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Belete MT, Kim SE, Gudeta WF, Igori D, Kwon JA, Lee SH, Moon JS. Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis. Virol J 2024; 21:86. [PMID: 38622686 PMCID: PMC11017662 DOI: 10.1186/s12985-024-02361-7] [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: 12/04/2023] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Viruses have notable effects on agroecosystems, wherein they can adversely affect plant health and cause problems (e.g., increased biosecurity risks and economic losses). However, our knowledge of their diversity and interactions with specific host plants in ecosystems remains limited. To enhance our understanding of the roles that viruses play in agroecosystems, comprehensive analyses of the viromes of a wide range of plants are essential. High-throughput sequencing (HTS) techniques are useful for conducting impartial and unbiased investigations of plant viromes, ultimately forming a basis for generating further biological and ecological insights. This study was conducted to thoroughly characterize the viral community dynamics in individual plants. RESULTS An HTS-based virome analysis in conjunction with proximity sampling and a tripartite network analysis were performed to investigate the viral diversity in chunkung (Cnidium officinale) plants. We identified 61 distinct chunkung plant-associated viruses (27 DNA and 34 RNA viruses) from 21 known genera and 6 unclassified genera in 14 known viral families. Notably, 12 persistent viruses (7 DNA and 5 RNA viruses) were exclusive to dwarfed chunkung plants. The detection of viruses from the families Partitiviridae, Picobirnaviridae, and Spinareoviridae only in the dwarfed plants suggested that they may contribute to the observed dwarfism. The co-infection of chunkung by multiple viruses is indicative of a dynamic and interactive viral ecosystem with significant sequence variability and evidence of recombination. CONCLUSIONS We revealed the viral community involved in chunkung. Our findings suggest that chunkung serves as a significant reservoir for a variety of plant viruses. Moreover, the co-infection rate of individual plants was unexpectedly high. Future research will need to elucidate the mechanisms enabling several dozen viruses to co-exist in chunkung. Nevertheless, the important insights into the chunkung virome generated in this study may be relevant to developing effective plant viral disease management and control strategies.
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Affiliation(s)
- Mesele Tilahun Belete
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Amhara Agricultural Research Institute, Plant Biotechnology Research Division, Bahir Dar, Ethiopia
| | - Se Eun Kim
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Workitu Firmosa Gudeta
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Davaajargal Igori
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Biology, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, Mongolia
| | - Jeong A Kwon
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Su-Heon Lee
- School of Applied Bioscience, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 98411, Republic of Korea.
| | - Jae Sun Moon
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
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Nemchinov LG, Grinstead S. Complete genome sequence of alfalfa-associated picorna-like virus 2. Microbiol Resour Announc 2024; 13:e0105223. [PMID: 38426729 PMCID: PMC11008146 DOI: 10.1128/mra.01052-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
We have previously reported on the detection of an unknown picorna-like virus in alfalfa samples. The exact host of the virus was unclear due to its similarity to the members of Iflaviridae family, which typically infect arthropods. The virus was provisionally named alfalfa-associated picorna-like virus 2. Here, we report a complete genomic sequence of the virus.
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Affiliation(s)
- Lev G. Nemchinov
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, USA
| | - Sam Grinstead
- USDA-ARS, Molecular Plant Pathology Laboratory, Beltsville, Maryland, USA
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3
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Nemchinov LG, Postnikova OA, Wintermantel WM, Palumbo JC, Grinstead S. Alfalfa vein mottling virus, a novel potyvirid infecting Medicago sativa L. Virol J 2023; 20:284. [PMID: 38037050 PMCID: PMC10690988 DOI: 10.1186/s12985-023-02250-5] [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: 09/08/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND We have recently identified a novel virus detected in alfalfa seed material. The virus was tentatively named alfalfa-associated potyvirus 1, as its genomic fragments bore similarities with potyvirids. In this study, we continued investigating this novel species, expanding information on its genomic features and biological characteristics. METHODS This research used a wide range of methodology to achieve end results: high throughput sequencing, bioinformatics tools, reverse transcription-polymerase chain reactions, differential diagnostics using indicator plants, virus purification, transmission electron microscopy, and others. RESULTS In this study, we obtained a complete genome sequence of the virus and classified it as a tentative species in the new genus, most closely related to the members of the genus Ipomovirus in the family Potyviridae. This assumption is based on the genome sequence and structure, phylogenetic relationships, and transmission electron microscopy investigations. We also demonstrated its mechanical transmission to the indicator plant Nicotiana benthamiana and to the natural host Medicago sativa, both of which developed characteristic symptoms therefore suggesting a pathogenic nature of the disease. CONCLUSIONS Consistent with symptomatology, the virus was renamed to alfalfa vein mottling virus. A name Alvemovirus was proposed for the new genus in the family Potyviridae, of which alfalfa vein mottling virus is a tentative member.
