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Sayiprathap BR, Patibanda AK, Mantesh M, Hiremath S, Sagar N, Reddy CNL, Jahir Basha CR, Diwakar Reddy SE, Kasi Rao M, Nair RM, Sudini HK. Sterility Mosaic Disease of Pigeonpea ( Cajanus cajan (L.) Huth): Current Status, Disease Management Strategies, and Future Prospects. PLANTS (BASEL, SWITZERLAND) 2024; 13:2146. [PMID: 39124264 PMCID: PMC11313807 DOI: 10.3390/plants13152146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024]
Abstract
Pigeonpea (Cajanus cajan) is one of the important grain legume crops cultivated in the semi-arid tropics, playing a crucial role in the economic well-being of subsistence farmers. India is the major producer of pigeonpea, accounting for over 75% of the world's production. Sterility mosaic disease (SMD), caused by Pigeonpea sterility mosaic virus (PPSMV) and transmitted by the eriophyid mite (Aceria cajani), is a major constraint to pigeonpea cultivation in the Indian subcontinent, leading to potential yield losses of up to 100%. The recent characterization of another Emaravirus associated with SMD has further complicated the etiology of this challenging viral disease. This review focuses on critical areas, including the current status of the disease, transmission and host-range, rapid phenotyping techniques, as well as available disease management strategies. The review concludes with insights into the future prospects, offering an overview and direction for further research and management strategies.
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Affiliation(s)
- B. R. Sayiprathap
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, Telangana, India
- World Vegetable Center, South and Central Asia, ICRISAT Campus, Patancheru, Hyderabad 502324, Telangana, India;
| | - A. K. Patibanda
- Department of Plant Pathology, Acharya NG Ranga Agricultural University, Lam, Guntur 522034, Andhra Pradesh, India;
| | - Muttappagol Mantesh
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, Gandhi Krishi Vigynan Kendra (GKVK), Bengaluru 560065, Karnataka, India (C.N.L.R.); (C.R.J.B.)
| | - Shridhar Hiremath
- CSIR—North East Institute of Science and Technology, Jorhat 785006, Assam, India
| | - N. Sagar
- Department of Plant Pathology, University of Agricultural Sciences, Dharwad 580005, Karnataka, India
| | - C. N. Lakshminarayana Reddy
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, Gandhi Krishi Vigynan Kendra (GKVK), Bengaluru 560065, Karnataka, India (C.N.L.R.); (C.R.J.B.)
| | - C. R. Jahir Basha
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, Gandhi Krishi Vigynan Kendra (GKVK), Bengaluru 560065, Karnataka, India (C.N.L.R.); (C.R.J.B.)
| | - S. E. Diwakar Reddy
- Department of Plant Pathology, University of Agricultural Sciences, Dharwad 580005, Karnataka, India
| | - M. Kasi Rao
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, Telangana, India
- School of Agriculture, Mohan Babu University, Tirupati 517102, Andhra Pradesh, India
| | - R. M. Nair
- World Vegetable Center, South and Central Asia, ICRISAT Campus, Patancheru, Hyderabad 502324, Telangana, India;
| | - H. K. Sudini
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, Telangana, India
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Nourinejhad Zarghani S, Al Kubrusli R, Iancev S, Jalkanen R, Büttner C, von Bargen S. Molecular Population Genetics of Aspen Mosaic-Associated Virus in Finland and Sweden. Viruses 2023; 15:1678. [PMID: 37632020 PMCID: PMC10460043 DOI: 10.3390/v15081678] [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: 07/20/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Aspen mosaic-associated virus (AsMaV) is a newly identified Emaravirus, in the family Fimoviridae, Bunyavirales, associated with mosaic symptoms in aspen trees (Populus tremula). Aspen trees are widely distributed in Europe and understanding the population structure of AsMaV may aid in the development of better management strategies. The virus genome consists of five negative-sense single-stranded RNA (-ssRNA) molecules. To investigate the genetic diversity and population parameters of AsMaV, different regions of the genome were amplified and analyzed and full-length sequence of the divergent isolates were cloned and sequenced. The results show that RNA3 or nucleoprotein is a good representative for studying genetic diversity in AsMaV. Developed RT-PCR-RFLP was able to identify areas with a higher number of haplotypes and could be applied for screening the large number of samples. In general, AsMaV has a conserved genome and based on the phylogenetic studies, geographical structuring was observed in AsMaV isolates from Sweden and Finland, which could be attributed to founder effects. The genome of AsMaV is under purifying selection but not distributed uniformly on genomic RNAs. Distant AsMaV isolates displayed amino acid sequence variations compared to other isolates, and bioinformatic analysis predicted potential post-translational modification sites in some viral proteins.
