1
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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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2
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Wang X, Larrea-Sarmiento A, Olmedo-Velarde A, Al Rwahnih M, Borth W, Suzuki JY, Wall MM, Melzer M, Hu J. Survey of Viruses Infecting Basella alba in Hawaii. PLANT DISEASE 2023; 107:1022-1026. [PMID: 36167515 DOI: 10.1094/pdis-02-22-0449-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Malabar spinach plants (Basella alba, Basellaceae) with leaves exhibiting symptoms of mosaic, rugosity, and malformation were found in a community garden on Oahu, HI in 2018. Preliminary studies using enzyme-linked immunosorbent assay and reverse-transcription (RT)-PCR identified Basella rugose mosaic virus (BaRMV) in symptomatic plants. However, nucleotide sequence analysis of RT-PCR amplicons indicated that additional potyviruses were also present in the symptomatic Malabar spinach. High-throughput sequencing (HTS) analysis was conducted on ribosomal RNA-depleted composite RNA samples of potyvirus-positive plants from three locations. Assembled contigs shared sequences similar to BaRMV, chilli veinal mottle virus (ChiVMV), Alternanthera mosaic virus (AltMV), Basella alba endornavirus (BaEV), broad bean wilt virus 2 (BBWV2), and Iresine viroid 1. Virus- and viroid-specific primers were designed based on HTS sequencing results and used in RT-PCR and Sanger sequencing to confirm the presence of these viruses and the viroid. We tested 63 additional samples from six community gardens for a survey of viruses in Malabar spinach and found that 21 of them were positive for BaRMV, 57 for ChiVMV, 21 for AltMV, 19 for BaEV, and 14 for BBWV2. This is the first characterization of the virome from B. alba.
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Affiliation(s)
- Xupeng Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Adriana Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Alejandro Olmedo-Velarde
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Wayne Borth
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - Jon Y Suzuki
- United States Department of Agriculture, Agricultural Research Service, Pacific Basin Agricultural Research Center, Hilo, HI 96720
| | - Marisa M Wall
- United States Department of Agriculture, Agricultural Research Service, Pacific Basin Agricultural Research Center, Hilo, HI 96720
| | - Michael Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
| | - John Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI 96822
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3
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Adeleke IA, Kavalappara SR, McGregor C, Srinivasan R, Bag S. Persistent, and Asymptomatic Viral Infections and Whitefly-Transmitted Viruses Impacting Cantaloupe and Watermelon in Georgia, USA. Viruses 2022; 14:1310. [PMID: 35746780 PMCID: PMC9227350 DOI: 10.3390/v14061310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Cucurbits in Southeastern USA have experienced a drastic decline in production over the years due to the effect of economically important viruses, mainly those transmitted by the sweet potato whitefly (Bemisia tabaci Gennadius). In cucurbits, these viruses can be found as a single or mixed infection, thereby causing significant yield loss. During the spring of 2021, surveys were conducted to evaluate the incidence and distribution of viruses infecting cantaloupe (n = 80) and watermelon (n = 245) in Georgia. Symptomatic foliar tissues were collected from six counties and sRNA libraries were constructed from seven symptomatic samples. High throughput sequencing (HTS) analysis revealed the presence of three different new RNA viruses in Georgia: cucumis melo endornavirus (CmEV), cucumis melo amalgavirus (CmAV1), and cucumis melo cryptic virus (CmCV). Reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed the presence of CmEV and CmAV1 in 25% and 43% of the total samples tested, respectively. CmCV was not detected using RT-PCR. Watermelon crinkle leaf-associated virus 1 (WCLaV-1), recently reported in GA, was detected in 28% of the samples tested. Furthermore, RT-PCR and PCR analysis of 43 symptomatic leaf tissues collected from the fall-grown watermelon in 2019 revealed the presence of cucurbit chlorotic yellows virus (CCYV), cucurbit yellow stunting disorder virus (CYSDV), and cucurbit leaf crumple virus (CuLCrV) at 73%, 2%, and 81%, respectively. This finding broadens our knowledge of the prevalence of viruses in melons in the fall and spring, as well as the geographical expansion of the WCLaV-1 in GA, USA.
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Affiliation(s)
| | | | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA;
| | | | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA;
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4
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Dong Z, Yin H, Wang X, Lu S, Zuo W, Liu Z, Li Y. Identification of a novel alphaendornavirus from Lonicera maackii. Arch Virol 2022; 167:675-679. [PMID: 35088205 DOI: 10.1007/s00705-021-05347-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/18/2021] [Indexed: 11/02/2022]
Abstract
A new alphaendornavirus, tentatively named "Lonicera maackii alphaendornavirus" (LmEV), was identified in a Lonicera maackii plant in Beijing, China, with leaf abnormality of interveinal chlorosis, and its complete genome sequence was determined using small-RNA deep sequencing. The RNA genome of LmEV is 16,176 nt in length and contains a large open reading frame encoding a polyprotein of 5363 aa with conserved domains including a cysteine-rich region, a viral helicase, and an RNA-dependent RNA polymerase. Sequence comparisons showed that LmEV shared the highest nt and aa sequence identity with Vicia faba alphaendornavirus (VfEV) of the genus Alphaendornavirus. In phylogenetic analysis of the RdRp aa sequence LmEV clustered with members of the genus Alphaendornavirus, closest to VfEV. To our knowledge, this is the first report of a novel alphaendornavirus identified in Lonicera maackii. Its effect on the host plant, if any, remains to be investigated.
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Affiliation(s)
- Zheng Dong
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China.,Key Laboratory for Northern Urban, Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Hang Yin
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China.,Key Laboratory for Northern Urban, Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Xulong Wang
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China.,Key Laboratory for Northern Urban, Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Shuhao Lu
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China.,Key Laboratory for Northern Urban, Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Wenjie Zuo
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China.,Key Laboratory for Northern Urban, Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Zhibin Liu
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China.,Key Laboratory for Northern Urban, Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Yongqiang Li
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China. .,Key Laboratory for Northern Urban, Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China.
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5
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Complete nucleotide sequence of an alphaendornavirus isolated from common buckwheat (Fagopyrum esculentum). Arch Virol 2021; 166:3483-3486. [PMID: 34608525 DOI: 10.1007/s00705-021-05264-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/20/2021] [Indexed: 12/25/2022]
Abstract
A double-stranded RNA (dsRNA) of approximately 16 kbp was isolated from symptomless common buckwheat (Fagopyrum esculentum) plants. The size of the dsRNA suggested that it was the replicative form of an endornavirus. The dsRNA was sequenced, and it consisted of 15,677 nt, containing a single open reading frame that potentially encoded a polyprotein of 5190 aa. The polyprotein contained conserved domains for a viral methyltransferase, viral RNA helicase 1, MSCRAMM family adhesion SdrC, UDP-glycosyltransferase, and viral RNA-dependent RNA polymerase 2. A site-specific nick in the plus strand was detected near the 5' end of the dsRNA. BLASTp analysis showed that the polyprotein shared the highest identity with the polyprotein of winged bean endornavirus 1. Results of phylogenetic analysis supported placing this novel virus from common buckwheat, which was provisionally named "Fagopyrum esculentum endornavirus 1", in the genus Alphaendornavirus of the family Endornaviridae.
