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Vlasava NB, Michener DC, Kharytonchyk S, Cortés-Ortiz L. Co-Infection of Tobacco Rattle and Cycas Necrotic Stunt Viruses in Paeonia lactiflora: Detection Strategies, Potential Origins of Infection, and Implications for Paeonia Germplasm Conservation. Viruses 2024; 16:893. [PMID: 38932185 PMCID: PMC11209033 DOI: 10.3390/v16060893] [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: 04/30/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Increasing reports of tobacco rattle virus (TRV) and cycas necrotic stunt virus (CNSV) in herbaceous Paeonia worldwide highlight the importance of conserving the genetic resources of this economically important ornamental and medicinal crop. The unknown origin(s) of infection, differential susceptibility of peony cultivars to these viruses, and elusive disease phenotypes for CNSV in peonies make early detection and management challenging. Here, we report the presence of TRV and CNSV in plants of the University of Michigan living peony collection in the United States and a molecular characterization of their strains. Using sequences of the TRV 194 K RNA polymerase gene, we confirmed TRV infections in seven symptomatic plants (1.07% of all plants in the collection). Using newly developed primers, we recovered sequences of the CNSV RdRp gene and the polyprotein 1 gene region from nine out of twelve samples analyzed, including three from symptomless plants. Four of the nine plants had TRV and CNSV co-infections and showed more severe disease symptoms than plants only infected with TRV. Phylogenetic analyses of isolates from the University of Michigan living peony collection and publicly available isolates point to multiple origins of TRV and CNSV infections in this collection. This is the first report of TRV/CNSV co-infection and of a symptomatic detection of CNSV on cultivated P. lactiflora.
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Affiliation(s)
- Nastassia B. Vlasava
- Matthaei Botanical Gardens and Nichols Arboretum, University of Michigan, Ann Arbor, MI 48105, USA;
- Central Botanical Garden, National Academy of Sciences of Belarus, 220012 Minsk, Belarus
| | - David C. Michener
- Matthaei Botanical Gardens and Nichols Arboretum, University of Michigan, Ann Arbor, MI 48105, USA;
| | - Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA;
| | - Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA;
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Atsumi G, Naramoto S, Nishihara M, Nakatsuka T, Tomita R, Matsushita Y, Hoshi N, Shirakawa A, Kobayashi K, Fukuda H, Sekine KT. Identification of a novel viral factor inducing tumorous symptoms by disturbing vascular development in planta. J Virol 2023; 97:e0046323. [PMID: 37668368 PMCID: PMC10537666 DOI: 10.1128/jvi.00463-23] [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: 03/28/2023] [Accepted: 06/14/2023] [Indexed: 09/06/2023] Open
Abstract
Plant viruses induce various disease symptoms that substantially impact agriculture, but the underlying mechanisms of viral disease in plants are poorly understood. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Here, we show that a gene fragment of gentian Kobu-sho-associated virus, which is designated as Kobu-sho-inducing factor (KOBU), induces gall formation accompanied by ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. Transgenic gentian expressing KOBU exhibited tumorous symptoms, confirming the gall-forming activity of KOBU. Surprisingly, KOBU expression can also induce differentiation of an additional leaf-like tissue on the abaxial side of veins in normal N. benthamiana and gentian leaves. Transcriptome analysis with Arabidopsis thaliana expressing KOBU revealed that KOBU activates signaling pathways that regulate xylem development. KOBU protein forms granules and plate-like structures and co-localizes with mRNA splicing factors within the nucleus. Our findings suggest that KOBU is a novel pleiotropic virulence factor that stimulates vascular and leaf development. IMPORTANCE While various mechanisms determine disease symptoms in plants depending on virus-host combinations, the details of how plant viruses induce symptoms remain largely unknown in most plant species. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Our findings demonstrate that a gene fragment of gentian Kobu-sho-associated virus (GKaV), which is designated as Kobu-sho-inducing factor, induces the gall formation accompanied by the ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. The molecular mechanism by which gentian Kobu-sho-associated virus induces the Kobu-sho symptoms will provide new insight into not only plant-virus interactions but also the regulatory mechanisms underlying vascular and leaf development.