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Affiliation(s)
- Shaheen Nourinejhad Zarghani
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Serghei Iancev
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | | | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Lentzeallee 55-57, 14197 Berlin, Germany; (S.N.Z.); (R.A.K.); (C.B.)
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Liang X, Mei S, Yu H, Zhang S, Wu J, Cao M. Mixed infection of an emaravirus, a crinivirus, and a begomovirus in Pueraria lobata (Willd) Ohwi. Front Microbiol 2022; 13:926724. [PMID: 36246248 PMCID: PMC9557060 DOI: 10.3389/fmicb.2022.926724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Pueraria lobata (Willd) (Pueraria montana var. lobata (Willd.) Maesen & S. M. Almeida ex Sanjappa & Predeep) is an important herbal medicine used in many countries. In P. lobata plants showing symptoms of mosaic, yellow spots, and mottling, mixed infection of new viruses provisionally named Pueraria lobata-associated emaravirus (PloAEV, genus Emaravirus), Pueraria lobata-associated crinivirus (PloACV, genus Crinivirus), and isolate CQ of the previously reported kudzu mosaic virus (KuMV-CQ, genus Begomovirus) was confirmed through high-throughput sequencing. PloAEV has five RNA segments, encoding a putative RNA-dependent RNA polymerase, glycoprotein precursor, nucleocapsid protein, movement protein, and P5, respectively. PloACV has two RNA segments, encoding 11 putative proteins. Only PloAEV could be mechanically transmitted from mixed infected symptomatic kudzu to Nicotiana benthamiana plants. All three viruses were detected in 35 symptomatic samples collected from five different growing areas, whereas no viruses were detected in 21 non-symptomatic plants, suggesting a high association between these three viruses. Thus, this study provides new knowledge on the diversity and molecular characteristics of viruses in P. lobata plants affected by the viral disease.
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Urrutia CD, Romay G, Shaw BD, Verchot J. Advancing the Rose Rosette Virus Minireplicon and Encapsidation System by Incorporating GFP, Mutations, and the CMV 2b Silencing Suppressor. Viruses 2022; 14:836. [PMID: 35458566 PMCID: PMC9031449 DOI: 10.3390/v14040836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/01/2022] [Accepted: 04/13/2022] [Indexed: 11/26/2022] Open
Abstract
Plant infecting emaraviruses have segmented negative strand RNA genomes and little is known about their infection cycles due to the lack of molecular tools for reverse genetic studies. Therefore, we innovated a rose rosette virus (RRV) minireplicon containing the green fluorescent protein (GFP) gene to study the molecular requirements for virus replication and encapsidation. Sequence comparisons among RRV isolates and structural modeling of the RNA dependent RNA polymerase (RdRp) and nucleocapsid (N) revealed three natural mutations of the type species isolate that we reverted to the common species sequences: (a) twenty-one amino acid truncations near the endonuclease domain (named delA), (b) five amino acid substitutions near the putative viral RNA binding loop (subT), and (c) four amino acid substitutions in N (NISE). The delA and subT in the RdRp influenced the levels of GFP, gRNA, and agRNA at 3 but not 5 days post inoculation (dpi), suggesting these sequences are essential for initiating RNA synthesis and replication. The NISE mutation led to sustained GFP, gRNA, and agRNA at 3 and 5 dpi indicating that the N supports continuous replication and GFP expression. Next, we showed that the cucumber mosaic virus (CMV strain FNY) 2b singularly enhanced GFP expression and RRV replication. Including agRNA2 with the RRV replicon produced observable virions. In this study we developed a robust reverse genetic system for investigations into RRV replication and virion assembly that could be a model for other emaravirus species.
