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Kwon SJ, Bodaghi S, Dang T, Gadhave KR, Ho T, Osman F, Al Rwahnih M, Tzanetakis IE, Simon AE, Vidalakis G. Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV). Front Microbiol 2021; 12:683130. [PMID: 34168635 PMCID: PMC8218546 DOI: 10.3389/fmicb.2021.683130] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/05/2021] [Indexed: 12/22/2022] Open
Abstract
Citrus yellow-vein disease (CYVD) was first reported in California in 1957. We now report that CYVD is associated with a virus-like agent, provisionally named citrus yellow-vein associated virus (CYVaV). The CYVaV RNA genome has 2,692 nucleotides and codes for two discernable open reading frames (ORFs). ORF1 encodes a protein of 190 amino acid (aa) whereas ORF2 is presumably generated by a −1 ribosomal frameshifting event just upstream of the ORF1 termination signal. The frameshift product (717 aa) encodes the RNA-dependent RNA polymerase (RdRp). Phylogenetic analyses suggest that CYVaV is closely related to unclassified virus-like RNAs in the family Tombusviridae. Bio-indexing and RNA-seq experiments indicate that CYVaV can induce yellow vein symptoms independently of known citrus viruses or viroids.
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Affiliation(s)
- Sun-Jung Kwon
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States.,Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, South Korea
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Kiran R Gadhave
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Thien Ho
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, United States
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, United States
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
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Herschlag R, Okada R, Alcalá-Briseño RI, de Souto ER, Valverde RA. Identification of a novel endornavirus in Geranium carolinianum and occurrence within three agroecosystems. Virus Res 2020; 288:198116. [PMID: 32795491 DOI: 10.1016/j.virusres.2020.198116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 10/23/2022]
Abstract
A putative endornavirus was detected in Carolina geranium (Geranium carolinianum) in Louisiana, USA. The virus was provisionally named Geranium carolinianum endornavirus 1 (GcEV1). The viral RNA was sequenced, and it consisted of 14,625 nt containing a single ORF coding a putative polyprotein of 4815 aa with conserved domains for a helicase 1, peptidase C97, glycosyl transferase GTB-type, and RNA-dependent RNA polymerase 2. The 5'end consisted of 130 nt while the 3'end consisted of 54 nt ending in nine cytosine residues. The closest relative to GcEV1 was Phaseolus vulgaris endornavirus 3. In phylogenetic analyses, GcEV1 clustered with members of the genus Alphaendornavirus. GcEV1 was detected in 57 of 60 G. carolinianum plants collected from three distinct agroecosystems. The virus was not detected in eight other species of the genus Geranium. There was no association of a particular phenotypic trait of the host with the presence or absence of the virus. GcEV1 was transmitted at a rate of 100% in seeds of a self-pollinated G. carolinianum plant.
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Affiliation(s)
- Rachel Herschlag
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Ryo Okada
- Laboratory of Molecular and Cellular Biology, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | | | - Eliezer Rodrigues de Souto
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Rodrigo A Valverde
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, USA.
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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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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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Kwon SJ, Jin M, Cho IS, Yoon JY, Choi GS. Identification of rehmannia virus 1, a novel putative member of the genus Closterovirus, from Rehmannia glutinosa. Arch Virol 2018; 163:3383-3388. [PMID: 30191375 DOI: 10.1007/s00705-018-4014-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/10/2018] [Indexed: 11/26/2022]
Abstract
Transcriptome sequencing analysis of a symptomatic Rehmannia glutinosa plant revealed a virome containing two known RNA viruses and one novel virus. In this study, we examined the molecular and biological characteristics of the novel virus. The complete genome of the novel virus is composed of monopartite single-stranded RNA of 15,322 nucleotides with 69% nucleotide sequence identity (with 68% coverage) to tobacco virus 1. Its genome organization is typical of the members of the genus Closterovirus, containing nine putative open reading frames. Molecular and phylogenetic analyses of the genome and encoded protein sequences strongly support that the identified virus is a new species of the genus Closterovirus in the family Closteroviridae. The name rehmannia virus 1 (ReV1) is proposed for this novel virus.