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Affiliation(s)
- Go Atsumi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Hokkaido, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Satoshi Naramoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | | | | | - Reiko Tomita
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Yosuke Matsushita
- National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Nobue Hoshi
- Iwate Agricultural Research Center, Kitakami, Iwate, Japan
| | | | - Kappei Kobayashi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- Faculty of Agriculture, Ehime University, Matsuyama, Ehime, Japan
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ken-Taro Sekine
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- Faculty of Agriculture, University of the Ryukyus, Nishihara, Okinawa, Japan
- Department of Environmental Sciences and Conservation Biology, The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Kagoshima, Japan
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Hammond J, Huang Q, Jordan R, Meekes E, Fox A, Vazquez-Iglesias I, Vaira AM, Copetta A, Delmiglio C. International Trade and Local Effects of Viral and Bacterial Diseases in Ornamental Plants. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:73-95. [PMID: 37257057 DOI: 10.1146/annurev-phyto-021621-114618] [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: 06/02/2023]
Abstract
Since the 1950s, there have been major changes in the scope, value, and organization of the ornamental plant industry. With fewer individual producers and a strong trend toward consolidation and globalization, increasing quantities of diverse plant genera and species are being shipped internationally. Many more ornamentals are propagated vegetatively instead of by seed, further contributing to disease spread. These factors have led to global movement of pathogens to countries where they were not formerly known. The emergence of some previously undescribed pathogens has been facilitated by high-throughput sequencing, but biological studies are often lacking, so their roles in economic diseases are not yet known. Case studies of diseases in selected ornamentals discuss the factors involved in their spread, control measures to reduce their economic impact, and some potential effects on agronomic crops. Advances in diagnostic techniques are discussed, and parallels are drawn to the international movement of human diseases.
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Affiliation(s)
- John Hammond
- Floral and Nursery Plants Research Unit, US National Arboretum, USDA-ARS, Beltsville, Maryland, USA;
| | - Qi Huang
- Floral and Nursery Plants Research Unit, US National Arboretum, USDA-ARS, Beltsville, Maryland, USA;
| | - Ramon Jordan
- Floral and Nursery Plants Research Unit, US National Arboretum, USDA-ARS, Beltsville, Maryland, USA;
| | | | - Adrian Fox
- Fera Science Ltd., York Biotech Campus, York, United Kingdom
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | | | - Andrea Copetta
- CREA Research Centre for Vegetable and Ornamental Crops, Sanremo, Italy
| | - Catia Delmiglio
- Plant Health & Environment Laboratory, Biosecurity New Zealand, Ministry for Primary Industries, Auckland, New Zealand
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Debat H, Bejerman N. Two novel flavi-like viruses shed light on the plant-infecting koshoviruses. Arch Virol 2023; 168:184. [PMID: 37338667 DOI: 10.1007/s00705-023-05813-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/09/2023] [Indexed: 06/21/2023]
Abstract
The family Flaviviridae is composed of viruses with a positive-sense single-stranded RNA genome and includes viruses that are important veterinary and human pathogens. Most members of the family are arthropod- and vertebrate-infecting viruses, but more recently, divergent flavi-like viruses have been identified in marine invertebrate and vertebrate hosts. The striking discovery of gentian Kobu-sho-associated virus (GKaV), along with a recent report of a related virus from carrot, has expanded the known host range of flavi-like viruses to plants, suggesting they could be grouped in a proposed genus tentatively named "Koshovirus". Here, we report the identification and characterization of two novel RNA viruses that show a genetic and evolutionary relationship to the previously identified "koshoviruses". Their genome sequences were obtained from transcriptomic datasets of the flowering plants Coptis teeta and Sonchus asper. These two new viruses, which we have named "coptis flavi-like virus 1" (CopFLV1) and "sonchus flavi-like virus 1" (SonFLV1), are members of novel species characterized by the longest monopartite RNA genome observed so far among plant-associated RNA viruses, which is ca. 24 kb in size. Structural and functional annotations of the polyproteins of all koshoviruses resulted in the detection not only of the expected helicase and RNA-dependent RNA polymerase but also of several additional divergent domains, including AlkB oxygenase, trypsin-like serine protease, methyltransferase, and envelope E1 flavi-like domains. Phylogenetic analysis showed that CopFLV1, SonFLV1, GKaV, and the carrot flavi-like virus were grouped together in a monophyletic clade, strongly supporting the recent proposal for creation of the genus "Koshovirus" for the group of related plant-infecting flavi-like viruses.