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Affiliation(s)
| | | | | | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77845, USA; (C.D.U.); (G.R.); (B.D.S.)
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Sayiprathap BR, Patibanda AK, Prasanna Kumari V, Jayalalitha K, Ramappa HK, Rajeswari E, Karthiba L, Saratbabu K, Sharma M, Sudini HK. Salient Findings on Host Range, Resistance Screening, and Molecular Studies on Sterility Mosaic Disease of Pigeonpea Induced by Pigeonpea sterility mosaic viruses ( PPSMV-I and PPSMV-II). Front Microbiol 2022; 13:838047. [PMID: 35432270 PMCID: PMC9012581 DOI: 10.3389/fmicb.2022.838047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Two distinct emaraviruses, Pigeonpea sterility mosaic virus-I (PPSMV-I) and Pigeonpea sterility mosaic virus-II (PPSMV-II) were found to be associated with sterility mosaic disease (SMD) of pigeonpea [Cajanus cajan (L.) Millsp.]. The host range of both these viruses and their vector are narrow, confined to Nicotiana benthamiana identified through mechanical transmission, and to Phaseolus vulgaris cvs. Top Crop, Kintoki, and Bountiful (F: Fabaceae) through mite transmission. A weed host Chrozophora rottleri (F: Euphorbiaceae) was also infected and tested positive for both the viruses in RT-PCR. Among the wild Cajanus species tested, Cajanus platycarpus accessions 15661, 15668, and 15671, and Cajanus scarabaeoides accessions 15683, 15686, and 15922 were infected by both the viruses and mite vector suggesting possible sources of SMD inoculum. Though accession 15666 of C. platycarpus, 15696 of C. scarabaeoides, and 15639 of Cajanus lanceolatus were infected by both the viruses, no mite infestation was observed on them. Phylogenetic analysis of nucleotide sequences of RNA-1 and RNA-2 of PPSMV-I and PPSMV-II isolates in southern India revealed significant divergence especially PPSMV-II, which is closely related to the Fig mosaic virus (FMV) than PPSMV-I. In multilocation testing of pigeonpea genotypes for their broad-based resistance to SMD for two consecutive years, genotypes ICPL-16086 and ICPL-16087 showed resistance reaction (<10% incidence) in all three locations studied. Overall, the present study gives a clear idea about the host range of PPSMV-I and PPSMV-II, their molecular relationship, and sources of resistance. This information is critical for the development of reliable diagnostic tools and improved disease management strategies.
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Affiliation(s)
- B. R. Sayiprathap
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
- Department of Plant Pathology, Acharya N. G. Ranga Agricultural University, Guntur, India
| | - A. K. Patibanda
- Department of Plant Pathology, Acharya N. G. Ranga Agricultural University, Guntur, India
| | - V. Prasanna Kumari
- Department of Plant Pathology, Acharya N. G. Ranga Agricultural University, Guntur, India
| | - K. Jayalalitha
- Department of Crop Physiology, Acharya N. G. Ranga Agricultural University, Guntur, India
| | - H. K. Ramappa
- Department of Plant Pathology, University of Agricultural Sciences, Bengaluru, India
| | - E. Rajeswari
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, India
| | - L. Karthiba
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, India
| | - K. Saratbabu
- Department of Plant Pathology, Acharya N. G. Ranga Agricultural University, Guntur, India
| | - Mamta Sharma
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - H. K. Sudini
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
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Tatineni S, Hein GL. High Plains wheat mosaic virus: An enigmatic disease of wheat and corn causing the High Plains disease. MOLECULAR PLANT PATHOLOGY 2021; 22:1167-1179. [PMID: 34375024 PMCID: PMC8435230 DOI: 10.1111/mpp.13113] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/10/2021] [Accepted: 07/13/2021] [Indexed: 05/03/2023]
Abstract
