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Dahan J, Orellana GE, Wald KB, Wenninger EJ, Cooper WR, Karasev AV. Bactericera cockerelli Picorna-like Virus and Three New Viruses Found Circulating in Populations of Potato/Tomato Psyllids ( Bactericera cockerelli). Viruses 2024; 16:415. [PMID: 38543780 PMCID: PMC10975263 DOI: 10.3390/v16030415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 04/01/2024] Open
Abstract
An investigation of viruses circulating in populations of field and laboratory potato/tomato psyllids (Bactericera cockerelli) was conducted using high-throughput sequencing (HTS) technology and conventional RT-PCR. Three new viruses were discovered: one from the family Tymoviridae and two from the family Solemoviridae. A tymo-like virus sequence represented a nearly complete 6843 nt genome of a virus named Bactericera cockerelli tymo-like virus (BcTLV) that spanned five open reading frames (ORFs) which encoded RNA-dependent RNA polymerase (RdRP), helicase, protease, methyltransferase, and a capsid protein. Phylogenetic analyses placed the RdRP of BcTLV inside a divergent lineage of the viruses from the family Tymoviridae found in insect and plant hosts in a sister clade to the genera Tymovirus, Marafivirus, and Maculavirus. Four solemo-like virus sequences were identified in the HTS outputs, representing two new viruses. One virus found only in field-collected psyllids and named Bactericera cockerelli solemo-like virus 1 (BcSLV-1) had a 5479 nt genome which spanned four ORFs encoding protease and RdRP. Three solemo-like sequences displayed 87.4-99.7% nucleotide sequence identity among themselves, representing variants or strains of the same virus named Bactericera cockerelli solemo-like virus 2 (BcSLV-2). The genome of BcSLV-2 spanned only two ORFs that encoded a protease and an RdRP. Phylogenetic analysis placed the RdRPs of BcSLV-1 and BcSLV-2 in two separate lineages as sister clades to viruses from the genus Sobemovirus found in plant hosts. All three new psyllid viruses were found circulating in psyllids collected from potato fields in southern Idaho along with a previously identified Bactericera cockerelli picorna-like virus. Any possible role of the three viruses in controlling populations of the field psyllids remains to be elucidated.
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Affiliation(s)
- Jennifer Dahan
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, 875 Perimeter Drive, MS 2329, Moscow, ID 83844-2329, USA; (J.D.); (G.E.O.); (K.B.W.)
| | - Gardenia E. Orellana
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, 875 Perimeter Drive, MS 2329, Moscow, ID 83844-2329, USA; (J.D.); (G.E.O.); (K.B.W.)
| | - Kaleigh B. Wald
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, 875 Perimeter Drive, MS 2329, Moscow, ID 83844-2329, USA; (J.D.); (G.E.O.); (K.B.W.)
| | - Erik J. Wenninger
- Department of Entomology, Plant Pathology, and Nematology, and Kimberly Research and Extension Center, University of Idaho, Kimberly, ID 83341-5082, USA;
| | - W. Rodney Cooper
- USDA-ARS, Temperate Tree Fruit and Vegetable Research Unit, Wapato, WA 98951, USA;
| | - Alexander V. Karasev
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, 875 Perimeter Drive, MS 2329, Moscow, ID 83844-2329, USA; (J.D.); (G.E.O.); (K.B.W.)