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Affiliation(s)
- Sun-Jung Kwon
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
| | - Meilan Jin
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, 27709, Republic of Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Ju-Yeon Yoon
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Gug-Seoun Choi
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
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Martínez RT, de Almeida MMS, Rodriguez R, de Oliveira AS, Melo FL, Resende RO. Identification and genome analysis of tomato chlorotic spot virus and dsRNA viruses from coinfected vegetables in the Dominican Republic by high-throughput sequencing. Virol J 2018; 15:24. [PMID: 29373979 PMCID: PMC5787326 DOI: 10.1186/s12985-018-0931-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 01/12/2018] [Indexed: 12/28/2022] Open
Abstract
The Tomato chlorotic spot virus (TCSV) was first reported in the 1980s, having its occurrence limited to Brazil and Argentina. Due to an apparent mild severity in the past, molecular studies concerning TCSV were neglected. However, TCSV has disseminated over the USA and Caribbean countries. In Dominican Republic TCSV has been recently reported on important cultivated crops such as pepper and beans. In this work, we provide the first complete genome of a TCSV isolate from symptomatic plants in Dominican Republic, which was obtained by high-throughput sequencing. In addition, three dsRNA viruses from different virus families were identified coinfecting these plants Bell pepper endornavirus (BPEV), Southern tomato virus (STV) and Pepper cryptic virus 2 (PCV-2). Phylogenetic analysis showed that the Dominican Republic TCSV isolate has a close relationship with other TCSV isolates and a reassortant isolate between TCSV and Groundnut ringspot virus (GRSV), all found in USA. BPEV, STV and PCV-2 isolates from Dominican Republic were close related to corresponding American isolates. The possible biological implications of these virus-mixed infections are discussed.
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Affiliation(s)
- Reina Teresa Martínez
- Universidad Autónoma de Santo Domingo-UASD and Instituto Dominicano de Investigaciones Agropecuarias y Florestales – IDIAF, Santo Domingo, Dominican Republic
| | | | - Rosalba Rodriguez
- Universidad Autónoma de Santo Domingo-UASD, Santo Domingo, Dominican Republic
| | | | - Fernando Lucas Melo
- Departamento de Biologia Celular, Universidade de Brasília, Brasilia, Brazil
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Complete genome sequence of a new strain of Lagenaria siceraria endornavirus from China. Arch Virol 2017; 163:805-808. [DOI: 10.1007/s00705-017-3664-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 11/28/2017] [Indexed: 10/18/2022]
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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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Kwon SJ, Choi GS, Yoon JY, Seo JK, Choi HS. Identification of Leonurus sibiricus as a Weed Reservoir for Three Pepper-Infecting Viruses. THE PLANT PATHOLOGY JOURNAL 2016; 32:65-9. [PMID: 26889117 PMCID: PMC4755677 DOI: 10.5423/ppj.nt.07.2015.0138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/30/2015] [Accepted: 08/30/2015] [Indexed: 06/05/2023]
Abstract
In plant virus ecology, weeds are regarded as wild reservoirs of viruses and as potential sources for insect-mediated transmission of viruses. During field surveys in 2013-2014, three Leonurus sibiricus plants showing virus-like symptoms were collected from pepper fields in Daegu, Seosan, and Danyang in Korea. Molecular diagnosis assays showed that the collected L. sibiricus samples were infected with either Tomato spotted wilt virus (TSWV), Pepper mild mottle virus (PMMoV), or Beet western yellow virus (BWYV), respectively. Since this is the first identification of TSWV, PMMoV, and BWYV from L. sibiricus, complete genome sequences of three virus isolates were determined to examine their phylogenetic relationships with the previously reported strains and isolates. Phylogenetic analyses performed using full genome sequences of the viruses showed the isolates of TSWV and PMMoV obtained from L. sibiricus are closely related to the pepper isolates of the corresponding viruses. Our results suggest that L. sibiricus could act an alternative host and reservoir of viruses that cause damages in pepper fields.
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Affiliation(s)
- Sun-Jung Kwon
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju 565-862,
Korea
| | - Gug-Seoun Choi
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju 565-862,
Korea
| | - Ju-Yeon Yoon
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju 565-862,
Korea
| | - Jang-Kyun Seo
- Crop Protection Division, National Academy of Agricultural Science, RDA, Wanju 565-851,
Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Academy of Agricultural Science, RDA, Wanju 565-851,
Korea
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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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