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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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7
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Hajake T, Matsuno K, Kasumba DM, Oda H, Kobayashi M, Miyata N, Shinji M, Kogure A, Kasajima N, Okamatsu M, Sakoda Y, Kato H, Fujita T. Broad and systemic immune-modulating capacity of plant-derived dsRNA. Int Immunol 2020; 31:811-821. [PMID: 31367737 DOI: 10.1093/intimm/dxz054] [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: 04/14/2019] [Accepted: 07/31/2019] [Indexed: 01/14/2023] Open
Abstract
Double-stranded RNA (dsRNA) is well characterized as an inducer of anti-viral interferon responses. We previously reported that dsRNA extracted from a specific edible plant possesses an immune-modulating capacity to confer, in mice, resistance against respiratory viruses, including the H1N1 strain of the influenza A virus (IAV). We report here that the systemic immune-activating capacity of the plant-derived dsRNA protected mice from infection by a highly virulent H5N1 strain of the IAV. In addition, subcutaneous inoculation of the dsRNA together with the inactivated virion of the H5N1 strain of the IAV suppressed the lethality of the viral infection as compared with individual inoculation of either dsRNA or HA protein, suggesting its potential usage as a vaccination adjuvant. Moreover, intra-peritoneal inoculation of the dsRNA limited the growth of B16-F10 melanoma cells through the activation of NK cells in murine models. Taken together, this study demonstrated the systemic immune-modulating capacity of a plant-derived dsRNA and its potential for nucleic acid-based clinical applications.
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Affiliation(s)
- Takara Hajake
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.,Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Keita Matsuno
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Kita, Nishi, Kita-ku, Sapporo, Japan
| | - Dacquin M Kasumba
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.,Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Haruka Oda
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.,Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Moe Kobayashi
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Nao Miyata
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.,Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Madoka Shinji
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.,Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Amane Kogure
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.,Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Nodoka Kasajima
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Kita, Nishi, Kita-ku, Sapporo, Japan
| | - Masatoshi Okamatsu
- Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Kita, Nishi, Kita-ku, Sapporo, Japan
| | - Yoshihiro Sakoda
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Kita, Nishi, Kita-ku, Sapporo, Japan.,Laboratory of Microbiology, Department of Disease Control, Graduate School of Veterinary Medicine, Hokkaido University, Kita, Nishi, Kita-ku, Sapporo, Japan
| | - Hiroki Kato
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.,Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.,Institute of Cardiovascular Immunology, University Hospital Bonn, University of Bonn, BMZ Sigmund-Freud-Str., Bonn, Germany
| | - Takashi Fujita
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.,Laboratory of Molecular and Cellular Immunology, Graduate School of Biostudies, Kyoto University, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan
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8
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Rodrigues TB, Petrick JS. Safety Considerations for Humans and Other Vertebrates Regarding Agricultural Uses of Externally Applied RNA Molecules. FRONTIERS IN PLANT SCIENCE 2020; 11:407. [PMID: 32391029 PMCID: PMC7191066 DOI: 10.3389/fpls.2020.00407] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 03/20/2020] [Indexed: 05/13/2023]
Abstract
The potential of double-stranded RNAs (dsRNAs) for use as topical biopesticides in agriculture was recently discussed during an OECD (Organisation for Economic Co-operation and Development) Conference on RNA interference (RNAi)-based pesticides. Several topics were presented and these covered different aspects of RNAi technology, its application, and its potential effects on target and non-target organisms (including both mammals and non-mammals). This review presents information relating to RNAi mechanisms in vertebrates, the history of safe RNA consumption, the biological barriers that contribute to the safety of its consumption, and effects related to humans and other vertebrates as discussed during the conference. We also review literature related to vertebrates exposed to RNA molecules and further consider human health safety assessments of RNAi-based biopesticides. This includes possible routes of exposure other than the ingestion of potential residual material in food and water (such as dermal and inhalation exposures during application in the field), the implications of different types of formulations and RNA structures, and the possibility of non-specific effects such as the activation of the innate immune system or saturation of the RNAi machinery.
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Affiliation(s)
| | - Jay S. Petrick
- Bayer Crop Science, Chesterfield, MO, United States
- *Correspondence: Jay S. Petrick,
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9
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Fukuhara T, Tabara M, Koiwa H, Takahashi H. Effect of asymptomatic infection with southern tomato virus on tomato plants. Arch Virol 2019; 165:11-20. [PMID: 31620899 DOI: 10.1007/s00705-019-04436-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 09/13/2019] [Indexed: 12/20/2022]
Abstract
Southern tomato virus (STV) is often found infecting healthy tomato plants (Solanum lycopersicum). In this study, we compared STV-free and STV-infected plants of cultivar M82 to determine the effect of STV infection on the host plant. STV-free plants exhibited a short and bushy phenotype, whereas STV-infected plants were taller. STV-infected plants produced more fruit than STV-free plants, and the germination rate of seeds from STV-infected plants was higher than that of seeds from STV-free plants. This phenotypic difference was also observed in progeny plants (siblings) derived from a single STV-infected plant in which the transmission rate of STV to progeny plants via the seeds was approximately 86%. These results suggest that the interaction between STV and host plants is mutualistic. Transcriptome analysis revealed that STV infection affects gene expression in the host plant and results in downregulation of genes involved in ethylene biosynthesis and signaling. STV-infected tomato plants might thus be artificially selected due to their superior traits as a crop.
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Affiliation(s)
- Toshiyuki Fukuhara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan. .,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
| | - Midori Tabara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.,Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Hisashi Koiwa
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.,Molecular and Environmental Plant Sciences, Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Hideki Takahashi
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza-Aoba, Sendai, 980-0845, Japan
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10
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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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11
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Velasco L, Arjona-Girona I, Cretazzo E, López-Herrera C. Viromes in Xylariaceae fungi infecting avocado in Spain. Virology 2019; 532:11-21. [PMID: 30986551 DOI: 10.1016/j.virol.2019.03.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/29/2019] [Accepted: 03/29/2019] [Indexed: 12/25/2022]
Abstract
Four isolates of Entoleuca sp., family Xylariaceae, Ascomycota, recovered from avocado rhizosphere in Spain were analyzed for mycoviruses presence. For that, the dsRNAs from the mycelia were extracted and subjected to metagenomics analysis that revealed the presence of eleven viruses putatively belonging to families Partitiviridae, Hypoviridae, Megabirnaviridae, and orders Tymovirales and Bunyavirales, in addition to one ourmia-like virus plus other two unclassified virus species. Moreover, a sequence with 98% nucleotide identity to plant endornavirus Phaseolus vulgaris alphaendornavirus 1 has been identified in the Entoleuca sp. isolates. Concerning the virome composition, the four isolates only differed in the presence of the bunyavirus and the ourmia-like virus, while all other viruses showed common patterns. Specific primers allowed the detection by RT-PCR of these viruses in a collection of Entoleuca sp. and Rosellinia necatrix isolates obtained from roots of avocado trees. Results indicate that intra- and interspecies horizontal virus transmission occur frequently in this pathosystem.
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Affiliation(s)
- Leonardo Velasco
- Instituto Andaluz de Investigación y Formación Agraria (IFAPA), 29140, Churriana, Málaga, Spain.
| | - Isabel Arjona-Girona
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, C.S.I.C, Córdoba, Spain
| | - Enrico Cretazzo
- Instituto Andaluz de Investigación y Formación Agraria (IFAPA), 29140, Churriana, Málaga, Spain
| | - Carlos López-Herrera
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, C.S.I.C, Córdoba, Spain
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12
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Discovery of Cucumis melo endornavirus by deep sequencing of human stool samples in Brazil. Virus Genes 2019; 55:332-338. [PMID: 30915664 DOI: 10.1007/s11262-019-01648-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 02/08/2019] [Indexed: 01/04/2023]
Abstract
The nearly complete genome sequences of two Cucumis melo endornavirus (CmEV) strains were obtained using deep sequencing while investigating fecal samples for the presence of gastroenteritis viruses. The Brazilian CmEV BRA/TO-23 (aa positions 116-5027) and BRA/TO-74 (aa positions 26-5057) strains were nearly identical to the reference CmEV CL-01 (USA) and SJ1 (South Korea) strains, showing 97% and 98% of nucleotide and amino acid identity, respectively. Endornaviruses are not known to be associated with human disease and their presence may simply reflect recent dietary consumption. Metagenomic analyses offered an opportunity to identify for the first time in Brazil a newly described endornavirus species.