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Affiliation(s)
- Humberto Debat
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Córdoba, Argentina.
| | - Nicolás Bejerman
- Instituto de Patología Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Córdoba, Argentina.
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Solovyev AG, Morozov SY. Uncovering Plant Virus Species Forming Novel Provisional Taxonomic Units Related to the Family Benyviridae. Viruses 2022; 14:v14122680. [PMID: 36560684 PMCID: PMC9781952 DOI: 10.3390/v14122680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/25/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022] Open
Abstract
Based on analyses of recent open-source data, this paper describes novel horizons in the diversity and taxonomy of beny-like viruses infecting hosts of the plant kingdom (Plantae or Archaeplastida). First, our data expand the known host range of the family Benyviridae to include red algae. Second, our phylogenetic analysis suggests that the evolution of this virus family may have involved cross-kingdom host change events and gene recombination/exchanges between distant taxa. Third, the identification of gene blocks encoding known movement proteins in beny-like RNA viruses infecting non-vascular plants confirms other evidence that plant virus genomic RNAs may have acquired movement proteins simultaneously or even prior to the evolutionary emergence of the plant vascular system. Fourth, novel data on plant virus diversity highlight that molecular evolution gave rise to numerous provisional species of land-plant-infecting viruses, which encode no known potential movement genetic systems.
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Affiliation(s)
- Andrey G. Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
- All Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Sergey Y. Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia
- Department of Virology, Biological Faculty, Moscow State University, 119234 Moscow, Russia
- Correspondence: ; Tel.: +7-(495)-9393198
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Schönegger D, Marais A, Faure C, Candresse T. A new flavi-like virus identified in populations of wild carrots. Arch Virol 2022; 167:2407-2409. [PMID: 35962825 DOI: 10.1007/s00705-022-05544-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022]
Abstract
We report the discovery of a new flavi-like virus identified in wild carrots (Daucus carota subsp. carota), using a double-stranded (ds)RNA high-throughput sequencing (HTS) approach. The new virus, tentatively named "carrot flavi-like virus 1" (CtFLV-1), has a large genome of 21.8 kb that harbours a single open reading frame encoding a 7,078-aa polyprotein with conserved RNA helicase (Hel) and RNA-dependent RNA polymerase (RdRp) domains. The new virus is phylogenetically related to recently described flavi-like viruses from arthropods, but its closest relative is a plant-associated virus, gentian Kobu-sho-associated virus (GKSaV). A pairwise comparison showed that these two viruses share 38.4% amino acid (aa) sequence identity in their polyproteins and 73% and 47.8% aa sequence identity in their conserved RdRp and Hel domains, respectively. Based on their similar genome organization and phylogenetic relationship, GKSaV and CtFLV-1 could form the basis for a new genus of plant-associated viruses, possibly within the family Flaviviridae, for which the name "Koshovirus" is proposed.
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Affiliation(s)
- Deborah Schönegger
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France.
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Complete genome sequence of peony leafroll-associated virus, a novel ampelovirus in subgroup I. Arch Virol 2022; 167:995-998. [PMID: 35133479 DOI: 10.1007/s00705-022-05389-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/04/2022] [Indexed: 11/02/2022]
Abstract
The complete genome sequence of peony leafroll-associated virus (PLRaV) was determined by deep sequencing of ribosomal-RNA-depleted total RNA extracted from a peony plant exhibiting leafroll symptoms. Further PCR and RACE analysis showed that the PLRaV genome consists of 15,406 nucleotides and contains 10 putative open reading frames, with an organization typical of members of the genus Ampelovirus, family Closteroviridae. Amino acid sequence comparisons showed that the viral heat shock protein 70 homolog (HSP70h) shared the highest sequence identity (41.7%) with the corresponding region of grapevine leafroll-associated virus 1, and the coat protein (CP) and RNA-dependent RNA polymerase (RdRp) shared the highest sequence identity (32.1% and 52.3%, respectively) with grapevine leafroll-associated virus 13. Phylogenetic analysis of the HSP70h, CP, and RdRp aa sequences showed that PLRaV clustered with members of subgroup I of the genus Ampelovirus.
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