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Affiliation(s)
- Lev G Nemchinov
- USDA-ARS, NEA, BARC, Molecular Plant Pathology Laboratory, Beltsville, MD, USA.
| | - Olga A Postnikova
- USDA-ARS, NEA, BARC, Animal Biosciences and Biotechnology Laboratory, Beltsville, MD, USA
| | | | - John C Palumbo
- University of Arizona Yuma Agricultural Center, Yuma, AZ, USA
| | - Sam Grinstead
- USDA-ARS, NEA, BARC, Molecular Plant Pathology Laboratory, Beltsville, MD, USA
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Iwai K, Kon T, Fujita Y, Abe H, Honma H, Kawasumi N, Kawakami H, Kawashimo M, Sakurai M, Fuji SI. Genetic diversity of viruses infecting cnidium plants ( Cnidium officinale) in Japan. Virusdisease 2023; 34:431-439. [PMID: 37780903 PMCID: PMC10533470 DOI: 10.1007/s13337-023-00835-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/01/2023] [Indexed: 10/03/2023] Open
Abstract
Cnidium vein yellowing virus (CnVYV), cnidium virus X (CnVX), cucumber mosaic virus (CMV) and cnidium virus 1 (CnV1) were detected at extremely high levels in Cnidium officinale plants showing viral symptoms collected from Iwate and Hokkaido Prefectures, Japan. The complete nucleotide sequence of the newly detected CnVYV and CnV1, and genetic diversity of the cnidium-infecting viruses (CnVYV, CnVX, and CnV1) indicated that South Korean and Japanese cnidium plants had close relationship with each other. All three viruses can infect vegetatively propagated perennials and are vertically transmitted once infection occurs. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00835-w.
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Affiliation(s)
- Kazuma Iwai
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Tatsuya Kon
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Yuito Fujita
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Haruki Abe
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Hiroshi Honma
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Naoki Kawasumi
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Hiroko Kawakami
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
| | - Midori Kawashimo
- Botanical Raw Materials Division, Tsumura & Co., 3586 Yoshiwara, Ami-machi, Inashiki-gun, Ibaraki 300-1192 Japan
| | - Miki Sakurai
- Botanical Raw Materials Division, Tsumura & Co., 3586 Yoshiwara, Ami-machi, Inashiki-gun, Ibaraki 300-1192 Japan
| | - Shin-ichi Fuji
- Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi, Nakano, Shimoshinjo, Akita, 010-0195 Japan
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Nemchinov LG, Irish BM, Uschapovsky IV, Grinstead S, Shao J, Postnikova OA. Composition of the alfalfa pathobiome in commercial fields. Front Microbiol 2023; 14:1225781. [PMID: 37692394 PMCID: PMC10491455 DOI: 10.3389/fmicb.2023.1225781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023] Open
Abstract
Through the recent advances of modern high-throughput sequencing technologies, the "one microbe, one disease" dogma is being gradually replaced with the principle of the "pathobiome". Pathobiome is a comprehensive biotic environment that not only includes a diverse community of all disease-causing organisms within the plant but also defines their mutual interactions and resultant effect on plant health. To date, the concept of pathobiome as a major component in plant health and sustainable production of alfalfa (Medicago sativa L.), the most extensively cultivated forage legume in the world, is non-existent. Here, we approached this subject by characterizing the biodiversity of the alfalfa pathobiome using high-throughput sequencing technology. Our metagenomic study revealed a remarkable abundance of different pathogenic communities associated with alfalfa in the natural ecosystem. Profiling the alfalfa pathobiome is a starting point to assess known and identify new and emerging stress challenges in the context of plant disease management. In addition, it allows us to address the complexity of microbial interactions within the plant host and their impact on the development and evolution of pathogenesis.