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13
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Endornaviruses: persistent dsRNA viruses with symbiotic properties in diverse eukaryotes. Virus Genes 2019; 55:165-173. [DOI: 10.1007/s11262-019-01635-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/07/2019] [Indexed: 10/27/2022]
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14
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Mutuku JM, Wamonje FO, Mukeshimana G, Njuguna J, Wamalwa M, Choi SK, Tungadi T, Djikeng A, Kelly K, Domelevo Entfellner JB, Ghimire SR, Mignouna HD, Carr JP, Harvey JJW. Metagenomic Analysis of Plant Virus Occurrence in Common Bean ( Phaseolus vulgaris) in Central Kenya. Front Microbiol 2018; 9:2939. [PMID: 30581419 PMCID: PMC6293961 DOI: 10.3389/fmicb.2018.02939] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/15/2018] [Indexed: 11/13/2022] Open
Abstract
Two closely related potyviruses, bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV), are regarded as major constraints on production of common bean (Phaseolus vulgaris L.) in Eastern and Central Africa, where this crop provides a high proportion of dietary protein as well as other nutritional, agronomic, and economic benefits. Previous studies using antibody-based assays and indicator plants indicated that BCMV and BCMNV are both prevalent in bean fields in the region but these approaches cannot distinguish between these potyviruses or detect other viruses that may threaten the crop. In this study, we utilized next generation shotgun sequencing for a metagenomic examination of viruses present in bean plants growing at two locations in Kenya: the University of Nairobi Research Farm in Nairobi's Kabete district and at sites in Kirinyaga County. RNA was extracted from leaves of bean plants exhibiting apparent viral symptoms and sequenced on the Illumina MiSeq platform. We detected BCMNV, cucumber mosaic virus (CMV), and Phaseolus vulgaris alphaendornaviruses 1 and 2 (PvEV1 and 2), with CMV present in the Kirinyaga samples. The CMV strain detected in this study was most closely related to Asian strains, which suggests that it may be a recent introduction to the region. Surprisingly, and in contrast to previous surveys, BCMV was not detected in plants at either location. Some plants were infected with PvEV1 and 2. The detection of PvEV1 and 2 suggests these seed transmitted viruses may be more prevalent in Eastern African bean germplasm than previously thought.
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Affiliation(s)
- J. Musembi Mutuku
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Francis O. Wamonje
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Gerardine Mukeshimana
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - Joyce Njuguna
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - Mark Wamalwa
- Biotechnology Department, Kenyatta University, Nairobi, Kenya
| | - Seung-Kook Choi
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Department of Vegetable Research, National Institute of Horticultural and Herbal Science, Rural Development Agency, Wanju County, South Korea
| | - Trisna Tungadi
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Appolinaire Djikeng
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - Krys Kelly
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | | | - Sita R. Ghimire
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - Hodeba D. Mignouna
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - John P. Carr
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Jagger J. W. Harvey
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
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Yang D, Wu M, Zhang J, Chen W, Li G, Yang L. Sclerotinia minor Endornavirus 1, a Novel Pathogenicity Debilitation-Associated Mycovirus with a Wide Spectrum of Horizontal Transmissibility. Viruses 2018; 10:E589. [PMID: 30373273 PMCID: PMC6266790 DOI: 10.3390/v10110589] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 12/02/2022] Open
Abstract
Sclerotinia minor is a phytopathogenic fungus causing sclerotinia blight on many economically important crops. Here, we have characterized the biological and molecular properties of a novel endornavirus, Sclerotinia minor endornavirus 1 (SmEV1), isolated from the hypovirulent strain LC22 of S. minor. The genome of SmEV1 is 12,626 bp long with a single, large open reading frame (ORF), coding for a putative protein of 4020 amino acids. The putative protein contains cysteine-rich region (CRR), viral methyltransferase (MTR), putative DEXDc, viral helicase (Hel), and RNA-dependent RNA polymerase (RdRp) domains. The putative protein and the conserved domains are phylogenetically related to endornaviruses. SmEV1 does not contain a site-specific nick characteristic of most previously described endornaviruses. Hypovirulence and associated traits of strain LC22 and SmEV1 were readily cotransmitted horizontally via hyphal contact to isolates of different vegetative compatibility groups of S. minor. Additionally, SmEV1 in strain LC22 was found capable of being transmitted vertically through sclerotia. Furthermore, mycelium fragments of hypovirulent strain LC22 have a protective activity against attack by S. minor. Taken together, we concluded that SmEV1 is a novel hypovirulence-associated mycovirus with a wide spectrum of transmissibility, and has potential for biological control (virocontrol) of diseases caused by S. minor.
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Affiliation(s)
- Dan Yang
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Mingde Wu
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jing Zhang
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Weidong Chen
- U.S. Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, WA 99164, USA.
| | - Guoqing Li
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Long Yang
- The State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China.
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Peng X, Gan S, Zhang X, Zhai Y, Cai L, Yan F, Zhang S. Complete sequence of a novel alphaendornavirus from the phytopathogenic fungus Arthrocladiella mougeotii. Arch Virol 2018; 163:3467-3470. [PMID: 30220032 DOI: 10.1007/s00705-018-4028-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/30/2018] [Indexed: 11/24/2022]
Abstract
A novel double-stranded RNA (dsRNA) virus, which was provisionally named Arthrocladiella mougeotii endornavirus (AmEV), was isolated from Arthrocladiella mougeotii, the phytopathogenic fungus infecting Lycium chinense in Beijing, China. The genome of AmEV is 11,683 nucleotides in length with a 5' and 3' non-coding region of 16 and 50 nt, respectively, as well as a single 11,617-nt long open reading frame potentially encoding a putative protein of 3,871 amino acids with conserved Helicase and RNA-dependent RNA polymerase (RdRp) domains. Phylogenetic analysis based on the the amino acid sequence of the RdRp showed that AmEV is most closely related to Erysiphe cichoracearum endornavirus (EcEV).
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Affiliation(s)
- Xiaoqin Peng
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Shexiang Gan
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Xiaoting Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Yingying Zhai
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Lina Cai
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Fei Yan
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Songbai Zhang
- Hubei Collaborative Innovation Center for Grain Industry, Engineering Research Center of Ecology and Agricultural Use of Wetland, China Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China.