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Rosario K, Van Bogaert N, López-Figueroa NB, Paliogiannis H, Kerr M, Breitbart M. Freshwater macrophytes harbor viruses representing all five major phyla of the RNA viral kingdom Orthornavirae. PeerJ 2022; 10:e13875. [PMID: 35990902 PMCID: PMC9390326 DOI: 10.7717/peerj.13875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/19/2022] [Indexed: 01/18/2023] Open
Abstract
Research on aquatic plant viruses is lagging behind that of their terrestrial counterparts. To address this knowledge gap, here we identified viruses associated with freshwater macrophytes, a taxonomically diverse group of aquatic phototrophs that are visible with the naked eye. We surveyed pooled macrophyte samples collected at four spring sites in Florida, USA through next generation sequencing of RNA extracted from purified viral particles. Sequencing efforts resulted in the detection of 156 freshwater macrophyte associated (FMA) viral contigs, 37 of which approximate complete genomes or segments. FMA viral contigs represent putative members from all five major phyla of the RNA viral kingdom Orthornavirae. Similar to viral types found in land plants, viral sequences identified in macrophytes were dominated by positive-sense RNA viruses. Over half of the FMA viral contigs were most similar to viruses reported from diverse hosts in aquatic environments, including phototrophs, invertebrates, and fungi. The detection of FMA viruses from orders dominated by plant viruses, namely Patatavirales and Tymovirales, indicate that members of these orders may thrive in aquatic hosts. PCR assays confirmed the presence of putative FMA plant viruses in asymptomatic vascular plants, indicating that viruses with persistent lifestyles are widespread in macrophytes. The detection of potato virus Y and oat blue dwarf virus in submerged macrophytes suggests that terrestrial plant viruses infect underwater plants and highlights a potential terrestrial-freshwater plant virus continuum. Defining the virome of unexplored macrophytes will improve our understanding of virus evolution in terrestrial and aquatic primary producers and reveal the potential ecological impacts of viral infection in macrophytes.
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Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
| | - Noémi Van Bogaert
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States,Present Address: FVPHouse, Berlare, Belgium
| | | | - Haris Paliogiannis
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States,Present Address: MIO-ECSDE, Athens, Greece
| | - Mason Kerr
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St Petersburg, Florida, United States
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Coat protein expression strategy of maize rayado fino virus and evidence for requirement of CP1 for leafhopper transmission. Virology 2022; 570:96-106. [DOI: 10.1016/j.virol.2022.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/19/2022]
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Silva LA, Jordan C, de Carvalho VR, Wilcken CF, Ribeiro BM. Identification and genome sequencing of RNA viruses in the eucalyptus snout beetle Gonipterus spp. (Coleoptera: Curculionidae). Arch Virol 2020; 165:2993-2997. [PMID: 32975676 DOI: 10.1007/s00705-020-04814-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/18/2020] [Indexed: 11/30/2022]
Abstract
The genomes of two putative new RNA viruses (macula-like virus and bunya-like virus) were identified in total RNA extracted from dead eucalyptus snout beetles (Gonipterus spp.) from a laboratory colony. However, only bunya-like virus was detected in field-collected insects. The macula-like virus has a monopartite single-stranded RNA genome that contains three open reading frames (ORFs) encoding an RNA-dependent RNA polymerase (RdRp), a capsid protein (CP), protein with unknown function. The bunya-like virus genome was predicted to consist of two RNA segments: a large segment (L) encoding a single protein (RdRp) and a small segment (S) encoding a putative nucleocapsid protein.
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Affiliation(s)
- Leonardo A Silva
- Laboratory of Baculovirus, Cell Biology Department, UnB-University of Brasília, 70910-900, Brasília, DF, Brazil
| | - Carolina Jordan
- Plant Protection Department, FCA/UNESP-São Paulo State University, Campus of Botucatu, 18610-307, Botucatu, SP, Brazil
| | - Vanessa Rafaela de Carvalho
- Plant Protection Department, FCA/UNESP-São Paulo State University, Campus of Botucatu, 18610-307, Botucatu, SP, Brazil
| | - Carlos F Wilcken
- Plant Protection Department, FCA/UNESP-São Paulo State University, Campus of Botucatu, 18610-307, Botucatu, SP, Brazil
| | - Bergmann M Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, UnB-University of Brasília, 70910-900, Brasília, DF, Brazil.