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Affiliation(s)
- Lev G. Nemchinov
- Molecular Plant Pathology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Brian M. Irish
- Plant Germplasm Introduction and Testing Research Unit, Prosser, WA, United States
| | | | - Sam Grinstead
- Molecular Plant Pathology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Jonathan Shao
- United States Department of Agriculture, Agricultural Research Service, Office of The Area Director, Beltsville, MD, United States
| | - Olga A. Postnikova
- Molecular Plant Pathology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Center, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
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6
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Nemchinov LG, Irish BM, Grinstead S, Postnikova OA. Characterization of the seed virome of alfalfa (Medicago sativa L). Virol J 2023; 20:96. [PMID: 37208777 DOI: 10.1186/s12985-023-02063-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/05/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Seed transmission of plant viruses can be important due to the role it plays in their dissemination to new areas and subsequent epidemics. Seed transmission largely depends on the ability of a virus to replicate in reproductive tissues and survive during the seed maturation process. It occurs through the infected embryo or mechanically through the contaminated seed coat. Alfalfa (Medicago sativa L.) is an important legume forage crop worldwide, and except for a few individual seedborne viruses infecting the crop, its seed virome is poorly known. The goal of this research was to perform initial seed screenings on alfalfa germplasm accessions maintained by the USDA ARS National Plant Germplasm System in order to identify pathogenic viruses and understand their potential for dissemination. METHODS For the detection of viruses, we used high throughput sequencing combined with bioinformatic tools and reverse transcription-polymerase chain reactions. RESULTS Our results suggest that, in addition to common viruses, alfalfa seeds are infected by other potentially pathogenic viral species that could be vertically transmitted to offspring. CONCLUSIONS To the best of our knowledge, this is the first study of the alfalfa seed virome carried out by HTS technology. This initial screening of alfalfa germplasm accessions maintained by the NPGS showed that the crop's mature seeds contain a broad range of viruses, some of which were not previously considered to be seed-transmitted. The information gathered will be used to update germplasm distribution policies and to make decisions on the safety of distributing germplasm based on viral presence.
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Affiliation(s)
- Lev G Nemchinov
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD, 20705, USA.
| | - Brian M Irish
- Plant Germplasm Introduction and Testing Research, USDA-ARS, Prosser, WA, 99352, USA
| | - Sam Grinstead
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
| | - Olga A Postnikova
- Molecular Plant Pathology Laboratory, USDA-ARS, Beltsville, MD, 20705, USA
- Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, MD, 20705, US
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7
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Molecular characterization of a novel endornavirus isolated from Ophiostoma bicolor associated with bark beetles. Arch Virol 2022; 167:2839-2843. [PMID: 36227426 DOI: 10.1007/s00705-022-05613-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/08/2022] [Indexed: 12/14/2022]
Abstract
Ophiostoma bicolor is a pathogenic fungus associated with bark beetles that can cause serious damage to host plants. In this study, a novel fungal virus, "Ophiostoma bicolor endornavirus 1" (ObEV1), was obtained from O. bicolor, and its complete genome sequence was determined. ObEV1 has a single-stranded positive-sense (+ ss) RNA genome of 10,119 nucleotides. Sequence annotation and comparison showed that the viral genome has a single large open reading frame (ORF) encoding a polyprotein of 362.48 kDa. The polyprotein contains seven conserved domains: RNA-dependent RNA polymerase (RdRp), viral RNA helicase 1 (VHel1), viral methyltransferase (VMet), DEAD-like helicase (DEXDc), gliding-GltJ (G1), large tegument protein UL36 (PHA), and YlqF-related-GTPase (Y). Sequence comparisons and phylogenetic analysis showed that ObEV1 is a novel mycovirus belonging to the genus Betaendornavirus of the family Endornaviridae. This is the first report of a mycovirus in the ophiostomatoid fungus O. bicolor.
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8
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Bejerman N, Debat H. Exploring the tymovirales landscape through metatranscriptomics data. Arch Virol 2022; 167:1785-1803. [PMID: 35708766 DOI: 10.1007/s00705-022-05493-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 05/12/2022] [Indexed: 11/26/2022]
Abstract
Tymovirales is an order of viruses with positive-sense RNA genomes that mostly infect plants, but also fungi and insects. The number of genome sequences of viruses that could fit this taxon has been growing in the last few years with the extensive use of high-throughput sequencing. Here, we report the discovery of 31 novel viral genome sequences associated with 27 different host plant species, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3,000 plant transcriptomes from the NCBI Sequence Read Archive (SRA) using known tymovirales sequences as queries. Identification, assembly, and curation of raw SRA reads resulted in 29 viral genome sequences with complete coding regions, and two representing partial genomes. Some of the obtained sequences highlight novel genome organizations for members of the order. Phylogenetic analysis showed that six of the novel viruses are related to alphaflexiviruses, 17 to betaflexiviruses, two to deltaflexiviruses, and six to tymovirids. These findings shed new light on the phylogenetic relationships and evolutionary landscape of this group of viruses. Furthermore, this study illustrates the complexity and genome diversity among members of the order and demonstrates that analyzing public SRA data provides an invaluable tool to accelerate virus discovery and refine virus taxonomy.
