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Cao C, Hu B, Li H, Wei Z, Li L, Zhang H, Chen J, Sun Z, Xu Z, Li Y. Metatranscriptome and small RNA sequencing revealed a mixed infection of newly identified bymovirus and bean yellow mosaic virus on peas. Virology 2024; 596:110116. [PMID: 38788336 DOI: 10.1016/j.virol.2024.110116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/11/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024]
Abstract
Peas (Pisum sativum L.) are widely cultivated in temperate regions and are susceptible hosts for various viruses across different families. The discovery and identification of new viruses in peas has significant implications for field disease management. Here, we identified a mixed infection of two viruses from field-collected peas exhibiting virus-like symptoms using metatranscriptome and small RNA sequencing techniques. Upon identification, one of the viruses was determined to be a newly isolated and discovered bymovirus from peas, named "pea bymovirus 1 (PBV1)". The other was identified as a novel variant of bean yellow mosaic virus (BYMV-HZ1). Subsequently, mechanical inoculation and RT-PCR assays confirmed that both viruses could be inoculated back onto peas and tobaccos, showing mixed infection by PBV1 and BYMV-HZ1. To our knowledge, this is the first isolation of a bymovirus from pea and the first documented case of mixed infection of peas by PBV1 and BYMV-HZ1 in China.
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Affiliation(s)
- Chen Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Biao Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Huajuan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Lulu Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Hehong Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zongtao Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhongtian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Yanjun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
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Shrestha N, Duvall MR, Bujarski JJ. Variability among the Isolates of Broad Bean Mottle Virus and Encapsidation of Host RNAs. Pathogens 2022; 11:pathogens11070817. [PMID: 35890061 PMCID: PMC9321246 DOI: 10.3390/pathogens11070817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/03/2022] [Accepted: 07/18/2022] [Indexed: 02/05/2023] Open
Abstract
Broad bean mottle bromovirus infects legume plants and is transmissible by insects. Several broad bean mottle virus (BBMV) isolates have been identified, including one in England (isolate Ba) and five in the Mediterranean countries: Libya (LyV), Morocco (MV), Syria (SV), Sudan (TU) and Tunisia (TV). Previously, we analyzed the nucleotide sequence of the Ba RNA and here we report on and compare it with another five Mediterranean variants. The RNA segments in the latter ones were extensively homologous, with some SNPs, single nucleotide deletions and insertions, while the number of mutations was higher in isolate Ba. Both the 5′ and 3′ untranslated terminal regions (UTRs) among the corresponding RNAs are highly conserved, reflecting their functionality in virus replication. The AUG initiation codons are within suboptimal contexts, possibly to adjust/regulate translation. The proteins 1a, 2a, 3a and coat protein (CP) are almost identical among the five isolates, but in Ba they have more amino acid (aa) substitutions. Phylogenetic analysis revealed the isolates from Morocco and Syria clustering with the isolate from England, while the variants from Libya, Tunisia and Sudan created a different clade. The BBMV isolates encapsidate a high content of host (ribosomal and messenger) RNAs. Our studies present BBMV as a useful model for bromoviruses infecting legumes.
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Affiliation(s)
- Nipin Shrestha
- Correspondence: (N.S.); (J.J.B.); Tel.: +1-305-684-2589 (N.S.); +1-815-753-0601 (J.J.B.); Fax: +1-815-753-7855 (J.J.B.)
| | | | - Jozef J. Bujarski
- Correspondence: (N.S.); (J.J.B.); Tel.: +1-305-684-2589 (N.S.); +1-815-753-0601 (J.J.B.); Fax: +1-815-753-7855 (J.J.B.)
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Šafářová D, Candresse T, Navrátil M. Complete genome sequence of a novel bromovirus infecting elderberry (Sambucus nigra L.) in the Czech Republic. Arch Virol 2017; 163:567-570. [PMID: 29094240 DOI: 10.1007/s00705-017-3629-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
Abstract
The genus Bromovirus currently contains six species whose members have relatively narrow host ranges. In the present work, a new bromovirus infecting elderberry (Sambucus nigra L.) is reported. dsRNA was purified and sequenced by next-generation sequencing, and with minimal additional completion by Sanger sequencing, the full tripartite genome was obtained. RNA1 is 3241 nt long and contains ORF1 (1a protein), RNA2 is 2810 nt long and contains ORF2 (2a protein), and RNA3 is 2244 nt long and contains ORF3a (movement protein) and ORF3b (coat protein, CP), separated by an intercistronic poly(A) stretch. Proteins 1a and 2a showed highest sequence identity (69.9% and 69.4%) to the corresponding proteins of melandrium yellow fleck virus. The coat protein showed highest sequence identity (67.9%) to that of brome mosaic virus. The genome shows a typical bromovirus organisation comprising of all the conserved protein domains within the genus. Phylogenetic analysis supports the assignment of this virus as a new member of the genus Bromovirus, for which the name "sambucus virus S" (SVS) is proposed.
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Affiliation(s)
- Dana Šafářová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic.
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Milan Navrátil
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic
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Hema M, Sreenivasulu P, Patil BL, Kumar PL, Reddy DVR. Tropical food legumes: virus diseases of economic importance and their control. Adv Virus Res 2015; 90:431-505. [PMID: 25410108 DOI: 10.1016/b978-0-12-801246-8.00009-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diverse array of food legume crops (Fabaceae: Papilionoideae) have been adopted worldwide for their protein-rich seed. Choice of legumes and their importance vary in different parts of the world. The economically important legumes are severely affected by a range of virus diseases causing significant economic losses due to reduction in grain production, poor quality seed, and costs incurred in phytosanitation and disease control. The majority of the viruses infecting legumes are vectored by insects, and several of them are also seed transmitted, thus assuming importance in the quarantine and in the epidemiology. This review is focused on the economically important viruses of soybean, groundnut, common bean, cowpea, pigeonpea, mungbean, urdbean, chickpea, pea, faba bean, and lentil and begomovirus diseases of three minor tropical food legumes (hyacinth bean, horse gram, and lima bean). Aspects included are geographic distribution, impact on crop growth and yields, virus characteristics, diagnosis of causal viruses, disease epidemiology, and options for control. Effectiveness of selection and planting with virus-free seed, phytosanitation, manipulation of crop cultural and agronomic practices, control of virus vectors and host plant resistance, and potential of transgenic resistance for legume virus disease control are discussed.
