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Rose Virome Analysis and Identification of a Novel Ilarvirus in Taiwan. Viruses 2022; 14:v14112537. [PMID: 36423147 PMCID: PMC9693529 DOI: 10.3390/v14112537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Rose (Rosa spp.), especially R. hybrida, is one of the most popular ornamental plants in the world and the third largest cut flower crop in Taiwan. Rose mosaic disease (RMD), showing mosaic, line patterns and ringspots on leaves, is a common rose disease caused by the complex infection of various viruses. Due to pests and diseases, the rose planting area in Taiwan has been decreasing since 2008; however, no rose virus disease has been reported in the past five decades. In the spring of 2020, rose samples showing RMD-like symptoms were observed at an organic farm in Chiayi, central Taiwan. The virome in the farm was analyzed by RNA-seq. Rose genomic sequences were filtered from the obtained reads. The remaining reads were de novo assembled to generate 294 contigs, 50 of which were annotated as viral sequences corresponding to 10 viruses. Through reverse transcription-polymerase chain reaction validation, a total of seven viruses were detected, including six known rose viruses, namely apple mosaic virus, prunus necrotic ringspot virus, rose partitivirus, apple stem grooving virus, rose spring dwarf-associated virus and rose cryptic virus 1, and a novel ilarvirus. After completing the whole genome sequencing and sequence analysis, the unknown ilarvirus was demonstrated as a putative new species, tentatively named rose ilarvirus 2. This is the first report of the rose virus disease in Taiwan.
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2
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Costa LC, Hu X, Malapi-Wight M, O'Connell M, Hendrickson LM, Turner RS, McFarland C, Foster J, Hurtado-Gonzales OP. Genomic characterization of silvergrass cryptic virus 1, a novel partitivirus infecting Miscanthus sinensis. Arch Virol 2021; 167:261-265. [PMID: 34757504 DOI: 10.1007/s00705-021-05294-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/15/2021] [Indexed: 11/29/2022]
Abstract
In the present study we report the identification of a novel partitivirus recovered from Miscanthus sinensis, for which the provisional name "silvergrass cryptic virus 1" (SgCV-1) is proposed. High-throughput sequencing (HTS) and rapid amplification of cDNA ends (RACE) allowed the assembly of the complete sequence of each double-stranded RNA genome segment of this novel virus. The largest dsRNA segment, dsRNA1 (1699 bp), was predicted to encode a viral RNA-dependent RNA polymerase protein (RdRp) with 478 aa, and dsRNA2 (1490 bp) and dsRNA3 (1508 bp) were predicted to encode putative capsid proteins (CPs) with 347 and 348 aa, respectively. SgCV-1 has the highest amino acid sequence identity (≤ 70.80% in RdPp and ≤ 34.5% in CPs) to members of the genus Deltapartitivirus, family Partitiviridae, especially to unclassified viruses related to members of this genus. Its genome segment and protein lengths are also within the range of those of deltapartitiviruses. Moreover, phylogenetic analysis based on RdRp amino acid sequences also showed clustering of this novel virus with the related unclassified deltapartitiviruses. An RT-PCR survey of 94 imported M. sinensis samples held in quarantine identified seven additional samples carrying SgCV-1. This new virus fulfils all ICTV criteria to be considered a new member of the genus Deltapartitivirus.
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Affiliation(s)
- Larissa C Costa
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Xiaojun Hu
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Martha Malapi-Wight
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA.,USDA-APHIS, Biotechnology Regulatory Services, Biotechnology Risk Analysis Program, Riverdale, MD, USA
| | - Mary O'Connell
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Leticia M Hendrickson
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Roy S Turner
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | | | - Joseph Foster
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA
| | - Oscar P Hurtado-Gonzales
- United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA.