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Rolland M, Villemot J, Marais A, Theil S, Faure C, Cadot V, Valade R, Vitry C, Rabenstein F, Candresse T. Classical and next generation sequencing approaches unravel Bymovirus diversity in barley crops in France. PLoS One 2017; 12:e0188495. [PMID: 29182661 PMCID: PMC5705140 DOI: 10.1371/journal.pone.0188495] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 11/08/2017] [Indexed: 11/18/2022] Open
Abstract
Despite the generalized use of cultivars carrying the rym4 resistance gene, the impact of viral mosaic diseases on winter barleys increased in recent years in France. This change could reflect i) an increased prevalence of the rym4 resistance-breaking pathotype of Barley yellow mosaic virus Y (BaYMV-2), ii) the emergence of rym4 resistance-breaking pathotypes of Barley mild mosaic virus (BaMMV) or iii) the emergence of other viruses. A study was undertaken to determine the distribution and diversity of viruses causing yellow mosaic disease. A collection of 241 symptomatic leaf samples from susceptible, rym4 and rym5 varieties was gathered from 117 sites. The viruses present in all samples were identified by specific RT-PCR assays and, for selected samples, by double-stranded RNA next-generation sequencing (NGS). The results show that BaYMV-2 is responsible for the symptoms observed in varieties carrying the resistance gene rym4. In susceptible varieties, both BaYMV-1 and BaYMV-2 were detected, together with BaMMV. Phylogenetic analyses indicate that the rym4 resistance-breaking ability independently evolved in multiple genetic backgrounds. Parallel analyses revealed a similar scenario of multiple independent emergence events in BaMMV for rym5 resistance-breaking, likely involving multiple amino acid positions in the viral-linked genome protein. NGS analyses and classical techniques provided highly convergent results, highlighting and validating the power of NGS approaches for diagnostics and viral population characterization.
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Affiliation(s)
- Mathieu Rolland
- Groupe d'Etude et de contrôle des Variétés Et des Semences, Beaucouzé, France
| | - Julie Villemot
- Groupe d'Etude et de contrôle des Variétés Et des Semences, Beaucouzé, France
| | - Armelle Marais
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
| | - Sébastien Theil
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
| | - Chantal Faure
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
| | - Valérie Cadot
- Groupe d'Etude et de contrôle des Variétés Et des Semences, Beaucouzé, France
| | - Romain Valade
- ARVALIS–Institut du végétal, Thiverval-Grignon, France
| | - Cindy Vitry
- ARVALIS–Institut du végétal, Thiverval-Grignon, France
| | | | - Thierry Candresse
- Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de Bordeaux, Villenave d’Ornon, France
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Kasumba DM, Hajake T, Oh SW, Kotenko SV, Kato H, Fujita T. A Plant-Derived Nucleic Acid Reconciles Type I IFN and a Pyroptotic-like Event in Immunity against Respiratory Viruses. THE JOURNAL OF IMMUNOLOGY 2017; 199:2460-2474. [DOI: 10.4049/jimmunol.1700523] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/23/2017] [Indexed: 12/14/2022]
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19
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Nordenstedt N, Marcenaro D, Chilagane D, Mwaipopo B, Rajamäki ML, Nchimbi-Msolla S, Njau PJR, Mbanzibwa DR, Valkonen JPT. Pathogenic seedborne viruses are rare but Phaseolus vulgaris endornaviruses are common in bean varieties grown in Nicaragua and Tanzania. PLoS One 2017; 12:e0178242. [PMID: 28542624 PMCID: PMC5444779 DOI: 10.1371/journal.pone.0178242] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 05/10/2017] [Indexed: 12/29/2022] Open
Abstract
Common bean (Phaseolus vulgaris) is an annual grain legume that was domesticated in Mesoamerica (Central America) and the Andes. It is currently grown widely also on other continents including Africa. We surveyed seedborne viruses in new common bean varieties introduced to Nicaragua (Central America) and in landraces and improved varieties grown in Tanzania (eastern Africa). Bean seeds, harvested from Nicaragua and Tanzania, were grown in insect-controlled greenhouse or screenhouse, respectively, to obtain leaf material for virus testing. Equal amounts of total RNA from different samples were pooled (30-36 samples per pool), and small RNAs were deep-sequenced (Illumina). Assembly of the reads (21-24 nt) to contiguous sequences and searches for homologous viral sequences in databases revealed Phaseolus vulgaris endornavirus 1 (PvEV-1) and PvEV-2 in the bean varieties in Nicaragua and Tanzania. These viruses are not known to cause symptoms in common bean and are considered non-pathogenic. The small-RNA reads from each pool of samples were mapped to the previously characterized complete PvEV-1 and PvEV-2 sequences (genome lengths ca. 14 kb and 15 kb, respectively). Coverage of the viral genomes was 87.9-99.9%, depending on the pool. Coverage per nucleotide ranged from 5 to 471, confirming virus identification. PvEV-1 and PvEV-2 are known to occur in Phaseolus spp. in Central America, but there is little previous information about their occurrence in Nicaragua, and no information about occurrence in Africa. Aside from Cowpea mild mosaic virus detected in bean plants grown from been seeds harvested from one region in Tanzania, no other pathogenic seedborne viruses were detected. The low incidence of infections caused by pathogenic viruses transmitted via bean seeds may be attributable to new, virus-resistant CB varieties released by breeding programs in Nicaragua and Tanzania.
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Affiliation(s)
- Noora Nordenstedt
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Delfia Marcenaro
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Nicaraguan Institute of Agricultural Technology (CNIAB-INTA), Managua, Nicaragua
| | - Daudi Chilagane
- Sokoine University of Agriculture, Morogoro, Tanzania
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | - Beatrice Mwaipopo
- Sokoine University of Agriculture, Morogoro, Tanzania
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | | | | | | | | | - Jari P. T. Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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Ong JW, Li H, Sivasithamparam K, Dixon KW, Jones MG, Wylie SJ. Novel Endorna-like viruses, including three with two open reading frames, challenge the membership criteria and taxonomy of the Endornaviridae. Virology 2016; 499:203-211. [DOI: 10.1016/j.virol.2016.08.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/11/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
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21
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Hao F, Zhou Z, Wu M, Li G. Molecular characterization of a novel endornavirus from the phytopathogenic fungus Botrytis cinerea. Arch Virol 2016; 162:313-316. [PMID: 27722992 DOI: 10.1007/s00705-016-3106-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 10/04/2016] [Indexed: 11/28/2022]
Abstract
The complete sequence of a novel endornavirus (Botrytis cinerea endornavirus 1, BcEV1) from the phytopathogenic fungus Botrytis cinerea strain HBtom-372 was determined. The BcEV1 coding strand is 11,557 nucleotides long, possessing an open reading frame (ORF) that codes for a polyprotein of 3,787 amino acid residues and lacks a site-specific nick. The polyprotein contains viral methyltransferase (MTR) domain, a cysteine-rich region (CRR), two putative viral helicase (DEXDc-like and Hel-1) domains, and an RNA-dependent RNA polymerase_2 (RdRp_2) domain. In phylogenetic analysis, BcEV1 clustered with several fungal endornaviruses, forming an independent clade, and it was detected in 4.2 % of B. cinerea strains collected from central China.
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Affiliation(s)
- Fangmin Hao
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ziliang Zhou
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mingde Wu
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. .,The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Guoqing Li
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,The Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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22
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Ecological risk assessment for DvSnf7 RNA: A plant-incorporated protectant with targeted activity against western corn rootworm. Regul Toxicol Pharmacol 2016; 81:77-88. [PMID: 27494948 DOI: 10.1016/j.yrtph.2016.08.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 12/31/2022]
Abstract
MON 87411 maize, which expresses DvSnf7 RNA, was developed to provide an additional mode of action to confer protection against corn rootworm (Diabrotica spp.). A critical step in the registration of a genetically engineered crop with an insecticidal trait is performing an ecological risk assessment to evaluate the potential for adverse ecological effects. For MON 87411, an assessment plan was developed that met specific protection goals by characterizing the routes and levels of exposure, and testing representative functional taxa that would be directly or indirectly exposed in the environment. The potential for toxicity of DvSnf7 RNA was evaluated with a harmonized battery of non-target organisms (NTOs) that included invertebrate predators, parasitoids, pollinators, soil biota as well as aquatic and terrestrial vertebrate species. Laboratory tests evaluated ecologically relevant endpoints such as survival, growth, development, and reproduction and were of sufficient duration to assess the potential for adverse effects. No adverse effects were observed with any species tested at, or above, the maximum expected environmental concentration (MEEC). All margins of exposure for NTOs were >10-fold the MEEC. Therefore, it is reasonable to conclude that exposure to DvSnf7 RNA, both directly and indirectly, is safe for NTOs at the expected field exposure levels.