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Affiliation(s)
- 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, Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, Argentina.
| | - 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, Camino 60 Cuadras Km 5,5 (X5020ICA), Córdoba, Argentina
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A Novel Flavi-like Virus in Alfalfa ( Medicago sativa L.) Crops along the Snake River Valley. Viruses 2022; 14:v14061320. [PMID: 35746792 PMCID: PMC9228291 DOI: 10.3390/v14061320] [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: 05/17/2022] [Revised: 06/07/2022] [Accepted: 06/14/2022] [Indexed: 11/18/2022] Open
Abstract
Alfalfa is an important perennial forage crop in Idaho supporting dairy and cattle industries that is typically grown in the same field for as many as 4 years. Alfalfa stands of different ages were subjected to screening for viruses using high-throughput sequencing and RT-PCR. The two most common viruses found were alfalfa mosaic virus and bean leafroll virus, along with Medicago sativa amalgavirus, two alphapartitiviruses, and one deltapartitivirus. Additionally, a new flavi-like virus with an unusual genome organization was discovered, dubbed Snake River alfalfa virus (SRAV). The 11,745 nt, positive-sense (+) RNA genome of SRAV encodes a single 3835 aa polyprotein with only two identifiable conserved domains, an RNA-dependent RNA polymerase (RdRP) and a predicted serine protease. Notably, unlike all +RNA virus genomes in the similar size range, the SRAV polyprotein contained no predicted helicase domain. In the RdRP phylogeny, SRAV was placed inside the flavi-like lineage as a sister clade to a branch consisting of hepaci-, and pegiviruses. To the best of our knowledge, SRAV is the first flavi-like virus identified in a plant host. Although commonly detected in alfalfa crops in southern Idaho, SRAV sequences were also amplified from thrips feeding in alfalfa stands in the area, suggesting a possible role of Frankliniella occidentalis in virus transmission.
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Adeleke IA, Kavalappara SR, McGregor C, Srinivasan R, Bag S. Persistent, and Asymptomatic Viral Infections and Whitefly-Transmitted Viruses Impacting Cantaloupe and Watermelon in Georgia, USA. Viruses 2022; 14:1310. [PMID: 35746780 PMCID: PMC9227350 DOI: 10.3390/v14061310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022] Open
Abstract
Cucurbits in Southeastern USA have experienced a drastic decline in production over the years due to the effect of economically important viruses, mainly those transmitted by the sweet potato whitefly (Bemisia tabaci Gennadius). In cucurbits, these viruses can be found as a single or mixed infection, thereby causing significant yield loss. During the spring of 2021, surveys were conducted to evaluate the incidence and distribution of viruses infecting cantaloupe (n = 80) and watermelon (n = 245) in Georgia. Symptomatic foliar tissues were collected from six counties and sRNA libraries were constructed from seven symptomatic samples. High throughput sequencing (HTS) analysis revealed the presence of three different new RNA viruses in Georgia: cucumis melo endornavirus (CmEV), cucumis melo amalgavirus (CmAV1), and cucumis melo cryptic virus (CmCV). Reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed the presence of CmEV and CmAV1 in 25% and 43% of the total samples tested, respectively. CmCV was not detected using RT-PCR. Watermelon crinkle leaf-associated virus 1 (WCLaV-1), recently reported in GA, was detected in 28% of the samples tested. Furthermore, RT-PCR and PCR analysis of 43 symptomatic leaf tissues collected from the fall-grown watermelon in 2019 revealed the presence of cucurbit chlorotic yellows virus (CCYV), cucurbit yellow stunting disorder virus (CYSDV), and cucurbit leaf crumple virus (CuLCrV) at 73%, 2%, and 81%, respectively. This finding broadens our knowledge of the prevalence of viruses in melons in the fall and spring, as well as the geographical expansion of the WCLaV-1 in GA, USA.