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3
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Nerva L, Vigani G, Di Silvestre D, Ciuffo M, Forgia M, Chitarra W, Turina M. Biological and Molecular Characterization of Chenopodium quinoa Mitovirus 1 Reveals a Distinct Small RNA Response Compared to Those of Cytoplasmic RNA Viruses. J Virol 2019; 93:e01998-18. [PMID: 30651361 PMCID: PMC6430534 DOI: 10.1128/jvi.01998-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/08/2019] [Indexed: 02/07/2023] Open
Abstract
Indirect evidence of mitochondrial viruses in plants comes from discovery of genomic fragments integrated into the nuclear and mitochondrial DNA of a number of plant species. Here, we report the existence of replicating mitochondrial virus in plants: from transcriptome sequencing (RNA-seq) data of infected Chenopodium quinoa, a plant species commonly used as a test plant in virus host range experiments, among other virus contigs, we could assemble a 2.7-kb contig that had highest similarity to mitoviruses found in plant genomes. Northern blot analyses confirmed the existence of plus- and minus-strand RNA corresponding to the mitovirus genome. No DNA corresponding to the genomic RNA was detected, excluding the endogenization of such virus. We have tested a number of C. quinoa accessions, and the virus was present in a number of commercial varieties but absent from a large collection of Bolivian and Peruvian accessions. The virus could not be transmitted mechanically or by grafting, but it is transmitted vertically through seeds at a 100% rate. Small RNA analysis of a C. quinoa line carrying the mitovirus and infected by alfalfa mosaic virus showed that the typical antiviral silencing response active against cytoplasmic viruses (21- to 22-nucleotide [nt] vsRNA peaks) is not active against CqMV1, since in this specific case the longest accumulating vsRNA length is 16 nt, which is the same as that corresponding to RNA from mitochondrial genes. This is evidence of a distinct viral RNA degradation mechanism active inside mitochondria that also may have an antiviral effect.IMPORTANCE This paper reports the first biological characterization of a bona fide plant mitovirus in an important crop, Chenopodium quinoa, providing data supporting that mitoviruses have the typical features of cryptic (persistent) plant viruses. We, for the first time, demonstrate that plant mitoviruses are associated with mitochondria in plants. In contrast to fungal mitoviruses, plant mitoviruses are not substantially affected by the antiviral silencing pathway, and the most abundant mitovirus small RNA length is 16 nt.
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Affiliation(s)
- L Nerva
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
- Council for Agricultural Research and Economics-Research Centre for Viticulture and Enology CREA-VE, Conegliano, Italy
| | - G Vigani
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - D Di Silvestre
- Institute for Biomedical Technology, CNR, Segrate, Milan, Italy
| | - M Ciuffo
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
| | - M Forgia
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - W Chitarra
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
- Council for Agricultural Research and Economics-Research Centre for Viticulture and Enology CREA-VE, Conegliano, Italy
| | - M Turina
- Institute for Sustainable Plant Protection, CNR, Turin, Italy
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4
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Genome segments encoding capsid protein-like variants of Pyrus pyrifolia cryptic virus. Virus Res 2017; 240:64-68. [PMID: 28760347 DOI: 10.1016/j.virusres.2017.07.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 12/27/2022]
Abstract
According to previous studies, three double-stranded (ds) RNA molecules (dsRNA1, 2, and 3) detected in Japanese pear are transmitted to the next generation with high frequency through both ovules and pollen. Nucleotide sequence analysis of dsRNA1-encoding RNA-dependent RNA polymerase (RdRp) has suggested that these dsRNAs are related to a cryptovirus named Pyrus pyrifolia cryptic virus (PpCV). In this study, purified dsRNA prepared from a PpCV-infected Japanese pear cultivar was subjected to next-generation deep sequencing. This sequencing generated two de novo assembled contigs corresponding to dsRNA2 and 3, with BLAST analysis of the predicted amino acid sequences indicating homology to capsid proteins (CPs) of the cryptoviruses persimmon cryptic virus and Sinapis alba cryptic virus 1, respectively. Relationships between the two contigs and dsRNA2 and 3 were confirmed by northern blot hybridization with probes generated using primers designed from the assembled contigs. Rapid amplification of cDNA ends analyses of 5'- and 3'-terminal sequences of dsRNA2 and 3 revealed that these two dsRNAs consist of 1523 and 1481bp, respectively. The 5'-terminal sequences (AGAAUUUC) of dsRNA1, 2 and 3 were found to be conserved. Phylogenetic analysis of deduced amino acid sequences of the two CP-like variants indicated that PpCV belongs to Deltapartitivirus (Partitiviridae). Our results imply that PpCV is tri-segmented.
