1
|
Lagzian A, Ghorbani A, Tabein S, Riseh RS. Genetic variations and gene expression profiles of Rice Black-streaked dwarf virus (RBSDV) in different host plants and insect vectors: insights from RNA-Seq analysis. BMC Genomics 2024; 25:736. [PMID: 39080552 PMCID: PMC11289972 DOI: 10.1186/s12864-024-10649-9] [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: 02/27/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
Rice black-streaked dwarf virus (RBSDV) is an etiological agent of a destructive disease infecting some economically important crops from the Gramineae family in Asia. While RBSDV causes high yield losses, genetic characteristics of replicative viral populations have not been investigated within different host plants and insect vectors. Herein, eleven publicly available RNA-Seq datasets from Chinese RBSDV-infected rice, maize, and viruliferous planthopper (Laodelphax striatellus) were obtained from the NCBI database. The patterns of SNP and RNA expression profiles of expected RBSDV populations were analyzed by CLC Workbench 20 and Geneious Prime software. These analyses discovered 2,646 mutations with codon changes in RBSDV whole transcriptome and forty-seven co-mutated hotspots with high variant frequency within the crucial regions of S5-1, S5-2, S6, S7-1, S7-2, S9, and S10 open reading frames (ORFs) which are responsible for some virulence and host range functions. Moreover, three joint mutations are located on the three-dimensional protein of P9-1. The infected RBSDV-susceptible rice cultivar KTWYJ3 and indigenous planthopper datasets showed more co-mutated hotspot numbers than others. Our analyses showed the expression patterns of viral genomic fragments varied depending on the host type. Unlike planthopper, S5-1, S2, S6, and S9-1 ORFs, respectively had the greatest read numbers in host plants; and S5-2, S9-2, and S7-2 were expressed in the lowest level. These findings underscore virus/host complexes are effective in the genetic variations and gene expression profiles of plant viruses. Our analysis revealed no evidence of recombination events. Interestingly, the negative selection was observed at 12 RBSDV ORFs, except for position 1015 in the P1 protein, where a positive selection was detected. The research highlights the potential of SRA datasets for analysis of the virus cycle and enhances our understanding of RBSDV's genetic diversity and host specificity.
Collapse
Affiliation(s)
- Arezoo Lagzian
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute, Karaj, Iran.
| | - Saeid Tabein
- Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Roohallah Saberi Riseh
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| |
Collapse
|
2
|
Guevara-Rivera EA, Rodríguez-Negrete EA, Lozano-Durán R, Bejarano ER, Torres-Calderón AM, Arce-Leal ÁP, Leyva-López NE, Méndez-Lozano J. From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species. Methods Mol Biol 2024; 2732:103-117. [PMID: 38060120 DOI: 10.1007/978-1-0716-3515-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Viruses comprise the most abundant genetic material in the biosphere; however, global viral genomic population (virome) has been largely underestimated. Recently, high-throughput sequencing (HTS) has provided a powerful tool for the detection of known viruses and the discovery of novel viral species from environmental and individual samples using metagenomics and ecogenomics approaches, respectively. Viruses with circular DNA single-stranded (ssDNA) genomes belonging to the begomovirus genera (family Geminiviridae) constitute the largest group of emerging plant viruses worldwide. The knowledge of begomoviruses viromes is mostly restricted to crop plant systems; nevertheless, it has been described that noncultivated plants specifically at the interface between wild and cultivated plants are important reservoirs leading to viral evolution and the emergence of new diseases. Here we present a protocol that allows the identification and isolation of known and novel begomoviruses species infecting cultivated and noncultivated plant species. The method consists of circular viral molecules enrichment by rolling circle amplification (RCA) from begomovirus-positive total plant DNA, followed by NGS-based metagenomic sequencing. Subsequently, metagenomic reads are processed for taxonomic classification using Viromescan software and a customized Geminiviridae family database, and begomovirus-related reads are used for contigs assembly and annotation using Spades software and Blastn algorithm, respectively. Then, the obtained begomovirus-related signatures are used as templates for specific primers design and implemented for PCR-based ecogenomic identification of individual samples harboring the corresponding viral species. Lastly, full-length begomovirus genomes are obtained by RCA-based amplification from total plant DNA of selected individual samples, cloning, and viral molecular identity corroborated by Sanger sequencing. Conclusively, the identification and isolation of a novel monopartite begomovirus species native to the New World (NW) named Gallium leaf deformation virus (GLDV) is shown.
Collapse
Affiliation(s)
- Enrique A Guevara-Rivera
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico
| | - Edgar A Rodríguez-Negrete
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico
| | - Rosa Lozano-Durán
- Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), Eberhard Karls University, Tübingen, Germany
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | | | - Ángela P Arce-Leal
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico
| | - Norma E Leyva-López
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico
| | - Jesús Méndez-Lozano
- Departamento de Biotecnología Agrícola, Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, Guasave, Sinaloa, Mexico.
| |
Collapse
|
3
|
Devendran R, Kavalappara SR, Simmons AM, Bag S. Whitefly-Transmitted Viruses of Cucurbits in the Southern United States. Viruses 2023; 15:2278. [PMID: 38005954 PMCID: PMC10675411 DOI: 10.3390/v15112278] [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: 10/24/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Cucurbits are economically important crops that are widely cultivated in many parts of the world, including the southern US. In recent years, higher temperatures have favored the rapid build-up of whiteflies in the fall-grown cucurbits in this region. As a result, whitefly-transmitted viruses (WTVs) have severely impacted the marketable yield of cucurbits. In this review, we discuss three major groups of WTVs negatively impacting cucurbit cultivation in the southern US, including begomoviruses, criniviruses, and ipomoviruses. Here, we discuss the available information on the biology, epidemiology and advances made toward detecting and managing these viruses, including sources of resistance and cultural practices.