BRIEF HISTORY In 1993, severe mosaic and necrosis symptoms were observed on corn (maize) and wheat from several Great Plains states of the USA. Based on the geographical location of infections, the disease was named High Plains disease and the causal agent was tentatively named High Plains virus. Subsequently, researchers renamed this virus as maize red stripe virus and wheat mosaic virus to represent the host and symptom phenotype of the virus. After sequencing the genome of the pathogen, the causal agent of High Plains disease was officially named as High Plains wheat mosaic virus. Hence, High Plains virus, maize red stripe virus, wheat mosaic virus, and High Plains wheat mosaic virus (HPWMoV) are synonyms for the causal agent of High Plains disease. TAXONOMY High Plains wheat mosaic virus is one of the 21 definitive species in the genus Emaravirus in the family Fimoviridae. VIRION The genomic RNAs are encapsidated in thread-like nucleocapsids in double-membrane 80-200 nm spherical or ovoid virions. GENOME CHARACTERIZATION The HPWMoV genome consists of eight single-stranded negative-sense RNA segments encoding a single open reading frame (ORF) in each genomic RNA segment. RNA 1 is 6,981-nucleotide (nt) long, coding for a 2,272 amino acid protein of RNA-dependent RNA polymerase. RNA 2 is 2,211-nt long and codes for a 667 amino acid glycoprotein precursor. RNA 3 has two variants of 1,439- and 1,441-nt length that code for 286 and 289 amino acid nucleocapsid proteins, respectively. RNA 4 is 1,682-nt long, coding for a 364 amino acid protein. RNA 5 and RNA 6 are 1,715- and 1,752-nt long, respectively, and code for 478 and 492 amino acid proteins, respectively. RNA 7 and RNA 8 are 1,434- and 1,339-nt long, code for 305 and 176 amino acid proteins, respectively. BIOLOGICAL PROPERTIES HPWMoV can infect wheat, corn (maize), barley, rye brome, oat, rye, green foxtail, yellow foxtail, and foxtail barley. HPWMoV is transmitted by the wheat curl mite and through corn seed. DISEASE MANAGEMENT Genetic resistance against HPWMoV in wheat is not available, but most commercial corn hybrids are resistant while sweet corn varieties remain susceptible. Even though corn hybrids are resistant to virus, it still serves as a green bridge host that enables mites to carry the virus from corn to new crop wheat in the autumn. The main management strategy for High Plains disease in wheat relies on the management of green bridge hosts. Cultural practices such as avoiding early planting can be used to avoid mite buildup and virus infections.
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Affiliation(s)
- Satyanarayana Tatineni
- USDA‐ARS and Department of Plant PathologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
| | - Gary L. Hein
- Department of EntomologyUniversity of Nebraska‐LincolnLincolnNebraskaUSA
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Kormelink R, Verchot J, Tao X, Desbiez C. The Bunyavirales: The Plant-Infecting Counterparts. Viruses 2021; 13:842. [PMID: 34066457 PMCID: PMC8148189 DOI: 10.3390/v13050842] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/18/2022] Open
Abstract
Negative-strand (-) RNA viruses (NSVs) comprise a large and diverse group of viruses that are generally divided in those with non-segmented and those with segmented genomes. Whereas most NSVs infect animals and humans, the smaller group of the plant-infecting counterparts is expanding, with many causing devastating diseases worldwide, affecting a large number of major bulk and high-value food crops. In 2018, the taxonomy of segmented NSVs faced a major reorganization with the establishment of the order Bunyavirales. This article overviews the major plant viruses that are part of the order, i.e., orthospoviruses (Tospoviridae), tenuiviruses (Phenuiviridae), and emaraviruses (Fimoviridae), and provides updates on the more recent ongoing research. Features shared with the animal-infecting counterparts are mentioned, however, special attention is given to their adaptation to plant hosts and vector transmission, including intra/intercellular trafficking and viral counter defense to antiviral RNAi.
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Affiliation(s)
- Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA;
| | - Xiaorong Tao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China;
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High-Throughput Sequencing Indicates Novel Varicosavirus, Emaravirus, and Deltapartitivirus Infections in Vitis coignetiae. Viruses 2021; 13:v13050827. [PMID: 34063722 PMCID: PMC8147796 DOI: 10.3390/v13050827] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/01/2021] [Accepted: 05/02/2021] [Indexed: 11/17/2022] Open
Abstract
Vitis coignetiae samples were collected from several locations in the northern area of Japan, and virome analysis using a high-throughput sequencing technique was performed. The data indicated that some of the collected samples were in mixed infections by various RNA viruses. Among these viruses, three were identified as newly recognized species with support of sequence identity and phylogenetic analysis. The viruses have been provisionally named the Vitis varicosavirus, Vitis emaravirus, and Vitis crypticvirus, and were assigned to the genus Varicosavirus, Emaravirus, and Deltapartitivirus, respectively.