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Li L, Liu J, Zhang Q, Fu R, Zhu X, Li C, Chen J. Seed-borne viral dsRNA elements in three cultivatedRaphanusandBrassicaplants suggest three cryptoviruses. Can J Microbiol 2016; 62:287-95. [DOI: 10.1139/cjm-2015-0788] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Since the 1970s, several dsRNA viruses, including Radish yellow edge virus, Raphanus sativus virus 1, Raphanus sativus virus 2, and Raphanus sativus virus 3, have been identified and reported as infecting radish. In the present study, in conjunction with a survey of seed-borne viruses in cultivated Brassica and Raphanus using the dsRNA diagnostic method, we discovered 3 novel cryptoviruses that infect Brassica and Raphanus: Raphanus sativus partitivirus 1, which infects radish (Raphanus sativus); Sinapis alba cryptic virus 1, which infects Sinapis alba; and Brassica rapa cryptic virus 1 (BrCV1), which infects Brassica rapa. The genomic organization of these cryptoviruses was analyzed and characterized. BrCV1 might represent the first plant partitivirus found in Gammapartitivirus. Additionally, the evolutionary relationships among all of the partitiviruses reported in Raphanus and Brassica were analyzed.
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Affiliation(s)
- Liqiang Li
- College of Life Science, Zhejiang University, Hangzhou, 310058, People’s Republic of China
| | - Jianning Liu
- Institute of Bioengineering, Zhejiang Sci-Tech University, Hangzhou, 310018, People’s Republic of China
| | - Qiong Zhang
- Institute of Bioengineering, Zhejiang Sci-Tech University, Hangzhou, 310018, People’s Republic of China
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, People’s Republic of China
| | - Runying Fu
- Shenzhen Seventh People’s Hospital, Shenzhen, 518081, People’s Republic of China
| | - Xiwu Zhu
- Institute of Bioengineering, Zhejiang Sci-Tech University, Hangzhou, 310018, People’s Republic of China
- Institute of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi, 41700, People’s Republic of China
| | - Chao Li
- College of Life Science, Shenzhen University, Shenzhen, 518068, People’s Republic of China
| | - Jishuang Chen
- College of Life Science, Zhejiang University, Hangzhou, 310058, People’s Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, People’s Republic of China
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Nibert ML, Ghabrial SA, Maiss E, Lesker T, Vainio EJ, Jiang D, Suzuki N. Taxonomic reorganization of family Partitiviridae and other recent progress in partitivirus research. Virus Res 2014; 188:128-41. [DOI: 10.1016/j.virusres.2014.04.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
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7
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Zhang T, Jiang Y, Huang J, Dong W. Genomic organization of a novel partitivirus from the phytopathogenic fungus Ustilaginoidea virens. Arch Virol 2013; 158:2415-9. [PMID: 23732929 DOI: 10.1007/s00705-013-1742-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/19/2013] [Indexed: 10/26/2022]
Abstract
From the plant pathogen Ustilaginoidea virens, four double-stranded RNA (dsRNA) segments designated Uv-dsRNA1, -2, -3, and -4 were isolated, cloned, and sequenced. Uv-dsRNA1 (1775 bp) and -2 (1588 bp) potentially encode an RNA-dependent RNA polymerase (RdRp) and a viral coat protein (CP), respectively. Since the RdRp and CP sequences encoded by Uv-dsRNA1 and -2, respectively, are most closely related to, but clearly distinct from, those of viruses of the genus Partitivirus, they appear to be the two genome segments of a new partitivirus, for which the name Ustilaginoidea virens partitivirus 1 is proposed. In contrast, Uv-dsRNA3 (1352 bp) did not share significant sequence similarity with GenBank sequences, and the ORF of Uv-dsRNA4 (1119 bp) was only 32 % identical to a functionally unknown protein (GaRVMS2s3gp1) encoded by Gremmeniella abietina RNA virus MS2.