Collapse
Affiliation(s)
| | | | - Alvin M. Simmons
- U.S. Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC 29414, USA
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA
| |
Collapse
|
4
|
Andika IB, Tian M, Bian R, Cao X, Luo M, Kondo H, Sun L. Cross-Kingdom Interactions Between Plant and Fungal Viruses. Annu Rev Virol 2023; 10:119-138. [PMID: 37406341 DOI: 10.1146/annurev-virology-111821-122539] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The large genetic and structural divergences between plants and fungi may hinder the transmission of viruses between these two kingdoms to some extent. However, recent accumulating evidence from virus phylogenetic analyses and the discovery of naturally occurring virus cross-infection suggest the occurrence of past and current transmissions of viruses between plants and plant-associated fungi. Moreover, artificial virus inoculation experiments showed that diverse plant viruses can multiply in fungi and vice versa. Thus, virus cross-infection between plants and fungi may play an important role in the spread, emergence, and evolution of both plant and fungal viruses and facilitate the interaction between them. In this review, we summarize current knowledge related to cross-kingdom virus infection in plants and fungi and further discuss the relevance of this new virological topic in the context of understanding virus spread and transmission in nature as well as developing control strategies for crop plant diseases.
Collapse
Affiliation(s)
- Ida Bagus Andika
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China;
| | - Mengyuan Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China;
| | - Ruiling Bian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China;
| | - Xinran Cao
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China;
| | - Ming Luo
- College of Agronomy, Xinjiang Agricultural University, Urumqi, China
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
| | - Liying Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China;
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan;
| |
Collapse
|
5
|
Claverie S, Hoareau M, Chéhida SB, Filloux D, Varsani A, Roumagnac P, Martin DP, Lett JM, Lefeuvre P. Metagenomics reveals the structure of Mastrevirus-host interaction network within an agro-ecosystem. Virus Evol 2023; 9:vead043. [PMID: 37475836 PMCID: PMC10354507 DOI: 10.1093/ve/vead043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/24/2023] [Accepted: 07/04/2023] [Indexed: 07/22/2023] Open
Abstract
As highly pervasive parasites that sometimes cause disease, viruses are likely major components of all natural ecosystems. An important step towards both understanding the precise ecological roles of viruses and determining how natural communities of viral species are assembled and evolve is obtaining full descriptions of viral diversity and distributions at ecosystem scales. Here, we focused on obtaining such 'community-scale' data for viruses in a single genus. We chose the genus Mastrevirus (family Geminiviridae), members of which have predominantly been found infecting uncultivated grasses (family Poaceae) throughout the tropical and sub-tropical regions of the world. We sampled over 3 years, 2,884 individual Poaceae plants belonging to thirty different species within a 2-ha plot which included cultivated and uncultivated areas on the island of Reunion. Mastreviruses were found in ∼8 per cent of the samples, of which 96 per cent did not have any discernible disease symptoms. The multitude of host-virus associations that we uncovered reveals both the plant species that most commonly host mastreviruses and the mastrevirus species (such as maize streak virus and maize streak Reunion virus) that have especially large host ranges. Our findings are consistent with the hypothesis that perennial plant species capable of hosting years-long mixed mastrevirus infections likely play a disproportionately important role in the generation of inter-species and inter-strain mastrevirus recombinants.
Collapse
Affiliation(s)
- Sohini Claverie
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France
- Université de La Réunion, UMR PVBMT, F-97410 St Pierre, La Réunion, France
| | | | | | - Denis Filloux
- CIRAD, UMR PHIM, Montpellier F-34090, France
- PHIM Plant Health Institute, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier 34090, France
| | | | - Philippe Roumagnac
- CIRAD, UMR PHIM, Montpellier F-34090, France
- PHIM Plant Health Institute, Université de Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier 34090, France
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
| | | | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa
| |
Collapse
|
6
|
Tatineni S, Alexander J, Nunna H. 6K1, NIa-VPg, NIa-Pro, and CP of Wheat Streak Mosaic Virus Are Collective Determinants of Wheat Streak Mosaic Disease in Wheat. PHYTOPATHOLOGY 2023; 113:1115-1127. [PMID: 36537846 DOI: 10.1094/phyto-10-22-0401-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Wheat streak mosaic virus (WSMV; genus Tritimovirus, family Potyviridae) is the causal agent of the most economically important wheat streak mosaic disease of wheat (Triticum aestivum) in the Great Plains region of the United States. WSMV determinants responsible for wheat streak mosaic disease in wheat are unknown. Triticum mosaic virus (TriMV), a wheat-infecting virus, was used as an expression vector for the transient expression of each of the WSMV-encoded cistrons in wheat. WSMV-encoded 6K1, NIa-VPg, NIa-Pro, and CP cistrons in TriMV elicited symptoms specific to different stages of wheat streak mosaic disease without significantly affecting the genomic RNA accumulation. WSMV 6K1 produced early wheat streak mosaic disease-like symptoms of severe chlorotic streaks and patches. NIa-VPg and CP caused severe chlorotic streaks, followed by moderate stunting (only with NIa-VPg) of wheat, mimicking early- and mid-stage symptoms of wheat streak mosaic disease. WSMV NIa-Pro caused mild chlorotic streaks, followed by dark green leaves with severe stunting, representing the late symptoms of wheat streak mosaic disease. Collectively, these data suggest that cumulative effects of WSMV-encoded 6K1, NIa-VPg, NIa-Pro, and CP are responsible for different stages of wheat streak mosaic disease symptoms in wheat. Furthermore, deletion analysis of wheat streak mosaic disease determinants revealed that complete 6K1 and NIa-Pro, amino acids 3 to 60 and 121 to 197 of NIa-VPg, and amino acids 101 to 294 of CP are responsible for wheat streak mosaic disease-like symptoms in wheat. This study suggests that management strategies for wheat streak mosaic disease in wheat should target WSMV determinants of the disease phenotype.