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Du Z, Lin W, Qiu P, Liu X, Guo L, Wu K, Zhang S, Wu Z. Complete sequence of a double-stranded RNA from the phytopathogenic fungus Erysiphe cichoracearum that might represent a novel endornavirus. Arch Virol 2016; 161:2343-6. [PMID: 27255746 DOI: 10.1007/s00705-016-2911-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/25/2016] [Indexed: 11/30/2022]
Abstract
A double-stranded RNA (dsRNA) HBJZ1506 recovered from the phytopathogenic fungus Erysiphe cichoracearum infecting Calendula officinalis in Jingzhou, Hubei Province, China, was sequenced. HBJZ1506 comprises 11,908 nucleotides (nt) and contains a 11,859-nt-long open reading frame (ORF) coding for a polypeptide that is 61 % identical to that of a putative endornavirus named grapevine endophyte endornavirus (GeEV). The putative polyprotein has an RNA-dependent RNA polymerase (RdRp) domain and an RNA helicase domain, which show homology to and have an arrangement that is similar to that of their counterparts in approved or putative endornaviruses. In a phylogenetic tree constructed using amino acid sequences of the RdRp region of HBJZ1506 and selected endornaviruses, HBJZ1506 clustered with endornaviruses and formed a well-supported monophyletic branch with GeEV. These results suggest that HBJZ1506 might represent a novel endornavirus, for which the name Erysiphe cichoracearum endornavirus (EcEV) is proposed.
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Affiliation(s)
- Zhenguo Du
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Wenzhong Lin
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ping Qiu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xiaojuan Liu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Lingfang Guo
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Kangcheng Wu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Songbai Zhang
- Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, 434025, Hubei, China.
| | - Zujian Wu
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Plant Protection College, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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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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25
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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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26
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Candresse T, Marais A, Sorrentino R, Faure C, Theil S, Cadot V, Rolland M, Villemot J, Rabenstein F. Complete genomic sequence of barley (Hordeum vulgare) endornavirus (HvEV) determined by next-generation sequencing. Arch Virol 2015; 161:741-3. [PMID: 26666441 DOI: 10.1007/s00705-015-2709-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/30/2015] [Indexed: 11/24/2022]
Abstract
Endornaviruses are unusual plant-, fungus- and oomycete-infecting viruses with a large, ca 14- to 17-kb linear double-stranded RNA (dsRNA) genome and a persistent lifestyle. The complete genome sequence of an endornavirus from the barley (Hordeum vulgare) Nerz variety was determined from paired Illumina MySeq reads derived from purified dsRNAs. The genome is 14,243 nt long, with 5' and 3' non-coding regions of 207 and 47 nt, respectively. It encodes a single large protein of 4663 amino acids that carries conserved motifs for a methyltransferase, a helicase and an RNA-dependent RNA polymerase. The sequence of Hordeum vulgare endornavirus (HvEV) carries all the hallmarks of a typical member of the genus Endornavirus, with the exception of an UDP-glycosyltransferase motif observed in many, but not all, endornaviral genomes.
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Affiliation(s)
- Thierry Candresse
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France. .,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France.
| | - Armelle Marais
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France.,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Roberto Sorrentino
- Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", 80055, Portici, Italy
| | - Chantal Faure
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France.,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- INRA, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France.,Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Valérie Cadot
- GEVES, 25 rue Georges Morel, CS 90024, 49071, Beaucouzé Cedex, France
| | - Mathieu Rolland
- GEVES, 25 rue Georges Morel, CS 90024, 49071, Beaucouzé Cedex, France
| | - Julie Villemot
- GEVES, 25 rue Georges Morel, CS 90024, 49071, Beaucouzé Cedex, France
| | - Frank Rabenstein
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kuhn-Institute, Federal Research Institute for Cultivated Plants, Erwin-Baur-Straße 27, 06484, Quedlinburg, Germany
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27
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Complete genome sequence of a novel endornavirus isolated from hot pepper. Arch Virol 2015; 160:3153-6. [DOI: 10.1007/s00705-015-2616-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/15/2015] [Indexed: 11/26/2022]
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28
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Bruenn JA, Warner BE, Yerramsetty P. Widespread mitovirus sequences in plant genomes. PeerJ 2015; 3:e876. [PMID: 25870770 PMCID: PMC4393810 DOI: 10.7717/peerj.876] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/13/2015] [Indexed: 11/25/2022] Open
Abstract
The exploration of the evolution of RNA viruses has been aided recently by the discovery of copies of fragments or complete genomes of non-retroviral RNA viruses (Non-retroviral Endogenous RNA Viral Elements, or NERVEs) in many eukaryotic nuclear genomes. Among the most prominent NERVEs are partial copies of the RNA dependent RNA polymerase (RdRP) of the mitoviruses in plant mitochondrial genomes. Mitoviruses are in the family Narnaviridae, which are the simplest viruses, encoding only a single protein (the RdRP) in their unencapsidated viral plus strand. Narnaviruses are known only in fungi, and the origin of plant mitochondrial mitovirus NERVEs appears to be horizontal transfer from plant pathogenic fungi. At least one mitochondrial mitovirus NERVE, but not its nuclear copy, is expressed.
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Affiliation(s)
- Jeremy A Bruenn
- Department of Biological Sciences, State University of New York at Buffalo , Buffalo, NY , USA
| | - Benjamin E Warner
- Department of Biological Sciences, State University of New York at Buffalo , Buffalo, NY , USA
| | - Pradeep Yerramsetty
- Department of Biological Sciences, State University of New York at Buffalo , Buffalo, NY , USA
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29
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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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30
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Abstract
Linear double-stranded RNAs (dsRNAs) of about 15 kbp in length are often found from healthy plants, such as bell pepper and rice plants. Nucleotide sequencing and phylogenetic analyses reveal that these dsRNAs are not transcribed from host genomic DNAs, encode a single long open reading frame (ORF) with a viral RNA-dependent RNA polymerase domain, and contain a site-specific nick in the 5' region of their coding strands. Consequently the International Committee on Taxonomy of Viruses has approved that these dsRNAs are viruses forming a distinct taxon, the family Endornaviridae the genus Endornavirus. Endornaviruses have common properties that differ from those of conventional viruses: they have no obvious effect on the phenotype of their host plants, and they are efficiently transmitted to the next generation via both pollen and ova, but their horizontal transfer to other plants has never been proven. Conventional single-stranded RNA viruses, such as cucumber mosaic virus, propagate hugely and systemically in host plants to sometime kill their hosts eventually and transmit horizontally (infect to other plants). In contrast, copy numbers of endornaviruses are low and constant (about 100 copies/cell), and they symbiotically propagate with host plants and transmit vertically. Therefore, endornaviruses are unique plant viruses with symbiotic properties.