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Affiliation(s)
- Tingting Zhang
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
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8
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Mollov D, Lockhart B, Zlesak D. Complete nucleotide sequence of rose yellow mosaic virus, a novel member of the family Potyviridae. Arch Virol 2013; 158:1917-23. [PMID: 23553457 DOI: 10.1007/s00705-013-1686-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 02/21/2013] [Indexed: 10/27/2022]
Abstract
The complete genomic sequence of rose yellow mosaic virus (RoYMV) was determined and found to have all the features that are characteristic of members of the family Potyviridae. The RoYMV genome is 9508 nucleotides long excluding the 3'-poly-(A) tail and contains a single open reading frame encoding a polyprotein of 3067 amino acids. The RoYMV P3 and CI cistrons are shorter than those of other members of the family Potyviridae, and the 6K1 cistron is completely absent. Comparative sequence analysis revealed that RoYMV had highest amino acid sequence identity across the entire genome sequence to brome streak mosaic virus (33 %) and to turnip mosaic virus (30 %) at the coat protein level. Based on its low sequence similarity to known members of the family Potyviridae and phylogenetic analysis, RoYMV appears to be a distinct, previously undescribed, member of this family.
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Affiliation(s)
- Dimitre Mollov
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA.
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Liu H, Fu Y, Xie J, Cheng J, Ghabrial SA, Li G, Yi X, Jiang D. Discovery of novel dsRNA viral sequences by in silico cloning and implications for viral diversity, host range and evolution. PLoS One 2012; 7:e42147. [PMID: 22848734 PMCID: PMC3407116 DOI: 10.1371/journal.pone.0042147] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 07/02/2012] [Indexed: 11/18/2022] Open
Abstract
Genome sequence of viruses can contribute greatly to the study of viral evolution, diversity and the interaction between viruses and hosts. Traditional molecular cloning methods for obtaining RNA viral genomes are time-consuming and often difficult because many viruses occur in extremely low titers. DsRNA viruses in the families, Partitiviridae, Totiviridae, Endornaviridae, Chrysoviridae, and other related unclassified dsRNA viruses are generally associated with symptomless or persistent infections of their hosts. These characteristics indicate that samples or materials derived from eukaryotic organisms used to construct cDNA libraries and EST sequencing might carry these viruses, which were not easily detected by the researchers. Therefore, the EST databases may include numerous unknown viral sequences. In this study, we performed in silico cloning, a procedure for obtaining full or partial cDNA sequence of a gene by bioinformatics analysis, using known dsRNA viral sequences as queries to search against NCBI Expressed Sequence Tag (EST) database. From this analysis, we obtained 119 novel virus-like sequences related to members of the families, Endornaviridae, Chrysoviridae, Partitiviridae, and Totiviridae. Many of them were identified in cDNA libraries of eukaryotic lineages, which were not known to be hosts for these viruses. Furthermore, comprehensive phylogenetic analysis of these newly discovered virus-like sequences with known dsRNA viruses revealed that these dsRNA viruses may have co-evolved with respective host supergroups over a long evolutionary time while potential horizontal transmissions of viruses between different host supergroups also is possible. We also found that some of the plant partitiviruses may have originated from fungal viruses by horizontal transmissions. These findings extend our knowledge of the diversity and possible host range of dsRNA viruses and offer insight into the origin and evolution of relevant viruses with their hosts.
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Affiliation(s)
- Huiquan Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Jiatao Xie
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Jiasen Cheng
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Said A. Ghabrial
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Xianhong Yi
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
- * E-mail:
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Properties and detection of two cryptoviruses from pepper (Capsicum annuum). Virus Genes 2011; 43:307-12. [PMID: 21695493 DOI: 10.1007/s11262-011-0634-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
Abstract
Pepper (Capsicum annuum L.) contains a range of endogenous dsRNA molecules resembling the genomes of cryptoviruses. In this work, we have completed the molecular characterization of Pepper cryptic virus 1 (PCV-1) from cv "Jalapeño M" and generated complete genomic sequences of another cryptovirus from cv "Hungarian Wax" designated Pepper cryptic virus 2 (PCV-2). The two viruses share limited identical amino acid content in both genomic segments and appear phylogenetically closer to cryptoviruses reported from other crops (i.e. Raphanus sativus cryptic virus 3, Black raspberry cryptic virus) than to each other. Two sets of virus-specific primers were successfully used in RT-PCR tests for the simultaneous and discriminative detection of these two viruses in pepper leaves and seeds. Both viruses were detected in several pepper cultivars tested, either as single or mixed infections.