Collapse
Affiliation(s)
- Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service, University of Nebraska-Lincoln, Lincoln, NE 68583
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68503
| | - Jeffrey Alexander
- U.S. Department of Agriculture-Agricultural Research Service, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Haritha Nunna
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68503
| |
Collapse
|
7
|
Maclot F, Debue V, Malmstrom CM, Filloux D, Roumagnac P, Eck M, Tamisier L, Blouin AG, Candresse T, Massart S. Long-Term Anthropogenic Management and Associated Loss of Plant Diversity Deeply Impact Virome Richness and Composition of Poaceae Communities. Microbiol Spectr 2023; 11:e0485022. [PMID: 36916941 PMCID: PMC10100685 DOI: 10.1128/spectrum.04850-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
Modern agriculture has influenced plant virus emergence through ecosystem simplification, introduction of new host species, and reduction in crop genetic diversity. Therefore, it is crucial to better understand virus distributions across cultivated and uncultivated communities in agro-ecological interfaces, as well as virus exchange among them. Here, we advance fundamental understanding in this area by characterizing the virome of three co-occurring replicated Poaceae community types that represent a gradient of grass species richness and management intensity, from highly managed crop monocultures to little-managed, species-rich grasslands. We performed a large-scale study on 950 wild and cultivated Poaceae over 2 years, combining untargeted virome analysis down to the virus species level with targeted detection of three plant viruses. Deep sequencing revealed (i) a diversified and largely unknown Poaceae virome (at least 51 virus species or taxa), with an abundance of so-called persistent viruses; (ii) an increase of virome richness with grass species richness within the community; (iii) stability of virome richness over time but a large viral intraspecific variability; and (iv) contrasting patterns of virus prevalence, coinfections, and spatial distribution among plant communities and species. Our findings highlight the complex structure of plant virus communities in nature and suggest the influence of anthropogenic management on viral distribution and prevalence. IMPORTANCE Because viruses have been mostly studied in cultivated plants, little is known about virus diversity and ecology in less-managed vegetation or about the influence of human management and agriculture on virome composition. Poaceae (grass family)-dominated communities provide invaluable opportunities to examine these ecological issues, as they are distributed worldwide across agro-ecological gradients, are essential for food security and conservation, and can be infected by numerous viruses. Here, we used multiple levels of analysis that considered plant communities, individual plants, virus species, and haplotypes to broaden understanding of the Poaceae virome and to evaluate host-parasite richness relationships within agro-ecological landscapes in our study area. We emphasized the influence of grass diversity and land use on the composition of viral communities and their life history strategies, and we demonstrated the complexity of plant-virus interactions in less-managed grass communities, such as the higher virus prevalence and overrepresentation of mixed virus infection compared to theoretical predictions.
Collapse
Affiliation(s)
- François Maclot
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Virginie Debue
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Carolyn M. Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, & Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Denis Filloux
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, CIRAD, INRAE, Institut Agro, IRD, University of Montpellier, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, CIRAD, INRAE, Institut Agro, IRD, University of Montpellier, Montpellier, France
| | - Mathilde Eck
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Lucie Tamisier
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Arnaud G. Blouin
- Virology-Phytoplasmology Laboratory, Agroscope, Nyon, Switzerland
| | - Thierry Candresse
- University of Bordeaux, INRAE, UMR BFP, CS20032, Villenave d’Ornon, France
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| |
Collapse
|
8
|
Tatineni S, Hein GL. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. PHYTOPATHOLOGY 2023; 113:117-141. [PMID: 36095333 DOI: 10.1094/phyto-05-22-0167-rvw] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.
Collapse
Affiliation(s)
- Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Gary L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583
| |
Collapse
|
9
|
Lombardi EM, Peters J, Jacob L, Power AG. Wild and weedy Hesperis matronalis hosts turnip mosaic virus across heterogeneous landscapes in upstate New York. Virus Res 2023; 323:199011. [PMID: 36511291 DOI: 10.1016/j.virusres.2022.199011] [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: 08/25/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022]
Abstract
Turnip mosaic virus (TuMV) is a widespread and economically important pathogen in agricultural crops and has the widest known host range in the virus family Potyviridae. While management of the virus and its aphid vectors in agricultural fields decreases virus incidence, many alternative wild hosts for TuMV may serve as source populations for crop infection through spillover. Over thirty years ago, research demonstrated that the introduced brassica, Dame's Rocket (Hesperis matronalis) hosts several viruses, including TuMV. Here, we use both enzyme-linked immunosorbent assays (ELISA) and next generation sequencing to document the frequent infection by TuMV of Dame's Rocket, which is common and widespread in disturbed areas around crop fields in upstate New York. Deep sequencing of multiple tissue types of symptomatic hosts indicate that the infection is systemic and causes diagnostic, visible symptoms. In a common garden experiment using host populations from across upstate New York, we found evidence for genetic tolerance to TuMV infection in H. matronalis. Field surveys show that TuMV prevalence varies across populations, but is generally higher in agricultural areas. Examining disease dynamics in this and other common alternative hosts will enhance our understanding of TuMV epidemiology and, more broadly, virus distribution in wild plants.
Collapse
Affiliation(s)
- Elizabeth M Lombardi
- Cornell University, Department of Ecology and Evolutionary Biology, E145 Corson Hall, Ithaca, New York 14853, USA.