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31
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Petrick JS, Moore WM, Heydens WF, Koch MS, Sherman JH, Lemke SL. A 28-day oral toxicity evaluation of small interfering RNAs and a long double-stranded RNA targeting vacuolar ATPase in mice. Regul Toxicol Pharmacol 2014; 71:8-23. [PMID: 25445299 DOI: 10.1016/j.yrtph.2014.10.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
Abstract
New biotechnology-derived crop traits have been developed utilizing the natural process of RNA interference (RNAi). However, plant-produced double stranded RNAs (dsRNAs) are not known to present a hazard to mammals because numerous biological barriers limit uptake and potential for activity. To evaluate this experimentally, dsRNA sequences matching the mouse vATPase gene (an established target for control of corn rootworms) were evaluated in a 28-day toxicity study with mice. Test groups were orally gavaged with escalating doses of either a pool of four 21-mer vATPase small interfering RNAs (siRNAs) or a 218-base pair vATPase dsRNA. There were no treatment-related effects on body weight, food consumption, clinical observations, clinical chemistry, hematology, gross pathology, or histopathology endpoints. The highest dose levels tested were considered to be the no observed adverse effect levels (NOAELs) for the 21-mer siRNAs (48 mg/kg/day) and the 218 bp dsRNA (64 mg/kg/day). As an additional exploratory endpoint, vATPase gene expression, was evaluated in selected gastrointestinal tract and systemic tissues. The results of this assay did not indicate treatment-related suppression of vATPase. The results of this study indicate that orally ingested dsRNAs, even those targeting a gene in the test species, do not produce adverse health effects in mammals.
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Affiliation(s)
- Jay S Petrick
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA.
| | - William M Moore
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA
| | - William F Heydens
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA
| | - Michael S Koch
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA
| | - James H Sherman
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA
| | - Shawna L Lemke
- Monsanto Company, 800 North Lindbergh Boulevard, Creve Coeur, MO 63167, USA
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32
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Okada R, Kiyota E, Moriyama H, Toshiyuki F, Valverde RA. A new endornavirus species infecting Malabar spinach (Basella alba L.). Arch Virol 2014; 159:807-9. [PMID: 24122112 DOI: 10.1007/s00705-013-1875-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 09/30/2013] [Indexed: 11/27/2022]
Abstract
A putative new endornavirus was isolated from Malabar spinach (Basella alba). The viral dsRNA consisted of 14,027 nt with a single ORF that coded for a polyprotein of 4,508 aa. The genome organization was similar to that of four other endornaviruses. Conserved domains for helicase-1, capsular synthase, UDP-glucose-glycosyltransferase (UGT), and RdRp were detected. Infected plants were phenotypically undistinguishable from healthy ones. The name Basella alba endornavirus is proposed for the virus isolated from Malabar spinach.
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33
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Complete nucleotide sequence and genome organization of an endornavirus from bottle gourd (Lagenaria siceraria) in California, U.S.A. Virus Genes 2014; 49:163-8. [PMID: 24818693 DOI: 10.1007/s11262-014-1064-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/21/2014] [Indexed: 10/25/2022]
Abstract
The full-length nucleotide sequence and genome organization of an Endornavirus isolated from ornamental hard shell bottle gourd plants (Lagenaria siceraria (Molina) Standl.) in California (CA), USA tentatively named L. siceraria endornavirus-California (LsEV-CA) was determined. The LsEV-CA genome was 15088 bp in length, with a G + C content of 36.55 %. The lengths of the 5' and 3' untranslated regions were 111 and 52 bp, respectively. The genome of LsEV-CA contained one large ORF encoding a 576 kDa polyprotein. The predicted protein contains two glycosyltransferase motifs, as well as RNA-dependent RNA polymerase and helicase domains. LsEV-CA was detected in healthy-looking field-grown gourd plants, as well as plants expressing yellows symptoms. It was also detected in non-symptomatic greenhouse-grown gourd seedlings grown from seed obtained from the same field sites. These preliminary data indicate that LsEV-CA is likely not associated with the gourd-yellows syndrome observed in the field.
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34
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Decker CJ, Parker R. Analysis of double-stranded RNA from microbial communities identifies double-stranded RNA virus-like elements. Cell Rep 2014; 7:898-906. [PMID: 24767992 PMCID: PMC4117469 DOI: 10.1016/j.celrep.2014.03.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 03/12/2014] [Accepted: 03/19/2014] [Indexed: 01/08/2023] Open
Abstract
Double-stranded RNA (dsRNA) can function as genetic information and may have served as genomic material before the existence of DNA-based life. By developing a method to purify dsRNA, we have investigated the diversity of dsRNA in microbial populations. We detect large dsRNAs in multiple microbial populations. Analysis of an aquatic microbial population reveals that some dsRNA sequences match metagenomic DNA, suggesting that microbes contain pools of sense-antisense transcripts. In addition, ∼30% of the dsRNA sequences are not present in the corresponding DNA pool and are strongly biased toward encoding novel proteins. Of these "dsRNA unique" sequences, only a small percentage share similarity to known viruses, a large fraction assemble into RNA virus-like contigs, and the remaining fraction has an unexplained origin. These results have uncovered dsRNA virus-like elements and underscore that dsRNA potentially represents an additional reservoir of genetic information in microbial populations.
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Affiliation(s)
- Carolyn J Decker
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80303, USA
| | - Roy Parker
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80303, USA.
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35
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Chen X, Punja ZK. Characterization of a novel dsRNA endornavirus in the plant pathogenic fungus Thielaviopsis basicola. Mycology 2014. [DOI: 10.1080/21501203.2014.884181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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36
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Abstract
Saccharomyces cerevisiae has been a key experimental organism for the study of infectious diseases, including dsRNA viruses, ssRNA viruses, and prions. Studies of the mechanisms of virus and prion replication, virus structure, and structure of the amyloid filaments that are the basis of yeast prions have been at the forefront of such studies in these classes of infectious entities. Yeast has been particularly useful in defining the interactions of the infectious elements with cellular components: chromosomally encoded proteins necessary for blocking the propagation of the viruses and prions, and proteins involved in the expression of viral components. Here, we emphasize the L-A dsRNA virus and its killer-toxin-encoding satellites, the 20S and 23S ssRNA naked viruses, and the several infectious proteins (prions) of yeast.
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37
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Complete genome of a novel endornavirus assembled from next-generation sequence data. J Virol 2013; 86:13142. [PMID: 23118465 DOI: 10.1128/jvi.02538-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Endornaviruses have large double-stranded RNA (dsRNA) genomes that carry a single open reading frame (ORF). Here we report the complete genome of a novel endornavirus, assembled from next-generation sequence data generated from Vitis vinifera-extracted dsRNA. Two different fungal hosts have been identified for this virus, suggesting that horizontal transmission of the virus is possible.
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38
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Okada R, Yong CK, Valverde RA, Sabanadzovic S, Aoki N, Hotate S, Kiyota E, Moriyama H, Fukuhara T. Molecular characterization of two evolutionarily distinct endornaviruses co-infecting common bean (Phaseolus vulgaris). J Gen Virol 2013; 94:220-229. [DOI: 10.1099/vir.0.044487-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
Two high-molecular-mass dsRNAs of approximately 14 and 15 kbp were isolated from the common bean (Phaseolus vulgaris) cultivar Black Turtle Soup. These dsRNAs did not appear to cause obvious disease symptoms, and were transmitted through seeds at nearly 100 % efficiency. Sequence information indicates that they are the genomes of distinct endornavirus species, for which the names Phaseolus vulgaris endornavirus 1 (PvEV-1) and Phaseolus vulgaris endornavirus 2 (PvEV-2) are proposed. The PvEV-1 genome consists of 13 908 bp and potentially encodes a single polyprotein of 4496 aa, while that of PvEV-2 consists of 14 820 bp and potentially encodes a single ORF of 4851 aa. PvEV-1 is more similar to Oryza sativa endornavirus, while PvEV-2 is more similar to bell pepper endornavirus. Both viruses have a site-specific nick near the 5′ region of the coding strand, which is a common property of the endornaviruses. Their polyproteins contain domains of RNA helicase, UDP-glycosyltransferase and RNA-dependent RNA polymerase, which are conserved in other endornaviruses. However, a viral methyltransferase domain was found in the N-terminal region of PvEV-2, but was absent in PvEV-1. Results of cell-fractionation studies suggested that their subcellular localizations were different. Most endornavirus-infected bean cultivars tested were co-infected with both viruses.
