Division, International Potato Center (CIP), Quito, Ecuador
| | - Kwame Ogero
- Crop and System Sciences Division, International Potato Center (CIP), Mwanza, Tanzania
| | - Aaron I. Plex Sulá
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Salih Yilmaz
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Southwest Florida Research and Education Center (SWFREC), Immokalee, FL, United States
| | - Karen A. Garrett
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Global Food Systems Institute, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
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6
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Chiquito-Almanza E, Caballero-Pérez J, Acosta-Gallegos JA, Montero-Tavera V, Mariscal-Amaro LA, Anaya-López JL. Diversity and Distribution of Viruses Infecting Wild and Domesticated Phaseolus spp. in the Mesoamerican Center of Domestication. Viruses 2021; 13:v13061153. [PMID: 34208696 PMCID: PMC8235658 DOI: 10.3390/v13061153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/26/2021] [Accepted: 06/11/2021] [Indexed: 11/16/2022] Open
Abstract
Viruses are an important disease source for beans. In order to evaluate the impact of virus disease on Phaseolus biodiversity, we determined the identity and distribution of viruses infecting wild and domesticated Phaseolus spp. in the Mesoamerican Center of Domestication (MCD) and the western state of Nayarit, Mexico. We used small RNA sequencing and assembly to identify complete or near-complete sequences of forty-seven genomes belonging to nine viral species of five genera, as well as partial sequences of two putative new endornaviruses and five badnavirus- and pararetrovirus-like sequences. The prevalence of viruses in domesticated beans was significantly higher than in wild beans (97% vs. 19%; p < 0.001), and all samples from domesticated beans were positive for at least one virus species. In contrast, no viruses were detected in 80-83% of the samples from wild beans. The Bean common mosaic virus and Bean common mosaic necrosis virus were the most prevalent viruses in wild and domesticated beans. Nevertheless, Cowpea mild mottle virus, transmitted by the whitefly Bemisia tabaci, has the potential to emerge as an important pathogen because it is both seed-borne and a non-persistently transmitted virus. Our results provide insights into the distribution of viruses in cultivated and wild Phaseolus spp. and will be useful for the identification of emerging viruses and the development of strategies for bean viral disease management in a center of diversity.
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Affiliation(s)
- Elizabeth Chiquito-Almanza
- Biotechnology Department, National Institute for Forestry Agriculture and Livestock Research (INIFAP), Celaya, Guanajuato 38110, Mexico; (E.C.-A.); (V.M.-T.)
| | - Juan Caballero-Pérez
- Faculty of Chemistry, Autonomous University of Querétaro, Santiago de Querétaro 76017, Mexico;
| | - Jorge A. Acosta-Gallegos
- Bean Breeding Program, National Institute for Forestry Agriculture and Livestock Research (INIFAP), Celaya, Guanajuato 38110, Mexico;
| | - Victor Montero-Tavera
- Biotechnology Department, National Institute for Forestry Agriculture and Livestock Research (INIFAP), Celaya, Guanajuato 38110, Mexico; (E.C.-A.); (V.M.-T.)
| | - Luis Antonio Mariscal-Amaro
- Forestry and Plant Protection Program, National Institute for Forestry Agriculture and Livestock Research (INIFAP), Celaya, Guanajuato 38110, Mexico;
| | - José Luis Anaya-López
- Biotechnology Department, National Institute for Forestry Agriculture and Livestock Research (INIFAP), Celaya, Guanajuato 38110, Mexico; (E.C.-A.); (V.M.-T.)
- Correspondence:
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7
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Chiba Y, Tomaru Y, Shimabukuro H, Kimura K, Hirai M, Takaki Y, Hagiwara D, Nunoura T, Urayama SI. Viral RNA Genomes Identified from Marine Macroalgae and a Diatom. Microbes Environ 2021; 35. [PMID: 32554943 PMCID: PMC7511793 DOI: 10.1264/jsme2.me20016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Protists provide insights into the diversity and function of RNA viruses in marine systems. Among them, marine macroalgae are good targets for RNA virome analyses because they have a sufficient biomass in nature. However, RNA viruses in macroalgae have not yet been examined in detail, and only partial genome sequences have been reported for the majority of RNA viruses. Therefore, to obtain further insights into the distribution and diversity of RNA viruses associated with marine protists, we herein examined RNA viruses in macroalgae and a diatom. We report the putative complete genome sequences of six novel RNA viruses from two marine macroalgae and one diatom holobiont. Four viruses were not classified into established viral genera or families. Furthermore, a virus classified into Totiviridae showed a genome structure that has not yet been reported in this family. These results suggest that a number of distinct RNA viruses are widespread in a broad range of protists.