| | - Jasmine Peters
- Cornell University, Department of Ecology and Evolutionary Biology, E145 Corson Hall, Ithaca, New York 14853, USA
| | - Lukin Jacob
- Cornell University, Department of Ecology and Evolutionary Biology, E145 Corson Hall, Ithaca, New York 14853, USA
| | - Alison G Power
- Cornell University, Department of Ecology and Evolutionary Biology, E145 Corson Hall, Ithaca, New York 14853, USA
| |
Collapse
|
10
|
Moubset O, François S, Maclot F, Palanga E, Julian C, Claude L, Fernandez E, Rott P, Daugrois JH, Antoine-Lorquin A, Bernardo P, Blouin AG, Temple C, Kraberger S, Fontenele RS, Harkins GW, Ma Y, Marais A, Candresse T, Chéhida SB, Lefeuvre P, Lett JM, Varsani A, Massart S, Ogliastro M, Martin DP, Filloux D, Roumagnac P. Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses. PHYTOPATHOLOGY 2022; 112:2253-2272. [PMID: 35722889 DOI: 10.1094/phyto-03-22-0096-rvw] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Oumaima Moubset
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | - François Maclot
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Essowè Palanga
- Institut Togolais de Recherche Agronomique (ITRA-CRASS), B.P. 129, Kara, Togo
| | - Charlotte Julian
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Lisa Claude
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Rott
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jean-Heinrich Daugrois
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | | | | | - Arnaud G Blouin
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
- Plant Protection Department, Agroscope, 1260, Nyon, Switzerland
| | - Coline Temple
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
| | - Gordon W Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics, Institute, University of the Western Cape, South Africa
| | - Yuxin Ma
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, 33140 Villenave d'Ornon, France
| | | | | | | | | | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, U.S.A
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Darren P Martin
- Division of Computational Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| |
Collapse
|
11
|
Mackie J, Kinoti WM, Chahal SI, Lovelock DA, Campbell PR, Tran-Nguyen LTT, Rodoni BC, Constable FE. Targeted Whole Genome Sequencing (TWG-Seq) of Cucumber Green Mottle Mosaic Virus Using Tiled Amplicon Multiplex PCR and Nanopore Sequencing. PLANTS (BASEL, SWITZERLAND) 2022; 11:2716. [PMID: 36297740 PMCID: PMC9607580 DOI: 10.3390/plants11202716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Rapid and reliable detection tools are essential for disease surveillance and outbreak management, and genomic data is essential to determining pathogen origin and monitoring of transmission pathways. Low virus copy number and poor RNA quality can present challenges for genomic sequencing of plant viruses, but this can be overcome by enrichment of target nucleic acid. A targeted whole genome sequencing (TWG-Seq) approach for the detection of cucumber green mottle mosaic virus (CGMMV) has been developed where overlapping amplicons generated using two multiplex RT-PCR assays are then sequenced using the Oxford Nanopore MinION. Near complete coding region sequences were assembled with ≥100× coverage for infected leaf tissue dilution samples with RT-qPCR cycle quantification (Cq) values from 11.8 to 38 and in seed dilution samples with Cq values 13.8 to 27. Consensus sequences assembled using this approach showed greater than 99% nucleotide similarity when compared to genomes produced using metagenomic sequencing. CGMMV could be confidently detected in historical seed isolates with degraded RNA. Whilst limited access to, and costs associated with second-generation sequencing platforms can influence diagnostic outputs, the portable Nanopore technology offers an affordable high throughput sequencing alternative when combined with TWG-Seq for low copy or degraded samples.
Collapse
Affiliation(s)
- Joanne Mackie
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Melbourne, VIC 3083, Australia
| | - Wycliff M. Kinoti
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
| | - Sumit I. Chahal
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
| | - David A. Lovelock
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
| | - Paul R. Campbell
- Horticulture and Forestry Science, Department of Agriculture and Fisheries, Ecosciences Precinct, Brisbane, QLD 4102, Australia
| | | | - Brendan C. Rodoni
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Melbourne, VIC 3083, Australia
| | - Fiona E. Constable
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3083, Australia
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Melbourne, VIC 3083, Australia
| |
Collapse
|
12
|
McLeish MJ, Zamfir AD, Babalola BM, Peláez A, Fraile A, García-Arenal F. Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, Cucumis melo, crops, and adjacent wild communities. Virus Evol 2022; 8:veac095. [PMID: 36405340 PMCID: PMC9667876 DOI: 10.1093/ve/veac095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/24/2022] [Accepted: 09/30/2022] [Indexed: 07/22/2023] Open
Abstract
The emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here, we implemented a high-throughput approach to compare the viromes of melon (Cucumis melo) and wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the 41-plant species examined was infected by at least one virus. The interactions of 104 virus operational taxonomic units (OTUs) with these hosts occurred largely within ecological compartments of either Crop or Edge, with Edge having traits of a reservoir community. Local scale patterns of infection were characterised by the positive correlation between plant and virus richness at each site, the tendency for increased specialist host use through seasons, and specialist host use by OTUs observed only in Crop, characterised local-scale patterns of infection. In this study of systematically sampled viromes of a crop and adjacent wild communities, most hosts showed no disease symptoms, suggesting non-antagonistic symbioses are common. The coexistence of viruses within species-rich ecological compartments of agro-systems might promote the evolution of a diversity of virus strategies for survival and transmission. These communities, including those suspected as reservoirs, are subject to sporadic changes in assemblages, and so too are the conditions that favour the emergence of disease.
Collapse
Affiliation(s)
- Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Adrián D Zamfir
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Bisola M Babalola
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Adrián Peláez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| |
Collapse
|
13
|
Kalyankumar KK, Malathi VG, Renukadevi P, S MK, Manivannan N, Patil SG, Karthikeyan G. Molecular epidemiology on seasonal variation of yellow mosaic disease incidence in blackgram (Vigna mungo L. Hepper) with its vector Bemisia tabaci. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2022; 66:1985-1995. [PMID: 35930085 DOI: 10.1007/s00484-022-02334-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
The yellow mosaic disease (YMD) of blackgram caused by Mungbean yellow mosaic virus has emerged as a serious threat to grain legume production, especially in Southeastern Asia. Seasonal incidence of YMD with its vector population was assessed in three different agroclimatic zones of Tamil Nadu in India for three consecutive cropping seasons namely, Rabi 2018 (October-December), Summer 2019 (March-May), and Kharif 2019 (June-August) at three different time intervals viz., 20, 40, and 60 days after sowing (DAS). For all three seasons, disease incidence and whitefly count were recorded for a resistant and susceptible variety of blackgram in fields without any vector control intervention. The highest disease incidence (87%) was observed in the Panpozhi location during the summer season followed by Vamban and Coimbatore locations. The whitefly count was made through both visual count and yellow sticky traps. The whitefly population was highest at 20 DAS and decreased with the increasing age of crop for all the three locations assessed. Molecular epidemiology was analyzed by determining latent infection of mungbean yellow mosaic virus (MYMV) using molecular diagnosis. Latent infection was found to be well pronounced in the Coimbatore location during the Kharif season, where the crop was asymptomatic in both the resistant and susceptible varieties for all the three time periods assessed. The latent infection of MYMV observed in Coimbatore and Vamban ranged from 16.6 to 83.3% in both resistant and susceptible varieties for all three seasons. In Panpozhi, the latent infection of MYMV ranged from 16.6 to 66.6% for the susceptible variety (CO-5) for all three seasons observed. However, in the Panpozhi location, the resistant variety (VBN-8) failed to record any latent infection.