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Affiliation(s)
| | | | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA;
| | | | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA;
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11
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Lai X, Wang H, Wu C, Zheng W, Leng J, Zhang Y, Yan L. Comparison of Potato Viromes Between Introduced and Indigenous Varieties. Front Microbiol 2022; 13:809780. [PMID: 35602024 PMCID: PMC9114672 DOI: 10.3389/fmicb.2022.809780] [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: 11/05/2021] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
Viral disease in potatoes has been a major problem in potato production worldwide. In addition to the potential risk of introducing new diseases in new areas, viral-disease epidemics/pandemics can be initiated by “spillover” of indigenous viruses from infected alternative hosts into introduced cultivars. To investigate the tendency of potential viral infection/resistance, we analyzed the viromes of introduced and indigenous varieties of potatoes among different tissues using RNA-seq libraries. Bioinformatics analyses revealed that potato viruses PVM, PVY, and PVS were dominant and the most frequently identified viruses infecting potato virus-free plants in the field, and showed an infection bias between introduced and indigenous cultivars. PVY and PVS were the major viruses in introduced varieties, whereas PVM showed an extraordinarily high percentage in the indigenous variety. Other three common viruses, PVH, potato mop-top virus, and potato leafroll virus were identified specifically in the indigenous variety. There was a tendency for tissue-specific infection and sequence variation in viruses: underground parts (tubers, roots) harbored more unusual viruses, and tubers harbored relatively more variation with a high frequency of single nucleotide polymorphisms than other tissues. Taken together, our study provides a comprehensive overview of the composition, distribution, and sequence variation of viruses between introduced and indigenous varieties of potatoes.
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Affiliation(s)
- Xianjun Lai
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Xichang, China
| | - Haiyan Wang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Caiyun Wu
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Xichang, China
| | - Wen Zheng
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Xichang, China
| | - Jing Leng
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Xichang, China
| | - Yizheng Zhang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lang Yan
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Xichang, China
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12
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Diversity of the virome associated with alfalfa (Medicago sativa L.) in the U.S. Pacific Northwest. Sci Rep 2022; 12:8726. [PMID: 35610325 PMCID: PMC9130302 DOI: 10.1038/s41598-022-12802-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/04/2022] [Indexed: 01/04/2023] Open
Abstract
Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage legumes in the world. It is currently the third most valuable field crop in the United States with an estimated value of over $9.3 billion. Alfalfa productivity is limited by various infectious diseases that can reduce forage yield and quality and shorten stand life. The crop can frequently be infected with a diverse array of pathogens and other organisms that have distinct life cycles, biology, and mode of action. Among them are many coinfecting viruses, that greatly contribute to the heterogeneity of within-host pathogenic communities, representing a ubiquitous and abundant background for all other host–pathogen interactions. Regrettably, the impact of viral diseases, their role in alfalfa health and involvement in the severity of multi-pathogen infections are often underestimated and not well understood. As high-throughput sequencing approaches have been developed, opportunities to delve into these complex interactions can be realized. In this work, we have characterized a diversity of viral populations in several commercial alfalfa production fields located in the U.S. Pacific Northwest. At least 45 distinct viruses have been identified in all alfalfa samples. Among them some were known to infect the crop prior to this study, and others were designated as emerging, novel and viruses integrated into the alfalfa genome. Known viruses included alfalfa mosaic virus, pea streak virus and bean leafroll virus, while among emerging and novel agents were alfalfa virus S, cherry virus Trakiya, several rhabdoviruses and others. Additional biological and impact studies will be needed to determine if newly identified viruses, especially those that have not been reported from alfalfa before, should be considered pathogens of this crop.
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Guo Z, Zhang T, Chen Z, Niu J, Cui X, Mao Y, Hassan MU, Kareem HA, Xu N, Sui X, Gao S, Roy M, Cui J, Wang Q. Occurrence, Distribution, and Genetic Diversity of Alfalfa ( Medicago sativa L.) Viruses in Four Major Alfalfa-Producing Provinces of China. Front Microbiol 2022; 12:771361. [PMID: 35095791 PMCID: PMC8793692 DOI: 10.3389/fmicb.2021.771361] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/22/2021] [Indexed: 01/12/2023] Open
Abstract
Alfalfa (Medicago sativa L.) is one of the most widely cultivated forage crops in the world. China is the second largest producer of alfalfa in terms of the planting area worldwide, with Gansu, Henan, Inner Mongolia, and Shaanxi provinces being the production hubs. Alfalfa viruses have been reported on a small-scale survey in some of these areas, but they have not been well characterized. In the present study, seven viruses were detected in 12 fields of 10 cities/counties of the four abovementioned provinces by high-throughput sequencing and assembly of small RNA. Their incidence, distribution, and genetic diversity were analyzed by enzyme-linked immunosorbent assay, polymerase chain reaction (PCR)/reverse transcription-PCR and clone sequencing. The results showed that alfalfa mosaic virus (AMV), pea streak virus (PeSV), lucerne transient streak virus (LTSV), alfalfa dwarf virus (ADV), Medicago sativa alphapartitivirus 1 (MsAPV1), MsAPV2, and alfalfa leaf curl virus (ALCV) were the main viruses infecting alfalfa in four examined provinces. AMV and MsAPV1 had the highest incidences in all 4 provinces. SDT analysis of the 7 viruses isolated in China revealed a highly conserved among AMV, LTSV, ADV, MsAPV1, MsAPV2, and ALCV, but the sequence was a high variation between China isolates to abroad isolates in PeSV, ADV, and ALCV. To our knowledge, this is the first report of ADV in Inner Mongolia and Gansu, ALCV in Inner Mongolia, MsAPV1 and MsAPV2 in all 4 provinces, and PeSV and LTSV in China. These findings provide a basis for future research on the genetic evolution of alfalfa viruses in China and on strategies to prevent diseases in alfalfa caused by these viruses.