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Affiliation(s)
- Yuto Chiba
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba.,Faculty of Science, International College of Arts and Science, Yokohama City University
| | - Yuji Tomaru
- Japan Fisheries Research and Education Agency, National Research Institute of Fisheries and Environment of the Inland Sea
| | - Hiromori Shimabukuro
- Japan Fisheries Research and Education Agency, National Research Institute of Fisheries and Environment of the Inland Sea
| | | | - Miho Hirai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, JAMSTEC
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, JAMSTEC
| | - Daisuke Hagiwara
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba.,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Syun-Ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba.,Microbiology Research Center for Sustainability (MiCS), University of Tsukuba.,Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
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8
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Uchida K, Sakuta K, Ito A, Takahashi Y, Katayama Y, Omatsu T, Mizutani T, Arie T, Komatsu K, Fukuhara T, Uematsu S, Okada R, Moriyama H. Two Novel Endornaviruses Co-infecting a Phytophthora Pathogen of Asparagus officinalis Modulate the Developmental Stages and Fungicide Sensitivities of the Host Oomycete. Front Microbiol 2021; 12:633502. [PMID: 33633714 PMCID: PMC7902037 DOI: 10.3389/fmicb.2021.633502] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/14/2021] [Indexed: 01/06/2023] Open
Abstract
Two novel endornaviruses, Phytophthora endornavirus 2 (PEV2) and Phytophthora endornavirus 3 (PEV3) were found in isolates of a Phytophthora pathogen of asparagus collected in Japan. A molecular phylogenetic analysis indicated that PEV2 and PEV3 belong to the genus Alphaendornavirus. The PEV2 and PEV3 genomes consist of 14,345 and 13,810 bp, and they contain single open reading frames of 4,640 and 4,603 codons, respectively. Their polyproteins contain the conserved domains of an RNA helicase, a UDP-glycosyltransferase, and an RNA-dependent RNA polymerase, which are conserved in other alphaendornaviruses. PEV2 is closely related to Brown algae endornavirus 2, whereas PEV3 is closely related to Phytophthora endornavirus 1 (PEV1), which infects a Phytophthora sp. specific to Douglas fir. PEV2 and PEV3 were detected at high titers in two original Phytophthora sp. isolates, and we found a sub-isolate with low titers of the viruses during subculture. We used the high- and low-titer isolates to evaluate the effects of the viruses on the growth, development, and fungicide sensitivities of the Phytophthora sp. host. The high-titer isolates produced smaller mycelial colonies and much higher numbers of zoosporangia than the low-titer isolate. These results suggest that PEV2 and PEV3 inhibited hyphal growth and stimulated zoosporangium formation. The high-titer isolates were more sensitive than the low-titer isolate to the fungicides benthiavalicarb-isopropyl, famoxadone, and chlorothalonil. In contrast, the high-titer isolates displayed lower sensitivity to the fungicide metalaxyl (an inhibitor of RNA polymerase I) when compared with the low-titer isolate. These results indicate that persistent infection with PEV2 and PEV3 may potentially affect the fungicide sensitivities of the host oomycete.