Collapse
Affiliation(s)
| | - V G Malathi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - P Renukadevi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - Mohan Kumar S
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - N Manivannan
- National Pulses Research Centre, Tamil Nadu Agricultural University, Vamban, 622303, Pudukkottai, India
| | - S G Patil
- Department of Physical Sciences and Information Technology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - G Karthikeyan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
- Department of Physical Sciences and Information Technology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
| |
Collapse
|
14
|
Koloniuk I, Matyášová A, Brázdová S, Veselá J, Přibylová J, Fránová J, Elena SF. Transmission of Diverse Variants of Strawberry Viruses Is Governed by a Vector Species. Viruses 2022; 14:v14071362. [PMID: 35891344 PMCID: PMC9316375 DOI: 10.3390/v14071362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
Advances in high-throughput sequencing methods have boosted the discovery of multistrain viral infections in diverse plant systems. This phenomenon appears to be pervasive for certain viral species. However, our knowledge of the transmission aspects leading to the establishment of such mixed infections is limited. Recently, we reported a mixed infection of a single strawberry plant with strawberry mottle virus (SMoV), strawberry crinkle virus (SCV) and strawberry virus 1 (StrV-1). While SCV and StrV-1 are represented by two and three molecular variants, respectively, SmoV has three different RNA1 and RNA2 segments. In this study, we focus on virus acquisition by individual adult aphids of the Aphis gossypii, Aphis forbesi and Chaetosiphon fragaefolii species. Single-aphid transmission trials are performed under experimental conditions. Both different viruses and individual virus strains show varying performances in single aphid acquisition. The obtained data suggests that numerous individual transmission events lead to the establishment of multistrain infections. These data will be important for the development of epidemiological models in plant virology.
Collapse
Affiliation(s)
- Igor Koloniuk
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (S.B.); (J.V.); (J.P.); (J.F.)
- Correspondence: ; Tel.: +420-38-777-5521
| | - Alena Matyášová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (S.B.); (J.V.); (J.P.); (J.F.)
| | - Sára Brázdová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (S.B.); (J.V.); (J.P.); (J.F.)
- Faculty of Agriculture, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
| | - Jana Veselá
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (S.B.); (J.V.); (J.P.); (J.F.)
| | - Jaroslava Přibylová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (S.B.); (J.V.); (J.P.); (J.F.)
| | - Jana Fránová
- Institute of Plant Molecular Biology, Department of Plant Virology, Biology Centre CAS, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (S.B.); (J.V.); (J.P.); (J.F.)
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Paterna, 46980 València, Spain;
- Santa Fe Institute, Santa Fe, NM 87501, USA
| |
Collapse
|
15
|
Guevara-Rivera EA, Rodríguez-Negrete EA, Aréchiga-Carvajal ET, Leyva-López NE, Méndez-Lozano J. From Metagenomics to Discovery of New Viral Species: Galium Leaf Distortion Virus, a Monopartite Begomovirus Endemic in Mexico. Front Microbiol 2022; 13:843035. [PMID: 35547137 PMCID: PMC9083202 DOI: 10.3389/fmicb.2022.843035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Begomoviruses (Family Geminiviridae) are a major group of emerging plant viruses worldwide. The knowledge of begomoviruses is mostly restricted to crop plant systems. Nevertheless, it has been described that non-cultivated plants are important reservoirs and vessels of viral evolution that leads to the emergence of new diseases. High-throughput sequencing (HTS) has provided a powerful tool for speeding up the understanding of molecular ecology and epidemiology of plant virome and for discovery of new viral species. In this study, by performing earlier metagenomics library data mining, followed by geminivirus-related signature single plant searching and RCA-based full-length viral genome cloning, and based on phylogenetic analysis, genomes of two isolates of a novel monopartite begomovirus species tentatively named Galium leaf distortion virus (GLDV), which infects non-cultivated endemic plant Galium mexicanum, were identified in Colima, Mexico. Analysis of the genetic structure of both isolates (GLDV-1 and GLDV-2) revealed that the GLDV genome displays a DNA-A-like structure shared with the new world (NW) bipartite begomoviruses. Nonetheless, phylogenetic analysis using representative members of the main begomovirus American clades for tree construction grouped both GLDV isolates in a clade of the monopartite NW begomovirus, Tomato leaf deformation virus (ToLDeV). A comparative analysis of viral replication regulatory elements showed that the GLDV-1 isolate possesses an array and sequence conservation of iterons typical of NW begomovirus infecting the Solanaceae and Fabaceae families. Interestingly, GLDV-2 showed iteron sequences described only in monopartite begomovirus from OW belonging to a sweepovirus clade that infects plants of the Convolvulaceae family. In addition, the rep iteron related-domain (IRD) of both isolates display FRVQ or FRIS amino acid sequences corresponding to NW and sweepobegomovirus clades for GMV-1 and GMV-2, respectively. Finally, the lack of the GLDV DNA-B segment (tested by molecular detection and biological assays using GLDV-1/2 infectious clones) confirmed the monopartite nature of GLDV. This is the first time that a monopartite begomovirus is described in Mexican ecosystems, and “in silico” geometagenomics analysis indicates that it is restricted to a specific region. These data revealed additional complexity in monopartite begomovirus genetics and geographic distribution and highlighted the importance of metagenomic approaches in understanding global virome ecology and evolution.
Collapse
Affiliation(s)
- Enrique A Guevara-Rivera
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
| | - Edgar A Rodríguez-Negrete
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
| | - Elva T Aréchiga-Carvajal
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología-Unidad de Manipulación Genética, San Nicolás de los Garza, Mexico
| | - Norma E Leyva-López
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
| | - Jesús Méndez-Lozano
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
| |
Collapse
|
16
|
Sukhorukov G, Khalili M, Gascuel O, Candresse T, Marais-Colombel A, Nikolski M. VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data. FRONTIERS IN BIOINFORMATICS 2022; 2:867111. [PMID: 36304258 PMCID: PMC9580956 DOI: 10.3389/fbinf.2022.867111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/24/2022] [Indexed: 10/15/2023] Open
Abstract
High-throughput sequencing has provided the capacity of broad virus detection for both known and unknown viruses in a variety of hosts and habitats. It has been successfully applied for novel virus discovery in many agricultural crops, leading to the current drive to apply this technology routinely for plant health diagnostics. For this, efficient and precise methods for sequencing-based virus detection and discovery are essential. However, both existing alignment-based methods relying on reference databases and even more recent machine learning approaches are not efficient enough in detecting unknown viruses in RNAseq datasets of plant viromes. We present VirHunter, a deep learning convolutional neural network approach, to detect novel and known viruses in assemblies of sequencing datasets. While our method is generally applicable to a variety of viruses, here, we trained and evaluated it specifically for RNA viruses by reinforcing the coding sequences' content in the training dataset. Trained on the NCBI plant viruses data for three different host species (peach, grapevine, and sugar beet), VirHunter outperformed the state-of-the-art method, DeepVirFinder, for the detection of novel viruses, both in the synthetic leave-out setting and on the 12 newly acquired RNAseq datasets. Compared with the traditional tBLASTx approach, VirHunter has consistently exhibited better results in the majority of leave-out experiments. In conclusion, we have shown that VirHunter can be used to streamline the analyses of plant HTS-acquired viromes and is particularly well suited for the detection of novel viral contigs, in RNAseq datasets.