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Affiliation(s)
- Zhipeng Guo
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Tingting Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhao Chen
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Junpeng Niu
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Xuewen Cui
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Yue Mao
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Mahmood Ul Hassan
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Hafiz Abdul Kareem
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Nan Xu
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Xin Sui
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Shuanghong Gao
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Momi Roy
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Jian Cui
- Department of Plant Science, College of Life Sciences, Northwest A&F University, Yangling, China
| | - Quanzhen Wang
- Department of Grassland Science, College of Grassland Agriculture, Northwest A&F University, Yangling, China
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Wang Q, Zhang Y, Hu H, Hu J, Xiang M, Yang Q. Comparative proteomics analysis of the responses to selenium in selenium-enriched alfalfa (Medicago sativa L.) leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 165:265-273. [PMID: 34087704 DOI: 10.1016/j.plaphy.2021.04.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
The mass of leaves and the chlorophyll and selenium content of alfalfa can be increased by the foliar spraying of selenite. To better understand the relationship between changes in the expression of specific proteins and the various metabolic and regulatory pathways affected by selenium treatment, labeling with Tandem Mass Tags (TMT) was used as a proteomics technique to compare control leaves with those enriched with Se. A total of 8,411 proteins were identified, the expression levels of 195 of which were significantly modified, 67 significantly up-regulated and 128 significantly down-regulated. Using gene functional classification and metabolic pathway annotation, selenium treatment was found to have a significant impact on metabolic processes. The energy and substances produced by the metabolic processes of a variety of carbohydrates, lipids, and amino acids, and the metabolism of carbon may be responsible for increasing the yield of alfalfa leaves. Administration of selenium substantially influenced Se-responsive proteins, including ABC transporter G family member 36, Probable glutathione S-transferase and cysteine tRNA ligase. Selenium treatment may also enhance photosynthesis and the defense response of cells. Furthermore, protein ubiquitination also played an important role in the selenium response of alfalfa leaves. In summary, a basic analysis of the selenium response pathway in alfalfa leaves at the proteomics level was conducted, which may assist in a more detailed elucidation of selenium enrichment in alfalfa in the future.
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Affiliation(s)
- Qingdong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China; Key Laboratory of Forage Nutrition Regulation and Innovative Utilization of Zhengzhou, Zhengzhou, Henan, 450046, China; Henan Grass and Animal Engineering Technology Research Center, Zhengzhou, Henan 450046, China
| | - Yaru Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China; Key Laboratory of Forage Nutrition Regulation and Innovative Utilization of Zhengzhou, Zhengzhou, Henan, 450046, China; Henan Grass and Animal Engineering Technology Research Center, Zhengzhou, Henan 450046, China
| | - Huafeng Hu
- Henan University of Animal Husbandry and Economy, Zhengzhou, Hennan, 450046, China; Key Laboratory of Forage Nutrition Regulation and Innovative Utilization of Zhengzhou, Zhengzhou, Henan, 450046, China; Henan Grass and Animal Engineering Technology Research Center, Zhengzhou, Henan 450046, China.