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Saxena RK, Hake A, Bohra A, Khan AW, Hingane A, Sultana R, Singh IP, Naik SJS, Varshney RK. A diagnostic marker kit for Fusarium wilt and sterility mosaic diseases resistance in pigeonpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:367-379. [PMID: 33079215 PMCID: PMC7813729 DOI: 10.1007/s00122-020-03702-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/03/2020] [Indexed: 05/29/2023]
Abstract
Fusarium wilt (FW) and sterility mosaic diseases (SMD) are key biotic constraints to pigeonpea production. Occurrence of these two diseases in congenial conditions is reported to cause complete yield loss in susceptible pigeonpea cultivars. Various studies to elucidate genomic architecture of the two traits have revealed significant marker-trait associations for use in breeding programs. However, these DNA markers could not be used effectively in genomics-assisted breeding for developing FW and SMD resistant varieties primarily due to pathogen variability, location or background specificity, lesser phenotypic variance explained by the reported QTL and cost-inefficiency of the genotyping assays. Therefore, in the present study, a novel approach has been used to develop a diagnostic kit for identification of suitable FW and SMD resistant lines. This kit was developed with 10 markers each for FW and SMD resistance. Investigation of the diversity of these loci has shown the role of different alleles in different resistant genotypes. Two genes (C.cajan_03691 and C.cajan_18888) for FW resistance and four genes (C.cajan_07858, C.cajan_20995, C.cajan_21801 and C.cajan_17341) for SMD resistance have been identified. More importantly, we developed a customized and cost-effective Kompetitive allele-specific PCR genotyping assay for the identified genes in order to encourage their downstream applications in pigeonpea breeding programs. The diagnostic marker kit developed here will offer great strength to pigeonpea varietal development program, since the resistance against these two diseases is essentially required for nominating an improved line in varietal release pipeline.
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Affiliation(s)
- Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India.
| | - Anil Hake
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Abhishek Bohra
- ICAR- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - Aamir W Khan
- ICAR- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - Anupama Hingane
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Rafat Sultana
- Bihar Agricultural University, Sabour, Bhagalpur, Bihar, India
| | - Indra Prakash Singh
- ICAR- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - S J Satheesh Naik
- ICAR- Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India.
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Kubota K, Chiaki Y, Yanagisawa H, Yamasaki J, Horikawa H, Tsunekawa K, Morita Y. Novel degenerate primer sets for the detection and identification of emaraviruses reveal new chrysanthemum species. J Virol Methods 2020; 288:113992. [PMID: 33045282 DOI: 10.1016/j.jviromet.2020.113992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/09/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022]
Abstract
Emaraviruses are a genus of plant viruses that have been newly described in the past decade. These viruses, some of which are transmitted by eriophyid mites, are important pathogens of cereals, fruits, and ornamental trees worldwide. This study used sequence data for emaraviruses to design new degenerate primer sets that identify an extensive range of known and unknown emaraviruses. Sequence alignment of the amino acid and nucleotide sequences of RNA-dependent RNA polymerases for 11 accessions among nine emaraviruses confirmed the presence of seven conserved motifs (Pre-A, F, A, B, C, D, and E). Subsequently, new degenerate primers were designed based on motifs F, A, and B, which were the most conserved among the seven motifs. Reverse transcription-polymerase chain reaction using these primers detected known emaraviruses more efficiently than previously known primers. These new primers enabled the identification of a partial nucleotide sequence of a putative novel emaravirus from chrysanthemum leaves showing mosaic or yellowish ringspot symptoms known to be associated with eriophyid mites, Paraphytoptus kikus. These sequences were specifically detected from the symptomatic leaves of a chrysanthemum, and the putative emaravirus was tentatively named chrysanthemum mosaic-associated virus.