Collapse
Affiliation(s)
- Grigorii Sukhorukov
- CNRS, IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France
- Bordeaux Bioinformatics Center, Université de Bordeaux, Bordeaux, France
| | - Maryam Khalili
- Université de Bordeaux, INRAE, UMR BFP, CS20032, CEDEX, Villenave d’Ornon, France
| | - Olivier Gascuel
- Institut de Systématique, Biodiversité, Evolution (ISYEB - UMR7205, Muséum National d’Histoire Naturelle, CNRS, SU, EPHE, UA), Paris, France
| | - Thierry Candresse
- Université de Bordeaux, INRAE, UMR BFP, CS20032, CEDEX, Villenave d’Ornon, France
| | | | - Macha Nikolski
- CNRS, IBGC, UMR 5095, Université de Bordeaux, Bordeaux, France
- Bordeaux Bioinformatics Center, Université de Bordeaux, Bordeaux, France
| |
Collapse
|
17
|
Roossinck MJ. The Ups and Downs of an Out-of-the-Box Scientist with a Curious Mind. Annu Rev Virol 2022; 9:19-38. [PMID: 35512631 DOI: 10.1146/annurev-virology-100520-013446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
My early life was challenging, and not conducive to the study of science, but my first introduction to viruses was an epiphany for me. I spent the whole of my career dedicated to understanding viruses, driven largely by curiosity. This led me down many different avenues of study, and to work with many wonderful colleagues, most of whom remain friends. Some highlights of my career include the discovery of a mutualistic three-way symbiosis involving a virus, a fungus, and a plant; genetic mapping of a pathogenicity gene in tomato; uncovering a virus in 1,000-year-old corncobs; exploring virus biodiversity in wild plants; and establishing a system to use a fungal virus to understand the epidemiology of its host. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Marilyn J Roossinck
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, State College, Pennsylvania, USA;
| |
Collapse
|
18
|
Ghosh D, Chakraborty S, Kodamana H, Chakraborty S. Application of machine learning in understanding plant virus pathogenesis: trends and perspectives on emergence, diagnosis, host-virus interplay and management. Virol J 2022; 19:42. [PMID: 35264189 PMCID: PMC8905280 DOI: 10.1186/s12985-022-01767-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/27/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Inclusion of high throughput technologies in the field of biology has generated massive amounts of data in the recent years. Now, transforming these huge volumes of data into knowledge is the primary challenge in computational biology. The traditional methods of data analysis have failed to carry out the task. Hence, researchers are turning to machine learning based approaches for the analysis of high-dimensional big data. In machine learning, once a model is trained with a training dataset, it can be applied on a testing dataset which is independent. In current times, deep learning algorithms further promote the application of machine learning in several field of biology including plant virology. MAIN BODY Plant viruses have emerged as one of the principal global threats to food security due to their devastating impact on crops and vegetables. The emergence of new viral strains and species help viruses to evade the concurrent preventive methods. According to a survey conducted in 2014, plant viruses are anticipated to cause a global yield loss of more than thirty billion USD per year. In order to design effective, durable and broad-spectrum management protocols, it is very important to understand the mechanistic details of viral pathogenesis. The application of machine learning enables precise diagnosis of plant viral diseases at an early stage. Furthermore, the development of several machine learning-guided bioinformatics platforms has primed plant virologists to understand the host-virus interplay better. In addition, machine learning has tremendous potential in deciphering the pattern of plant virus evolution and emergence as well as in developing viable control options. CONCLUSIONS Considering a significant progress in the application of machine learning in understanding plant virology, this review highlights an introductory note on machine learning and comprehensively discusses the trends and prospects of machine learning in the diagnosis of viral diseases, understanding host-virus interplay and emergence of plant viruses.
Collapse
Affiliation(s)
- Dibyendu Ghosh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Srija Chakraborty
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016 India
| | - Hariprasad Kodamana
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016 India
- School of Artificial Intelligence, Indian Institute of Technology Delhi, New Delhi, 110016 India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| |
Collapse
|
19
|
Takahashi H, Tabara M, Miyashita S, Ando S, Kawano S, Kanayama Y, Fukuhara T, Kormelink R. Cucumber Mosaic Virus Infection in Arabidopsis: A Conditional Mutualistic Symbiont? Front Microbiol 2022; 12:770925. [PMID: 35069476 PMCID: PMC8776717 DOI: 10.3389/fmicb.2021.770925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
A cucumber mosaic virus isolate, named Ho [CMV(Ho)], was isolated from a symptomless Arabidopsis halleri field sample containing low virus titers. An analysis of CMV(Ho) RNA molecules indicated that the virus isolate, besides the usual cucumovirus tripartite RNA genome, additionally contained defective RNA3 molecules and a satellite RNA. To study the underlying mechanism of the persistent CMV(Ho) infection in perennial A. halleri, infectious cDNA clones were generated for all its genetic elements. CMV, which consists of synthetic transcripts from the infectious tripartite RNA genomes, and designated CMV(Ho)tr, multiplied in A. halleri and annual Arabidopsis thaliana Col-0 to a similar level as the virulent strain CMV(Y), but did not induce any symptoms in them. The response of Col-0 to a series of reassortant CMVs between CMV(Ho)tr and CMV(Y) suggested that the establishment of an asymptomatic phenotype of CMV(Ho) infection was due to the 2b gene of CMV RNA2, but not due to the presence of the defective RNA3 and satellite RNA. The accumulation of CMV(Ho) 2b protein tagged with the FLAG epitope (2b.Ho-FLAG) in 2b.Ho-FLAG-transformed Col-0 did not induce any symptoms, suggesting a 2b-dependent persistency of CMV(Ho)tr infection in Arabidopsis. The 2b protein interacted with Argonaute 4, which is known to regulate the cytosine methylation levels of host genomic DNA. Whole genomic bisulfite sequencing analysis of CMV(Ho)tr- and mock-inoculated Col-0 revealed that cytosine hypomethylation in the promoter regions of 82 genes, including two genes encoding transcriptional regulators (DOF1.7 and CBP1), was induced in response to CMV(Ho)tr infection. Moreover, the increased levels of hypomethylation in the promoter region of both genes, during CMV(Ho)tr infection, were correlated with the up- or down-regulation of their expression. Taken altogether, the results indicate that during persistent CMV(Ho) infection in Arabidopsis, host gene expression may be epigenetically modulated resulting from a 2b-mediated cytosine hypomethylation of host genomic DNA.