| | - Jinke Hu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China; Key Laboratory of Forage Nutrition Regulation and Innovative Utilization of Zhengzhou, Zhengzhou, Henan, 450046, China; Henan Grass and Animal Engineering Technology Research Center, Zhengzhou, Henan 450046, China
| | - Meiling Xiang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China; Key Laboratory of Forage Nutrition Regulation and Innovative Utilization of Zhengzhou, Zhengzhou, Henan, 450046, China; Henan Grass and Animal Engineering Technology Research Center, Zhengzhou, Henan 450046, China
| | - QiaoFeng Yang
- Henan University of Animal Husbandry and Economy, Zhengzhou, Hennan, 450046, China; Key Laboratory of Forage Nutrition Regulation and Innovative Utilization of Zhengzhou, Zhengzhou, Henan, 450046, China; Henan Grass and Animal Engineering Technology Research Center, Zhengzhou, Henan 450046, China
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15
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Chatzivassiliou EK. An Annotated List of Legume-Infecting Viruses in the Light of Metagenomics. PLANTS 2021; 10:plants10071413. [PMID: 34371616 PMCID: PMC8309371 DOI: 10.3390/plants10071413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022]
Abstract
Legumes, one of the most important sources of human food and animal feed, are known to be susceptible to a plethora of plant viruses. Many of these viruses cause diseases which severely impact legume production worldwide. The causal agents of some important virus-like diseases remain unknown. In recent years, high-throughput sequencing technologies have enabled us to identify many new viruses in various crops, including legumes. This review aims to present an updated list of legume-infecting viruses. Until 2020, a total of 168 plant viruses belonging to 39 genera and 16 families, officially recognized by the International Committee on Taxonomy of Viruses (ICTV), were reported to naturally infect common bean, cowpea, chickpea, faba-bean, groundnut, lentil, peas, alfalfa, clovers, and/or annual medics. Several novel legume viruses are still pending approval by ICTV. The epidemiology of many of the legume viruses are of specific interest due to their seed-transmission and their dynamic spread by insect-vectors. In this review, major aspects of legume virus epidemiology and integrated control approaches are also summarized.
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Affiliation(s)
- Elisavet K Chatzivassiliou
- Plant Pathology Laboratory, Department of Crop Science, School of Plant Sciences, Agricultural University of Athens, 11855 Athens, Greece
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16
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Mahony J, van Sinderen D. Virome studies of food production systems: time for 'farm to fork' analyses. Curr Opin Biotechnol 2021; 73:22-27. [PMID: 34252795 DOI: 10.1016/j.copbio.2021.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022]
Abstract
The food industry is under increasing pressure to produce high quality, traceable and minimally processed foods that are produced using sustainable approaches and ingredients. In line with the latter, there is an increased pressure for plant-based products to replace animal-derived products. Until recently, research efforts have mainly focused on dairy and meat products owing to their economic importance. The shift towards plant-based diets and food production requires a corresponding shift in research efforts to define the microbial requirements for and composition of (novel) plant-based foods, the (micro)organisms that are beneficial to such production systems, and the abundance and role of (bacterio)phages in shaping the microbial landscape of these foods. In this review, we explore current efforts in the area of virome analysis of foods and food production environments and highlight the need for more unified approaches to understand the contribution of phages in food safety and quality, and to develop novel tools to enhance the traceability of foods.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland.
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17
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Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data. Viruses 2021; 13:v13071304. [PMID: 34372509 PMCID: PMC8310260 DOI: 10.3390/v13071304] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/25/2021] [Accepted: 06/26/2021] [Indexed: 01/06/2023] Open
Abstract
Rhabdoviruses infect a large number of plant species and cause significant crop diseases. They have a negative-sense, single-stranded unsegmented or bisegmented RNA genome. The number of plant-associated rhabdovirid sequences has grown in the last few years in concert with the extensive use of high-throughput sequencing platforms. Here, we report the discovery of 27 novel rhabdovirus genomes associated with 25 different host plant species and one insect, which were hidden in public databases. These viral sequences were identified through homology searches in more than 3000 plant and insect transcriptomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using known plant rhabdovirus sequences as the query. The identification, assembly and curation of raw SRA reads resulted in sixteen viral genome sequences with full-length coding regions and ten partial genomes. Highlights of the obtained sequences include viruses with unique and novel genome organizations among known plant rhabdoviruses. Phylogenetic analysis showed that thirteen of the novel viruses were related to cytorhabdoviruses, one to alphanucleorhabdoviruses, five to betanucleorhabdoviruses, one to dichorhaviruses and seven to varicosaviruses. These findings resulted in the most complete phylogeny of plant rhabdoviruses to date and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant viruses. Furthermore, this study provided additional evidence for the complexity and diversity of plant rhabdovirus genomes and demonstrated that analyzing SRA public data provides an invaluable tool to accelerate virus discovery, gain evolutionary insights and refine virus taxonomy.