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Affiliation(s)
- Kenji Kubota
- Central Region Agricultural Research Center, NARO, Kannondai, Tsukuba, Ibaraki 305-8666, Japan.
| | - Yuya Chiaki
- Central Region Agricultural Research Center, NARO, Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Hironobu Yanagisawa
- Central Region Agricultural Research Center, NARO, Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Junki Yamasaki
- Kochi Agricultural Research Center, Hataeda, Nankoku, Kochi 783-0023, Japan
| | - Hidenori Horikawa
- Aichi Agricultural Research Center, Sagamine, Yazako, Nagakute, Aichi 480-1193, Japan
| | - Kenta Tsunekawa
- Aichi Agricultural Research Center, Sagamine, Yazako, Nagakute, Aichi 480-1193, Japan
| | - Yasuaki Morita
- Kochi Agricultural Research Center, Hataeda, Nankoku, Kochi 783-0023, Japan
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Bejerman N, Debat H, Dietzgen RG. The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes. Front Microbiol 2020; 11:588427. [PMID: 33042103 PMCID: PMC7524893 DOI: 10.3389/fmicb.2020.588427] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
The use of high-throughput sequencing (HTS) for virus diagnostics, as well as the importance of this technology as a valuable tool for discovery of novel viruses has been extensively investigated. In this review, we consider the application of HTS approaches to uncover novel plant viruses with a focus on the negative-sense, single-stranded RNA virosphere. Plant viruses with negative-sense and ambisense RNA (NSR) genomes belong to several taxonomic families, including Rhabdoviridae, Aspiviridae, Fimoviridae, Tospoviridae, and Phenuiviridae. They include both emergent pathogens that infect a wide range of plant species, and potential endophytes which appear not to induce any visible symptoms. As a consequence of biased sampling based on a narrow focus on crops with disease symptoms, the number of NSR plant viruses identified so far represents only a fraction of this type of viruses present in the virosphere. Detection and molecular characterization of NSR viruses has often been challenging, but the widespread implementation of HTS has facilitated not only the identification but also the characterization of the genomic sequences of at least 70 NSR plant viruses in the last 7 years. Moreover, continuing advances in HTS technologies and bioinformatic pipelines, concomitant with a significant cost reduction has led to its use as a routine method of choice, supporting the foundations of a diverse array of novel applications such as quarantine analysis of traded plant materials and genetic resources, virus detection in insect vectors, analysis of virus communities in individual plants, and assessment of virus evolution through ecogenomics, among others. The insights from these advancements are shedding new light on the extensive diversity of NSR plant viruses and their complex evolution, and provide an essential framework for improved taxonomic classification of plant NSR viruses as part of the realm Riboviria. Thus, HTS-based methods for virus discovery, our ‘new eyes,’ are unraveling in real time the richness and magnitude of the plant RNA virosphere.
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Affiliation(s)
- Nicolás Bejerman
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Humberto Debat
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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Kubota K, Usugi T, Tomitaka Y, Shimomoto Y, Takeuchi S, Kadono F, Yanagisawa H, Chiaki Y, Tsuda S. Perilla Mosaic Virus Is a Highly Divergent Emaravirus Transmitted by Shevtchenkella sp. (Acari: Eriophyidae). PHYTOPATHOLOGY 2020; 110:1352-1361. [PMID: 32202482 DOI: 10.1094/phyto-01-20-0013-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Shiso (Perilla frutescens var. crispa) is widely grown as an important vegetable or herb crop in Japan. Beginning around the year 2000, occurrences of severe mosaic symptoms on shiso were documented and gradually spread across Kochi Prefecture, one of four major shiso production areas in Japan. Next generation sequencing and cloning indicated the presence of a previously unknown virus related to the members of the genus Emaravirus, for which we proposed the name Perilla mosaic virus (PerMV). The genome of PerMV consists of 10 RNA segments, each encoding a single protein in the negative-sense orientation. Of these proteins, P1, P2, P3a, P3b, P4, and P5 show amino acid sequence similarities with those of known emaraviruses, whereas no similarities were found in P6a, P6b, P6c, and P7. Characteristics of the RNA segments as well as phylogenetic analysis of P1 to P4 indicate that PerMV is a distinct and highly divergent emaravirus. Electron microscopy observations and protein analyses corresponded to presence of an emaravirus. Transmission experiments demonstrated that an eriophyid mite, Shevtchenkella sp. (family Eriophyidae), transmits PerMV with a minimum 30-min acquisition access period. Only plants belonging to the genus Perilla tested positive for PerMV, and the plant-virus-vector interactions were evaluated. The nucleotide sequences reported here are available in the DDBJ/ENA/GenBank databases under accession numbers LC496090 to LC496099.