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Affiliation(s)
- Ryo Okada
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Chee Keat Yong
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Rodrigo A. Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, 70803, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Nanako Aoki
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Shunsuke Hotate
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Eri Kiyota
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Toshiyuki Fukuhara
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
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39
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Feldman TS, Morsy MR, Roossinck MJ. Are communities of microbial symbionts more diverse than communities of macrobial hosts? Fungal Biol 2012; 116:465-77. [DOI: 10.1016/j.funbio.2012.01.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 01/12/2012] [Accepted: 01/19/2012] [Indexed: 11/16/2022]
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40
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Abstract
A number of avocado (Persea americana) cultivars are known to contain high-molecular-weight double-stranded RNA (dsRNA) molecules for which a viral nature has been suggested, although sequence data are not available. Here we report the cloning and complete sequencing of a 13.5-kbp dsRNA virus isolated from avocado and show that it corresponds to the genome of a new species of the genus Endornavirus (family Endornaviridae), tentatively named Persea americana endornavirus (PaEV).
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41
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Okada R, Kiyota E, Sabanadzovic S, Moriyama H, Fukuhara T, Saha P, Roossinck MJ, Severin A, Valverde RA. Bell pepper endornavirus: molecular and biological properties, and occurrence in the genus Capsicum. J Gen Virol 2011; 92:2664-2673. [DOI: 10.1099/vir.0.034686-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Bell peppers (Capsicum annuum) harbour a large dsRNA virus. The linear genome (14.7 kbp) of two isolates from Japanese and USA bell pepper cultivars were completely sequenced and compared. They shared extensive sequence identity and contained a single, long ORF encoding a 4815 aa protein. This polyprotein contained conserved motifs of putative viral methyltransferase (MTR), helicase 1 (Hel-1), UDP-glycosyltransferase and RNA-dependent RNA polymerase. This unique arrangement of conserved domains has not been reported in any of the known endornaviruses. Hence this virus, for which the name Bell pepper endornavirus (BPEV) is proposed, is a distinct species in the genus Endornavirus (family Endornaviridae). The BPEV-encoded polyprotein contains a cysteine-rich region between the MTR and Hel-1 domains, with conserved CXCC motifs shared among several endornaviruses, suggesting an additional functional domain. In agreement with general endornavirus features, BPEV contains a nick in the positive-strand RNA molecule. The virus was detected in all bell pepper cultivars tested and transmitted through seed but not by graft inoculations. Analysis of dsRNA patterns and RT-PCR using degenerate primers revealed putative variants of BPEV, or closely related species, infecting other C. annuum genotypes and three other Capsicum species (C. baccatum, C. chinense and C. frutescens).
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Affiliation(s)
- Ryo Okada
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Eri Kiyota
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Hiromitsu Moriyama
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Toshiyuki Fukuhara
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Prasenjit Saha
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA
| | - Marilyn J. Roossinck
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA
| | - Ake Severin
- Laboratoire de Physiologie Vegetale, Universite de Cocody-Abidjan, UFR Biosciences, 22 BP, 582 Abidjan 22, Côte d'Ivoire
| | - Rodrigo A. Valverde
- Department of Plant Pathology & Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
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42
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Roossinck MJ, Sabanadzovic S, Okada R, Valverde RA. The remarkable evolutionary history of endornaviruses. J Gen Virol 2011; 92:2674-2678. [DOI: 10.1099/vir.0.034702-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The family Endornaviridae contains several members from diverse hosts, including plants, fungi and oomycetes. They are found as large dsRNA elements with a nick in the coding strand. All members encode a conserved RNA-dependent RNA polymerase, but no other domain that is conserved among all members. Based on the conserved domain database comparison the various domains have different origins, indicating a highly modular evolutionary history. In some cases, domains with similar putative functions are found that are derived from different protein families, indicating convergent evolution for a required function.
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Affiliation(s)
- Marilyn J. Roossinck
- The Samuel Roberts Noble Foundation, Plant Biology Division, Ardmore, OK 73402, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Ryo Okada
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Rodrigo A. Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
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43
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Desbiez C, Moury B, Lecoq H. The hallmarks of "green" viruses: do plant viruses evolve differently from the others? INFECTION GENETICS AND EVOLUTION 2011; 11:812-24. [PMID: 21382520 DOI: 10.1016/j.meegid.2011.02.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 02/22/2011] [Accepted: 02/24/2011] [Indexed: 12/13/2022]
Abstract
All viruses are obligatory parasites that must develop tight interactions with their hosts to complete their infectious cycle. Viruses infecting plants share many structural and functional similarities with those infecting other organisms, particularly animals and fungi. Quantitative data regarding their evolutionary mechanisms--generation of variability by mutation and recombination, changes in populations by selection and genetic drift have been obtained only recently, and appear rather similar to those measured for animal viruses.This review presents an update of our knowledge of the phylogenetic and evolutionary characteristics of plant viruses and their relation to their plant hosts, in comparison with viruses infecting other organisms.
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Affiliation(s)
- C Desbiez
- INRA, Unité de Pathologie Végétale UR407, F-84140 Montfavet, France.
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44
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Fukuhara T, Urayama S, Okada R, Kiyota E, Moriyama H. Detection of long and short double-stranded RNAs. Methods Mol Biol 2011; 744:129-44. [PMID: 21533690 DOI: 10.1007/978-1-61779-123-9_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In RNA interference (RNAi), long double-stranded RNAs (dsRNAs) of more than 100 nucleotides (nt) are diced into short dsRNAs (small interfering RNAs, siRNAs) of about 21-24 nt, the guide strand of which is incorporated into the RNA-induced silencing complex (RISC) that slices a specific mRNA. Consequently viral dsRNAs are known as potent inducers for RNAi, which probably originated from a defense mechanism against nucleic acid parasites. Therefore detection of long and short dsRNAs must be crucial techniques for RNAi or virus research. The methods for simple and sensitive detection of short dsRNAs (siRNAs) by northern hybridization, isolation of long dsRNAs by CF-11 cellulose chromatography, and detection of long dsRNAs by agarose gel electrophoresis and northern hybridization are described here.
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Affiliation(s)
- Toshiyuki Fukuhara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Tokyo, Japan.
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45
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Stielow B, Klenk HP, Menzel W. Complete genome sequence of the first endornavirus from the ascocarp of the ectomycorrhizal fungus Tuber aestivum Vittad. Arch Virol 2010; 156:343-5. [DOI: 10.1007/s00705-010-0875-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 11/24/2010] [Indexed: 11/28/2022]
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46
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Abstract
The vast majority of well-characterized eukaryotic viruses are those that cause acute or chronic infections in humans and domestic plants and animals. However, asymptomatic persistent viruses have been described in animals, and are thought to be sources for emerging acute viruses. Although not previously described in these terms, there are also many viruses of plants that maintain a persistent lifestyle. They have been largely ignored because they do not generally cause disease. The persistent viruses in plants belong to the family Partitiviridae or the genus Endornavirus. These groups also have members that infect fungi. Phylogenetic analysis of the partitivirus RNA-dependent RNA polymerase genes suggests that these viruses have been transmitted between plants and fungi. Additional families of viruses traditionally thought to be fungal viruses are also found frequently in plants, and may represent a similar scenario of persistent lifestyles, and some acute or chronic viruses of crop plants may maintain a persistent lifestyle in wild plants. Persistent, chronic and acute lifestyles of plant viruses are contrasted from both a functional and evolutionary perspective, and the potential role of these lifestyles in host evolution is discussed.