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Mlotshwa S, Xu J, Willie K, Khatri N, Marty D, Stewart LR. Engineering Maize rayado fino virus for virus-induced gene silencing. PLANT DIRECT 2020; 4:e00224. [PMID: 32783020 PMCID: PMC7409111 DOI: 10.1002/pld3.224] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 05/09/2023]
Abstract
Maize rayado fino virus (MRFV) is the type species of the genus Marafivirus in the family Tymoviridae. It infects maize (Zea mays), its natural host, to which it is transmitted by leafhoppers including Dalbulus maidis and Graminella nigrifrons in a persistent-propagative manner. The MRFV monopartite RNA genome encodes a precursor polyprotein that is processed into replication-associated proteins. The genome is encapsidated by two carboxy co-terminal coat proteins, CP1 and CP2. Cloned MRFV can be readily transmitted to maize by vascular puncture inoculation (VPI), and such virus systems that can be used in maize are valuable to examine plant gene function by gene silencing. However, the efficacy of marafiviruses for virus-induced gene silencing (VIGS) has not been investigated to date. To this end, MRFV genomic loci were tested for their potential to host foreign insertions without attenuating virus viability. This was done using infectious MRFV clones engineered to carry maize phytoene desaturase (PDS) gene fragments (ZmPDS) at various genomic regions. Several MRFV-PDS constructs were generated and tested for infectivity and VIGS in maize. This culminated in identification of the helicase/polymerase (HEL/POL) junction as a viable insertion site that preserved virus infectivity, as well as several sites at which sequence insertion caused loss of virus infectivity. Transcripts of viable constructs, carrying PDS inserts in the HEL/POL junction, induced stable local and systemic MRFV symptoms similar to wild-type infections, and triggered PDS VIGS initiating in veins and spreading into both inoculated and noninoculated leaves. These constructs were remarkably stable, retaining inserted sequences for at least four VPI passages while maintaining transmissibility by D. maidis. Our data thus identify the MRFV HEL/POL junction as an insertion site useful for gene silencing in maize.
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Affiliation(s)
| | - Junhuan Xu
- Department of Plant PathologyOhio State UniversityWoosterOhioUSA
| | - Kristen Willie
- USDA‐ARS Corn Soybean and Wheat Quality Research UnitWoosterOhioUSA
| | - Nitika Khatri
- Department of Plant PathologyOhio State UniversityWoosterOhioUSA
| | - DeeMarie Marty
- USDA‐ARS Corn Soybean and Wheat Quality Research UnitWoosterOhioUSA
| | - Lucy R. Stewart
- USDA‐ARS Corn Soybean and Wheat Quality Research UnitWoosterOhioUSA
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Kant R, Dasgupta I. Gene silencing approaches through virus-based vectors: speeding up functional genomics in monocots. PLANT MOLECULAR BIOLOGY 2019; 100:3-18. [PMID: 30850930 DOI: 10.1007/s11103-019-00854-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 03/02/2019] [Indexed: 05/20/2023]
Abstract
The design and use of existing VIGS vectors for revealing monocot gene functions are described and potential new vectors are discussed, which may expand their repertoire. Virus induced gene silencing (VIGS) is a method of transient gene silencing in plants, triggered by the use of modified viral vectors. VIGS has found widespread use in deciphering the functions of plant genes, mainly for dicots. In the last decade, however, its use in monocots has increased noticeably, involving not only previously described viruses for monocots, but also those described for dicots. Additional viruses have been modified for VIGS to bring a larger collection of monocots under the ambit of this method. For monocots, new methods of inoculation have been tried to obtain increased silencing efficiency. The issue of insert stability and duration of silencing have also been addressed by various research groups. VIGS has been used to unravel the functions of a fairly large collection of monocot genes. This review summarizes the above developments, bringing out some of the gaps in our understanding and identifies directions to develop this technology further in the coming years.