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Affiliation(s)
- Kenji Kubota
- Central Region Agricultural Research Center, NARO, Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Tomio Usugi
- Central Region Agricultural Research Center, NARO, Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Yasuhiro Tomitaka
- Kyushu Okinawa Agricultural Research Center, NARO, Suya, Koshi, Kumamoto 861-1192, Japan
| | | | - Shigeharu Takeuchi
- Kochi Agricultural Research Center, Hataeda, Nankoku, Kochi 783-0023, Japan
| | - Fujio Kadono
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Kajino-cho, Koganei, Tokyo 184-8584, Japan
| | - Hironobu Yanagisawa
- Central Region Agricultural Research Center, NARO, Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Yuya Chiaki
- Central Region Agricultural Research Center, NARO, Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Shinya Tsuda
- Central Region Agricultural Research Center, NARO, Kannondai, Tsukuba, Ibaraki 305-8666, Japan
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Katsiani A, Stainton D, Lamour K, Tzanetakis IE. The population structure of Rose rosette virus in the USA. J Gen Virol 2020; 101:676-684. [PMID: 32375952 DOI: 10.1099/jgv.0.001418] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rose rosette virus (RRV) (genus Emaravirus) is the causal agent of the homonymous disease, the most destructive malady of roses in the USA. Although the importance of the disease is recognized, little sequence information and no full genomes are available for RRV, a multi-segmented RNA virus. To better understand the population structure of the virus we implemented a Hi-Plex PCR amplicon high-throughput sequencing approach to sequence all 7 segments and to quantify polymorphisms in 91 RRV isolates collected from 16 states in the USA. Analysis revealed insertion/deletion (indel) polymorphisms primarily in the 5' and 3' non-coding, but also within coding regions, including some resulting in changes of protein length. Phylogenetic analysis showed little geographical structuring, suggesting that topography does not have a strong influence on virus evolution. Overall, the virus populations were homogeneous, possibly because of regular movement of plants, the recent emergence of RRV and/or because the virus is under strong purification selection to preserve its integrity and biological functions.
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Affiliation(s)
- Asimina Katsiani
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
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Chen Y, Dessau M, Rotenberg D, Rasmussen DA, Whitfield AE. Entry of bunyaviruses into plants and vectors. Adv Virus Res 2019; 104:65-96. [PMID: 31439153 DOI: 10.1016/bs.aivir.2019.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The majority of plant-infecting viruses are transmitted by arthropod vectors that deliver them directly into a living plant cell. There are diverse mechanisms of transmission ranging from direct binding to the insect stylet (non-persistent transmission) to persistent-propagative transmission in which the virus replicates in the insect vector. Despite this diversity in interactions, most arthropods that serve as efficient vectors have feeding strategies that enable them to deliver the virus into the plant cell without extensive damage to the plant and thus effectively inoculate the plant. As such, the primary virus entry mechanism for plant viruses is mediated by the biological vector. Remarkably, viruses that are transmitted in a propagative manner (bunyaviruses, rhabdoviruses, and reoviruses) have developed an ability to replicate in hosts from two kingdoms. Viruses in the order Bunyavirales are of emerging importance and with the advent of new sequencing technologies, we are getting unprecedented glimpses into the diversity of these viruses. Plant-infecting bunyaviruses are transmitted in a persistent, propagative manner must enter two unique types of host cells, plant and insect. In the insect phase of the virus life cycle, the propagative viruses likely use typical cellular entry strategies to traverse cell membranes. In this review, we highlight the transmission and entry strategies of three genera of plant-infecting bunyaviruses: orthotospoviruses, tenuiviruses, and emaraviruses.
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Affiliation(s)
- Yuting Chen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Moshe Dessau
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Dorith Rotenberg
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States.
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