Collapse
Affiliation(s)
- Hideki Takahashi
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Midori Tabara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Japan
- Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, Kusatsu, Japan
| | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Sugihiro Ando
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shuichi Kawano
- Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Japan
| | - Yoshinori Kanayama
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| |
Collapse
|
20
|
Narayan A, Zahra S, Singh A, Kumar S. In Silico Methods for the Identification of Viral-Derived Small Interfering RNAs (vsiRNAs) and Their Application in Plant Genomics. Methods Mol Biol 2022; 2408:71-84. [PMID: 35325416 DOI: 10.1007/978-1-0716-1875-2_4] [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] [Indexed: 06/14/2023]
Abstract
The current era of high-throughput sequencing (HTS) technology has expedited the detection and diagnosis of viruses and viroids in the living system including plants. HTS data has become vital to study the etiology of the infection caused by both known as well as novel viral elements in planta, and their impact on overall crop health and productivity. Viral-derived small interfering RNAs are generated as a result of defence response by the host via RNAi machinery. They are immensely exploited for performing exhaustive viral investigations in plants using bioinformatics as well as experimental approaches.This chapter briefly presents the basics of virus-derived small interfering RNAs (vsiRNAs ) biology in plants and their applications in plant genomics and highlights in silico strategies exploited for virus/viroid detection. It gives a systematic pipeline for vsiRNAs identification using currently available bioinformatics tools and databases. This will surely work as a quick beginner's recipe for the in silico revelation of plant vsiRNAs as well as virus/viroid diagnosis using high-throughput sequencing data.
Collapse
Affiliation(s)
| | - Shafaque Zahra
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Ajeet Singh
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
| |
Collapse
|
21
|
Kyrychenko AN, Shcherbatenko IS, Kovalenko AG. Viruses of Wild Plants and Current Metagenomic Methods for Their Investigation. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721030038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
22
|
Ma Y, Fort T, Marais A, Lefebvre M, Theil S, Vacher C, Candresse T. Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2021; 2:87-99. [PMID: 37284285 PMCID: PMC10168098 DOI: 10.1002/pei3.10043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 06/08/2023]
Abstract
Plants are colonized by diverse fungal and viral communities that influence their growth and survival as well as ecosystem functioning. Viruses interact with both plants and the fungi they host. Our understanding of plant-fungi-virus interactions is very limited, especially in wild plants. Combining metagenomic and culturomic approaches, we assessed the richness, diversity, and composition of leaf-associated fungal and viral communities from pools of herbaceous wild plants representative of four sites corresponding to cultivated or natural ecosystems. We identified 161 fungal families and 18 viral families comprising 249 RNA-dependent RNA polymerase-based operational taxonomic units (RdRp OTUs) from leaves. Fungal culturomics captured 12.3% of the fungal diversity recovered with metagenomic approaches and, unexpectedly, retrieved viral OTUs that were almost entirely different from those recovered by leaf metagenomics. Ecosystem management had a significant influence on both leaf mycobiome and virome, with a higher fungal community richness in natural ecosystems and a higher viral family richness in cultivated ecosystems, suggesting that leaf-associated fungal and viral communities are under the influence of different ecological drivers. Both the leaf-associated fungal and viral community compositions showed a strong site-specificity. Further research is needed to confirm these trends and unravel the factors structuring plant-fungi-virus interactions in wild plant populations.
Collapse
Affiliation(s)
- Yuxin Ma
- Univ. BordeauxINRAEUMR 1332 BFPVillenave d’Ornon cedexFrance
| | | | - Armelle Marais
- Univ. BordeauxINRAEUMR 1332 BFPVillenave d’Ornon cedexFrance
| | - Marie Lefebvre
- Univ. BordeauxINRAEUMR 1332 BFPVillenave d’Ornon cedexFrance
| | - Sébastien Theil
- Univ. BordeauxINRAEUMR 1332 BFPVillenave d’Ornon cedexFrance
- Present address:
INRA UMRF20, côte de ReyneAurillac15000France
| | | | | |
Collapse
|
23
|
Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review. Viruses 2021; 13:v13030412. [PMID: 33807625 PMCID: PMC7999175 DOI: 10.3390/v13030412] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.