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Affiliation(s)
- Keiko Uchida
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Kohei Sakuta
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Aori Ito
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Yumi Takahashi
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Tsutomu Arie
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Toshiyuki Fukuhara
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Seiji Uematsu
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Ryo Okada
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
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9
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Herschlag R, Okada R, Alcalá-Briseño RI, de Souto ER, Valverde RA. Identification of a novel endornavirus in Geranium carolinianum and occurrence within three agroecosystems. Virus Res 2020; 288:198116. [PMID: 32795491 DOI: 10.1016/j.virusres.2020.198116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
Abstract
A putative endornavirus was detected in Carolina geranium (Geranium carolinianum) in Louisiana, USA. The virus was provisionally named Geranium carolinianum endornavirus 1 (GcEV1). The viral RNA was sequenced, and it consisted of 14,625 nt containing a single ORF coding a putative polyprotein of 4815 aa with conserved domains for a helicase 1, peptidase C97, glycosyl transferase GTB-type, and RNA-dependent RNA polymerase 2. The 5'end consisted of 130 nt while the 3'end consisted of 54 nt ending in nine cytosine residues. The closest relative to GcEV1 was Phaseolus vulgaris endornavirus 3. In phylogenetic analyses, GcEV1 clustered with members of the genus Alphaendornavirus. GcEV1 was detected in 57 of 60 G. carolinianum plants collected from three distinct agroecosystems. The virus was not detected in eight other species of the genus Geranium. There was no association of a particular phenotypic trait of the host with the presence or absence of the virus. GcEV1 was transmitted at a rate of 100% in seeds of a self-pollinated G. carolinianum plant.
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Affiliation(s)
- Rachel Herschlag
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Ryo Okada
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | | | - Eliezer Rodrigues de Souto
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Rodrigo A Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA.
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Chiquito-Almanza E, Zamora-Aboytes JM, Medina HR, Acosta-Gallegos JA, Anaya-López JL. Complete genome sequence of a novel comovirus infecting common bean. Arch Virol 2020; 165:1505-1509. [PMID: 32277282 DOI: 10.1007/s00705-020-04610-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/11/2020] [Indexed: 10/24/2022]
Abstract
The complete genome sequence of a novel comovirus identified in Guanajuato, Mexico, in a common bean plant (Phaseolus vulgaris L.) coinfected with Phaseolus vulgaris alphaendornavirus 1 (PvEV-1) and Phaseolus vulgaris alphaendornavirus 2 (PvEV-2) is presented. According to the current ICTV taxonomic criteria, this comovirus corresponds to a new species, and the name "Phaseolus vulgaris severe mosaic virus" (PvSMV) is proposed for this virus based on the observed symptoms of "severe mosaic" syndrome caused by comoviruses in common bean. PvSMV is closely related to bean pod mosaic virus (BPMV), and its genome consists of two polyadenylated RNAs. RNA-1 (GenBank accession number MN837498) is 5969 nucleotides (nt) long and encodes a single polyprotein of 1856 amino acids (aa), with an estimated molecular weight (MW) of 210 kDa, that contains putative proteins responsible for viral replication and proteolytic processing. RNA-2 (GenBank accession number MN837499) is 3762 nt long and encodes a single polyprotein of 1024 aa, with an estimated MW of 114 kDa, that contains putative movement and coat proteins. Cleavage sites were predicted based on similarities in size and homology to aa sequences of other comoviruses available in the GenBank database. Symptoms associated with PvSMV include mosaic, local necrotic lesions, and apical necrosis. This is the first report of a comovirus infecting common bean in Mexico.
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Affiliation(s)
- E Chiquito-Almanza
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Bajío, km 6.5 carretera Celaya-San Miguel de Allende S/N. C.P. 38110, Celaya, GTO, Mexico
| | - J M Zamora-Aboytes
- Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México en Celaya, Celaya, GTO, Mexico
| | - H R Medina
- Departamento de Ingeniería Bioquímica, Tecnológico Nacional de México en Celaya, Celaya, GTO, Mexico
| | - J A Acosta-Gallegos
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Bajío, km 6.5 carretera Celaya-San Miguel de Allende S/N. C.P. 38110, Celaya, GTO, Mexico
| | - J L Anaya-López
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Campo Experimental Bajío, km 6.5 carretera Celaya-San Miguel de Allende S/N. C.P. 38110, Celaya, GTO, Mexico.
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Herschlag R, Escalante C, de Souto ER, Khankhum S, Okada R, Valverde RA. Occurrence of putative endornaviruses in non-cultivated plant species in South Louisiana. Arch Virol 2019; 164:1863-1868. [DOI: 10.1007/s00705-019-04270-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/30/2019] [Indexed: 01/12/2023]
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