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Affiliation(s)
- Ravi Kant
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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Edwards MC, Weiland JJ, Todd J, Stewart LR. Infectious Maize rayado fino virus from Cloned cDNA. PHYTOPATHOLOGY 2015; 105:833-839. [PMID: 25651051 DOI: 10.1094/phyto-09-14-0250-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A full-length cDNA clone was produced from a U.S. isolate of Maize rayado fino virus (MRFV), the type member of the genus Marafivirus within the family Tymoviridae. Infectivity of transcripts derived from cDNA clones was demonstrated by infection of maize plants and protoplasts, as well as by transmission via the known leafhopper vectors Dalbulus maidis and Graminella nigrifrons that transmit the virus in a persistent-propagative manner. Infection of maize plants through vascular puncture inoculation of seed with transcript RNA resulted in the induction of fine stipple stripe symptoms typical of those produced by wild-type MRFV and a frequency of infection comparable with that of the wild type. Northern and Western blotting confirmed the production of MRFV-specific RNAs and proteins in infected plants and protoplasts. An unanticipated increase in subgenomic RNA synthesis over levels in infected plants was observed in protoplasts infected with either wild-type or cloned virus. A conserved cleavage site motif previously demonstrated to function in both Oat blue dwarf virus capsid protein and tymoviral nonstructural protein processing was identified near the amino terminus of the MRFV replicase polyprotein, suggesting that cleavage at this site also may occur.
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Affiliation(s)
- Michael C Edwards
- First and second authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Crops Research Unit, Fargo, ND 58102-2765; third and fourth authors: USDA-ARS Corn, Soybean, and Wheat Quality Research Unit, Wooster, OH 44691
| | - John J Weiland
- First and second authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Crops Research Unit, Fargo, ND 58102-2765; third and fourth authors: USDA-ARS Corn, Soybean, and Wheat Quality Research Unit, Wooster, OH 44691
| | - Jane Todd
- First and second authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Crops Research Unit, Fargo, ND 58102-2765; third and fourth authors: USDA-ARS Corn, Soybean, and Wheat Quality Research Unit, Wooster, OH 44691
| | - Lucy R Stewart
- First and second authors: United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Cereal Crops Research Unit, Fargo, ND 58102-2765; third and fourth authors: USDA-ARS Corn, Soybean, and Wheat Quality Research Unit, Wooster, OH 44691
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Edwards MC, Weiland JJ. Coat protein expression strategy of oat blue dwarf virus. Virology 2014; 450-451:290-6. [PMID: 24503092 PMCID: PMC7173039 DOI: 10.1016/j.virol.2013.12.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 10/19/2013] [Accepted: 12/15/2013] [Indexed: 02/03/2023]
Abstract
Oat blue dwarf virus (OBDV) is a member of the genus Marafivirus whose genome encodes a 227 kDa polyprotein (p227) ostensibly processed post-translationally into its functional components. Encoded near the 3' terminus and coterminal with the p227 ORF are ORFs specifying major and minor capsid proteins (CP). Since the CP expression strategy of marafiviruses has not been thoroughly investigated, we produced a series of point mutants in the OBDV CP encoding gene and examined expression in protoplasts. Results support a model in which the 21 kDa major CP is the product of direct translation of a sgRNA, while the 24 kDa minor CP is a cleavage product derived from both the polyprotein and a larger ~26 kDa precursor translated directly from the sgRNA. Cleavage occurs at an LXG[G/A] motif conserved in many viruses that use papain-like proteases for polyprotein processing and protection against degradation via the ubiquitin-proteasome system.
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Affiliation(s)
- Michael C Edwards
- USDA-Agricultural Research Service, Cereal Crops Research Unit, Northern Crop Science Laboratory, 1605 Albrecht Blvd. N., Fargo, ND 58102-2765, USA.
| | - John J Weiland
- USDA-Agricultural Research Service, Cereal Crops Research Unit, Northern Crop Science Laboratory, 1605 Albrecht Blvd. N., Fargo, ND 58102-2765, USA
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Iwanaga M, Hitotsuyama T, Katsuma S, Ishihara G, Daimon T, Shimada T, Imanishi S, Kawasaki H. Infection study of Bombyx mori macula-like virus (BmMLV) using a BmMLV-negative cell line and an infectious cDNA clone. J Virol Methods 2012; 179:316-24. [DOI: 10.1016/j.jviromet.2011.11.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 09/12/2011] [Accepted: 11/16/2011] [Indexed: 10/15/2022]
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Presence of a polyA tail at the 3’ end of maize rayado fino virus RNA. Arch Virol 2010; 156:331-4. [DOI: 10.1007/s00705-010-0880-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 11/26/2010] [Indexed: 10/18/2022]
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