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Affiliation(s)
- Marilyn J Roossinck
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73402, USA.
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47
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Rastgou M, Habibi MK, Izadpanah K, Masenga V, Milne RG, Wolf YI, Koonin EV, Turina M. Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin. J Gen Virol 2009; 90:2525-2535. [PMID: 19535502 PMCID: PMC4091139 DOI: 10.1099/vir.0.013086-0] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 06/15/2009] [Indexed: 01/12/2023] Open
Abstract
Ourmia melon virus (OuMV), Epirus cherry virus (EpCV) and Cassava virus C (CsVC) are three species placed in the genus Ourmiavirus. We cloned and sequenced their RNA genomes. The sizes of the three genomic RNAs of OuMV, the type member of the genus, were 2814, 1064 and 974 nt and each had one open reading frame. RNA1 potentially encoded a 97.5 kDa protein carrying the GDD motif typical of RNA-dependent RNA polymerases (RdRps). The putative RdRps of ourmiaviruses are distantly related to known viral RdRps, with the closest similarity and phylogenetic affinity observed with fungal viruses of the genus Narnaviridae. RNA2 encoded a 31.6 kDa protein which, expressed in bacteria as a His-tag fusion protein and in plants through agroinfiltration, reacted specifically with antibodies made against tubular structures found in the cytoplasm. The ORF2 product is significantly similar to movement proteins of the genus Tombusviridae, and phylogenetic analysis supported this evolutionary relationship. The product of OuMV ORF3 is a 23.8 kDa protein. This protein was also expressed in bacteria and plants, and reacted specifically with antisera against the OuMV coat protein. The sequence of the ORF3 protein showed limited but significant similarity to capsid proteins of several plant and animal viruses, although phylogenetic analysis failed to reveal its most likely origin. Taken together, these results indicate that ourmiaviruses comprise a unique group of plant viruses that might have evolved by reassortment of genomic segments of RNA viruses infecting hosts belonging to different eukaryotic kingdoms, in particular, fungi and plants.
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Affiliation(s)
- M Rastgou
- Department of Plant Protection, College of Agriculture, Urmia University, Urmia, Iran
- Plant Protection Department, Faculty of Horticultural Science & Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - M K Habibi
- Plant Protection Department, Faculty of Horticultural Science & Plant Protection, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - K Izadpanah
- Plant Virology Research Center, Shiraz University, Shiraz, Iran
| | - V Masenga
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - R G Milne
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135 Torino, Italy
| | - Y I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - E V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - M Turina
- Istituto di Virologia Vegetale, CNR, Strada delle Cacce 73, 10135 Torino, Italy
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Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M. Metagenomic analysis of viruses in reclaimed water. Environ Microbiol 2009; 11:2806-20. [PMID: 19555373 DOI: 10.1111/j.1462-2920.2009.01964.x] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Reclaimed water use is an important component of sustainable water resource management. However, there are concerns regarding pathogen transport through this alternative water supply. This study characterized the viral community found in reclaimed water and compared it with viruses in potable water. Reclaimed water contained 1000-fold more virus-like particles than potable water, having approximately 10(8) VLPs per millilitre. Metagenomic analyses revealed that most of the viruses in both reclaimed and potable water were novel. Bacteriophages dominated the DNA viral community in both reclaimed and potable water, but reclaimed water had a distinct phage community based on phage family distributions and host representation within each family. Eukaryotic viruses similar to plant pathogens and invertebrate picornaviruses dominated RNA metagenomic libraries. Established human pathogens were not detected in reclaimed water viral metagenomes, which contained a wealth of novel single-stranded DNA and RNA viruses related to plant, animal and insect viruses. Therefore, reclaimed water may play a role in the dissemination of highly stable viruses. Information regarding viruses present in reclaimed water but not in potable water can be used to identify new bioindicators of water quality. Future studies will need to investigate the infectivity and host range of these viruses to evaluate the impacts of reclaimed water use on human and ecosystem health.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, St. Petersburg, Florida, USA
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Annotated ESTs from various tissues of the brown planthopper Nilaparvata lugens: a genomic resource for studying agricultural pests. BMC Genomics 2008; 9:117. [PMID: 18315884 PMCID: PMC2311293 DOI: 10.1186/1471-2164-9-117] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Accepted: 03/03/2008] [Indexed: 11/21/2022] Open
Abstract
Background The brown planthopper (BPH), Nilaparvata lugens (Hemiptera, Delphacidae), is a serious insect pests of rice plants. Major means of BPH control are application of agricultural chemicals and cultivation of BPH resistant rice varieties. Nevertheless, BPH strains that are resistant to agricultural chemicals have developed, and BPH strains have appeared that are virulent against the resistant rice varieties. Expressed sequence tag (EST) analysis and related applications are useful to elucidate the mechanisms of resistance and virulence and to reveal physiological aspects of this non-model insect, with its poorly understood genetic background. Results More than 37,000 high-quality ESTs, excluding sequences of mitochondrial genome, microbial genomes, and rDNA, have been produced from 18 libraries of various BPH tissues and stages. About 10,200 clusters have been made from whole EST sequences, with average EST size of 627 bp. Among the top ten most abundantly expressed genes, three are unique and show no homology in BLAST searches. The actin gene was highly expressed in BPH, especially in the thorax. Tissue-specifically expressed genes were extracted based on the expression frequency among the libraries. An EST database is available at our web site. Conclusion The EST library will provide useful information for transcriptional analyses, proteomic analyses, and gene functional analyses of BPH. Moreover, specific genes for hemimetabolous insects will be identified. The microarray fabricated based on the EST information will be useful for finding genes related to agricultural and biological problems related to this pest.
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Blawid R, Stephan D, Maiss E. Molecular characterization and detection of Vicia cryptic virus in different Vicia faba cultivars. Arch Virol 2007; 152:1477-88. [PMID: 17533556 DOI: 10.1007/s00705-007-0966-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 03/06/2007] [Indexed: 10/23/2022]
Abstract
After extraction of double-stranded (ds) RNAs from Vicia faba, dsRNA1 and dsRNA2 of Vicia cryptic virus (VCV), a member of the genus Alphacryptovirus (family Partitiviridae), were detected in six out of seven different cultivars by agarose gel electrophoresis. In attempts to sequence the complete VCV genome, the dsRNA1 and dsRNA2 sequences from a total of five different V. faba cultivars were determined. Analysis of these sequences indicated that V. faba cultivars contain almost indistinguishable VCV sequences. The larger dsRNA1 was 2012 bp in length and contained a major open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp). The smaller dsRNA2 was 1779 bp in length and comprised a single ORF on its plus-strand encoding the coat protein (CP). The sequences of the dsRNA1 and dsRNA2 ORFs shared highest amino acid sequence identities (84 and 56%, respectively) with the corresponding gene products of the alphacryptovirus white clover cryptic virus 1 (WCCV-1). The 5'-terminal untranslated regions of dsRNA1 and dsRNA2 of VCV were highly conserved and were strikingly similar to the corresponding regions of WCCV-1. RdRp amino acid sequence alignments revealed conserved motifs, which correlate with the phylogenetic clustering of the family Partitiviridae.
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Affiliation(s)
- R Blawid
- Faculty of Natural Sciences, Institute of Plant Diseases and Plant Protection, Leibniz Universität Hannover, Hannover, Germany
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