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François S, Antoine-Lorquin A, Kulikowski M, Frayssinet M, Filloux D, Fernandez E, Roumagnac P, Froissart R, Ogliastro M. Characterisation of the Viral Community Associated with the Alfalfa Weevil ( Hypera postica) and Its Host Plant, Alfalfa ( Medicago sativa). Viruses 2021; 13:791. [PMID: 33925168 PMCID: PMC8145008 DOI: 10.3390/v13050791] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 12/22/2022] Open
Abstract
Advances in viral metagenomics have paved the way of virus discovery by making the exploration of viruses in any ecosystem possible. Applied to agroecosystems, such an approach opens new possibilities to explore how viruses circulate between insects and plants, which may help to optimise their management. It could also lead to identifying novel entomopathogenic viral resources potentially suitable for biocontrol strategies. We sampled the larvae of a natural population of alfalfa weevils (Hypera postica), a major herbivorous pest feeding on legumes, and its host plant alfalfa (Medicago sativa). Insect and plant samples were collected from a crop field and an adjacent meadow. We characterised the diversity and abundance of viruses associated with weevils and alfalfa, and described nine putative new virus species, including four associated with alfalfa and five with weevils. In addition, we found that trophic accumulation may result in a higher diversity of plant viruses in phytophagous pests compared to host plants.
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Affiliation(s)
- Sarah François
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, South Park Road, Oxford OX1 3SY, UK
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Aymeric Antoine-Lorquin
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Maximilien Kulikowski
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Marie Frayssinet
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France; (D.F.); (E.F.); (P.R.)
- PHIM Plant Health Institute, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Rémy Froissart
- MIVEGEC Infectious and Vector Diseases: Ecology, Genetics, Evolution and Control, University of Montpellier, CNRS, IRD, 34394 Montpellier, France;
| | - Mylène Ogliastro
- DGIMI Diversity, Genomes and Microorganisms–Insects Interactions, University of Montpellier, INRAE, 34095 Montpellier, France; (A.A.-L.); (M.K.); (M.F.)
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Li J, Gu H, Liu Y, Wei S, Hu G, Wang X, McNeill MR, Ban L. RNA-seq reveals plant virus composition and diversity in alfalfa, thrips, and aphids in Beijing, China. Arch Virol 2021; 166:1711-1722. [PMID: 33866416 DOI: 10.1007/s00705-021-05067-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/22/2021] [Indexed: 11/27/2022]
Abstract
Viruses are widespread in alfalfa (Medicago sativa L.), representing a key limitation to the production of this important forage plant. Understanding the diversity of plant viruses in alfalfa and their potential vectors will play an important role in management to minimize the emergence, transmission, and impact of viruses. Next-generation sequencing (NGS) targeting the transcriptome was applied to monitor the virus communities in alfalfa and its two main pests, thrips (Odontothrips loti Haliday and Frankliniella intonsa Trybom) and aphids (Acyrthosiphon pisum Mordvilko and Therioaphis trifolii Monell). A comparison of transcriptome datasets with reference databases revealed the presence of eight candidate viruses. Five out of the eight viruses, alfalfa mosaic virus (AMV), Medicago sativa alphapartitivirus 1 (MsAPV1), Medicago sativa deltapartitivirus 1 (MsDPV1), Medicago sativa amalgavirus 1 (MsAV1), and bean yellow mosaic virus (BYMV), were confirmed by RT-PCR. We identified and determined the presence of four RNA viruses from alfalfa samples, two viruses (AMV and MsAPV1) from thrips samples, and one virus (BYMV) from T. trifolii. All sequences isolated from the insect samples were more than 95% identical to the sequences from the alfalfa samples or to sequences from the National Center for Biotechnology Information (NCBI) reference database. The RNA-seq results of this study suggest that AMV and MsAPV1 are the predominant RNA plant viruses infecting alfalfa and that they are carried by the major pests. This lays the foundation for future research on the vectors and transmission of these viruses. In addition, the sequence data have enabled the assembly of the first complete genome sequence of MsDPV1 from alfalfa.
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Affiliation(s)
- Jin Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Hongchang Gu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yanqi Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Shuhua Wei
- Ningxia Academy of Agriculture and Forestry Sciences, Institute of Plant Protection, Yinchuan, Ningxia, China
| | - Guixin Hu
- Pratacultural College, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xuemin Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mark Richard McNeill
- AgResearch, Resilient Agriculture Innovative Centre of Excellence, Lincoln, New Zealand
| | - Liping Ban
- College of Grassland Science and Technology, China Agricultural University, Beijing, China.
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