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Affiliation(s)
- Masarapu Hema
- Department of Virology, Sri Venkateswara University, Tirupati, India
| | - Pothur Sreenivasulu
- Formerly Professor of Virology, Sri Venkateswara University, Tirupati, India
| | - Basavaprabhu L Patil
- National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi, India
| | - P Lava Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Dodla V R Reddy
- Formerly Principal Virologist, ICRISAT, Patancheru, Hyderabad, India.
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Ghannam A, Kumari S, Muyldermans S, Abbady AQ. Camelid nanobodies with high affinity for broad bean mottle virus: a possible promising tool to immunomodulate plant resistance against viruses. PLANT MOLECULAR BIOLOGY 2015; 87:355-69. [PMID: 25648551 DOI: 10.1007/s11103-015-0282-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 01/06/2015] [Indexed: 05/03/2023]
Abstract
Worldwide, plant viral infections decrease seriously the crop production yield, boosting the demand to develop new strategies to control viral diseases. One of these strategies to prevent viral infections, based on the immunomodulation faces many problems related to the ectopic expression of specific antibodies in planta. Camelid nanobodies, expressed in plants, may offer a solution as they are an attractive tool to bind efficiently to viral epitopes, cryptic or not accessible to conventional antibodies. Here, we report a novel, generic approach that might lead to virus resistance based on the expression of camelid specific nanobodies against Broad bean mottle virus (BBMV). Eight nanobodies, recognizing BBMV with high specificity and affinity, were retrieved after phage display from a large 'immune' library constructed from an immunized Arabic camel. By an in vitro assay we demonstrate how three nanobodies attenuate the BBMV spreading in inoculated Vicia faba plants. Furthermore, the in planta transient expression of these three selected nanobodies confirms their virus neutralizing capacity. In conclusion, this report supports that plant resistance against viral infections can be achieved by the in vivo expression of camelid nanobodies.
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Affiliation(s)
- Ahmed Ghannam
- Division of Plant Pathology, Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), P. O. Box 6091, Damascus, Syria,
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Abstract
Cool-season grain legume crops become infected with a wide range of viruses, many of which cause serious diseases and major yield losses. This review starts by discussing which viruses are important in the principal cool-season grain legume crops in different parts of the world, the losses they cause and their economic impacts in relation to control. It then describes the main types of control measures available: host resistance, phytosanitary measures, cultural measures, chemical control, and biological control. Examples are provided of successful deployment of the different types of measures to control virus epidemics in cool-season grain legume crops. Next it emphasizes the need for integrated approaches to control because single control measures used alone rarely suffice to adequately reduce virus-induced yield losses in these crops. Development of effective integrated disease management (IDM) strategies depends on an interdisciplinary team approach to (i) understand the ecological and climatic factors which lead to damaging virus epidemics and (ii) evaluate the effectiveness of individual control measures. In addition to using virus-resistant cultivars, other IDM components include sowing virus-tested seed stocks, selecting cultivars with low seed transmission rates, using diverse phytosanitary or cultural practices that minimize the virus source or reduce its spread, and using selective pesticides in an environmentally responsible way. The review finishes by briefly discussing the implications of climate change in increasing problems associated with control and the opportunities to control virus diseases more effectively through new technologies.
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Abstract
In the Mediterranean region, pea, bean, and faba bean production is affected by around 17 major viruses. These viruses do not have the same ecology and consequently require a variety of different preventive measures to control them. Some of these viruses have a narrow host range, such as Faba bean necrotic yellows virus (FBNYV), and others, such as Alfalfa mosaic virus (AMV) and Cucumber mosaic virus (CMV), a very wide host range. Such features are important when identifying sources of virus inoculum in a region, and the vectors can transmit viruses from natural reservoirs to the crop plants. Some of these viruses are seed borne and, consequently, can be disseminated long distances through infected seeds. Crop losses caused by these viruses are variable, depending on the sensitivity and susceptibility of the crop to infection. Host resistance genes have been identified for some of these viruses, but in others, such as FBNYV, no resistance genes in faba bean have been identified yet. Significant progress was made in developing precise methods for the identification of these viruses, and new virus problems are being identified every year. This chapter is not intended to be a review for pea, bean, and faba bean viruses, but rather focuses on the major viruses which affect these crops in the Mediterranean basin with focus on the progress made over the past two decades.
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Affiliation(s)
- Khaled Makkouk
- National Council for Scientific Research, Beirut, Lebanon
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Broad bean mottle virus in Morocco; curculionid vectors, and natural occurrence in food legumes other than faba bean (Vicia faba). ACTA ACUST UNITED AC 1993. [DOI: 10.1007/bf01974666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Broad bean mottle virus in Morocco; variability, interaction with food legume species, and seed transmission in faba bean, pea, and chickpea. ACTA ACUST UNITED AC 1992. [DOI: 10.1007/bf01974461] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Fortass M, Bos L. Survey of faba bean (Vicia faba L.) for viruses in Morocco. ACTA ACUST UNITED AC 1991. [DOI: 10.1007/bf03041385] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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