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11
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Elbeaino T, Kubaa RA, Digiaro M, Minafra A, Martelli GP. The complete nucleotide sequence and genome organization of Fig cryptic virus, a novel bipartite dsRNA virus infecting fig, widely distributed in the Mediterranean basin. Virus Genes 2011; 42:415-21. [DOI: 10.1007/s11262-011-0581-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 01/31/2011] [Indexed: 11/28/2022]
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12
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Szego A, Enünlü N, Deshmukh SD, Veliceasa D, Hunyadi-Gulyás E, Kühne T, Ilyés P, Potyondi L, Medzihradszky K, Lukács N. The genome of Beet cryptic virus 1 shows high homology to certain cryptoviruses present in phylogenetically distant hosts. Virus Genes 2010; 40:267-76. [PMID: 20058060 DOI: 10.1007/s11262-009-0432-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 12/05/2009] [Indexed: 11/28/2022]
Abstract
UNLABELLED This study determined the complete nucleotide sequence of Beet cryptic virus 1 (BCV1). As expected by analogy to previously sequenced alphacryptoviruses, dsRNA1 (2008 bp) encodes a 72.5-kDa protein containing sequence motifs characteristic for RNA-dependent RNA polymerases (RdRp). In addition to the full-length dsRNA1, a truncated form was also detected in dsRNA extracts. dsRNA2 (1783 bp) codes for the viral coat protein (CP) as proven by the identity of the predicted CP sequence to peptide sequences of the purified virion protein. The amino acid sequence of BCV1 RdRp as well as the 5'- and 3'-UTRs show 81-85% identity to the corresponding regions of Vicia cryptic virus (VCV), White clover cryptic virus 1 (WCCV1) and Carrot cryptic virus (CaCV). The amino acid sequence identity of the CP is about 55-62%, moreover, a strong conservation of predicted alpha-helical regions was observed. The high degree of similarity of these seed- and pollen-transmitted viruses persisting in phylogenetically distant hosts, together with their high similarity to fungal partitiviruses strongly supports the hypothesis that horizontal transfer by a fungus played a role in the emergence of the present cryptovirus species. The change in the distribution of cryptic viruses may also be due to human influence: While earlier BCV1 occurred frequently in sugar beet cultivars, it is very rare in cultivars currently used in agricultural practice and was detected in only one of the 28 cultivars investigated in our experiments. ELECTRONIC SUPPLEMENTARY MATERIAL The online version of this article (doi:10.1007/s11262-009-0432-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anita Szego
- Department of Plant Physiology and Plant Biochemistry, Corvinus University of Budapest, Ménesi út 44, 1118 Budapest, Hungary
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Liu W, Chen J. A double-stranded RNA as the genome of a potential virus infecting Vicia faba. Virus Genes 2009; 39:126-31. [DOI: 10.1007/s11262-009-0362-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 04/19/2009] [Indexed: 11/30/2022]
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14
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Li L, Tian Q, Du Z, Duns GJ, Chen J. A novel double-stranded RNA virus detected in Primula malacoides is a plant-isolated partitivirus closely related to partitivirus infecting fungal species. Arch Virol 2009; 154:565-72. [PMID: 19267226 DOI: 10.1007/s00705-009-0342-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2008] [Accepted: 02/19/2009] [Indexed: 11/24/2022]
Abstract
A novel virus was detected in ornamental plants of Primula malacoides Franch exhibiting typical yellow-edge symptoms. Two double-stranded RNA (dsRNA) segments, of 2390 bp and 2344 bp, respectively, were extracted from plant tissues, and these same dsRNAs were detected from purified virions of about 35 nm in diameter. The two dsRNAs, putatively encoding partitivirus-related RNA-dependent RNA polymerase and capsid protein, were sequenced. Analysis of phylogenetic relationships and genomic structures indicated that these two dsRNAs together make up the genome of a novel partitivirus. This virus was found to be more closely related to the fungus-infecting partitiviruses than to the ones that infect plants and was designated as Primula malacoides virus 1 (PmV1). It is strongly suggested that this novel virus be classified as a member of the genus Partitivirus.
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Affiliation(s)
- Liqiang Li
- Institute of Bioengineering, Zhejiang Sci-Tech University, Hangzhou, China
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15
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Genomic characterization of a novel partitivirus infecting Aspergillus ochraceus. Virus Genes 2008; 37:322-7. [DOI: 10.1007/s11262-008-0265-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Accepted: 07/17/2008] [Indexed: 11/25/2022]
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