Collapse
|
24
|
Sempéré G, Pétel A, Abbé M, Lefeuvre P, Roumagnac P, Mahé F, Baurens G, Filloux D. metaXplor: an interactive viral and microbial metagenomic data manager. Gigascience 2021; 10:6126034. [PMID: 33527143 PMCID: PMC7931823 DOI: 10.1093/gigascience/giab001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/13/2020] [Accepted: 01/10/2021] [Indexed: 12/02/2022] Open
Abstract
Background Efficiently managing large, heterogeneous data in a structured yet flexible way is a challenge to research laboratories working with genomic data. Specifically regarding both shotgun- and metabarcoding-based metagenomics, while online reference databases and user-friendly tools exist for running various types of analyses (e.g., Qiime, Mothur, Megan, IMG/VR, Anvi'o, Qiita, MetaVir), scientists lack comprehensive software for easily building scalable, searchable, online data repositories on which they can rely during their ongoing research. Results metaXplor is a scalable, distributable, fully web-interfaced application for managing, sharing, and exploring metagenomic data. Being based on a flexible NoSQL data model, it has few constraints regarding dataset contents and thus proves useful for handling outputs from both shotgun and metabarcoding techniques. By supporting incremental data feeding and providing means to combine filters on all imported fields, it allows for exhaustive content browsing, as well as rapid narrowing to find specific records. The application also features various interactive data visualization tools, ways to query contents by BLASTing external sequences, and an integrated pipeline to enrich assignments with phylogenetic placements. The project home page provides the URL of a live instance allowing users to test the system on public data. Conclusion metaXplor allows efficient management and exploration of metagenomic data. Its availability as a set of Docker containers, making it easy to deploy on academic servers, on the cloud, or even on personal computers, will facilitate its adoption.
Collapse
Affiliation(s)
- Guilhem Sempéré
- CIRAD, UMR INTERTRYP, F-34398 Montpellier, France.,South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, Montpellier, France.,INTERTRYP, Université de Montpellier, CIRAD, IRD, 34398 Montpellier, France
| | - Adrien Pétel
- CIRAD, UMR PVBMT, F-97410 St Pierre, La Réunion, France
| | - Magsen Abbé
- CIRAD, UMR INTERTRYP, F-34398 Montpellier, France.,INTERTRYP, Université de Montpellier, CIRAD, IRD, 34398 Montpellier, France
| | | | - Philippe Roumagnac
- CIRAD, BGPI, 34398 Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Université de Montpellier, 34398 Montpellier, France
| | - Frédéric Mahé
- CIRAD, BGPI, 34398 Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Université de Montpellier, 34398 Montpellier, France
| | - Gaël Baurens
- CIRAD, UMR INTERTRYP, F-34398 Montpellier, France.,INTERTRYP, Université de Montpellier, CIRAD, IRD, 34398 Montpellier, France
| | - Denis Filloux
- CIRAD, BGPI, 34398 Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Université de Montpellier, 34398 Montpellier, France
| |
Collapse
|
25
|
Maclot F, Candresse T, Filloux D, Malmstrom CM, Roumagnac P, van der Vlugt R, Massart S. Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales. Front Microbiol 2020; 11:578064. [PMID: 33178159 PMCID: PMC7596190 DOI: 10.3389/fmicb.2020.578064] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/24/2020] [Indexed: 01/08/2023] Open
Abstract
The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.
Collapse
Affiliation(s)
- François Maclot
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | | | - Denis Filloux
- CIRAD, BGPI, Montpellier, France
- BGPI, INRAE, CIRAD, Institut Agro, Montpellier University, Montpellier, France
| | - Carolyn M. Malmstrom
- Department of Plant Biology and Graduate Program in Ecology, Evolution and Behavior, Michigan State University, East Lansing, MI, United States
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France
- BGPI, INRAE, CIRAD, Institut Agro, Montpellier University, Montpellier, France
| | - René van der Vlugt
- Laboratory of Virology, Wageningen University and Research Centre (WUR-PRI), Wageningen, Netherlands
| | - Sébastien Massart
- Plant Pathology Laboratory, Terra-Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| |
Collapse
|
26
|
Abstract
Virus-virus interactions in plants can modify host symptoms. As a result, disease management strategies may be unsuccessful if they are based solely on visual assessment and diagnostic assays for known individual viruses. Papaya ringspot virus is an important limiting factor for papaya production and likely has interactions with other viruses that are not yet known. Using high-throughput sequencing, we recovered known and novel RNA and DNA viruses from papaya orchards in Chiapas, Mexico, and categorized them by host and, in the case of papaya, symptom type: asymptomatic papaya, papaya with ringspot virus symptoms, papaya with nonringspot symptoms, weeds, and insects. Using network analysis, we demonstrated virus associations within and among host types and described the ecological community patterns. Recovery of viruses from weeds and asymptomatic papaya suggests the need for additional management attention. These analyses contribute to the understanding of the community structure of viruses in the agroecological landscape. The study of complex ecological interactions, such as those among host, pathogen, and vector communities, can help to explain host ranges and the emergence of novel pathogens. We evaluated the viromes of papaya orchards, including weed and insect viromes, to identify common viruses in intensive production of papaya in the Pacific Coastal Plain and the Central Depression of Chiapas, Mexico. Samples of papaya cultivar Maradol, susceptible to papaya ringspot virus (PRSV), were categorized by symptoms by local farmers (papaya ringspot symptoms, non-PRSV symptoms, or asymptomatic). These analyses revealed the presence of 61 viruses, where only 4 species were shared among both regions, 16 showed homology to known viruses, and 36 were homologous with genera including Potyvirus, Comovirus, and Tombusvirus (RNA viruses) and Begomovirus and Mastrevirus (DNA viruses). We analyzed the network of associations between viruses and host-location combinations, revealing ecological properties of the network, such as an asymmetric nested pattern, and compared the observed network to null models of network association. Understanding the network structure informs management strategies, for example, revealing the potential role of PRSV in asymptomatic papaya and that weeds may be an important pathogen reservoir. We identify three key management implications: (i) each region may need a customized management strategy; (ii) visual assessment of papaya may be insufficient for PRSV, requiring diagnostic assays; and (iii) weed control within orchards may reduce the risk of virus spread to papaya. Network analysis advances understanding of host-pathogen interactions in the agroecological landscape. IMPORTANCE Virus-virus interactions in plants can modify host symptoms. As a result, disease management strategies may be unsuccessful if they are based solely on visual assessment and diagnostic assays for known individual viruses. Papaya ringspot virus is an important limiting factor for papaya production and likely has interactions with other viruses that are not yet known. Using high-throughput sequencing, we recovered known and novel RNA and DNA viruses from papaya orchards in Chiapas, Mexico, and categorized them by host and, in the case of papaya, symptom type: asymptomatic papaya, papaya with ringspot virus symptoms, papaya with nonringspot symptoms, weeds, and insects. Using network analysis, we demonstrated virus associations within and among host types and described the ecological community patterns. Recovery of viruses from weeds and asymptomatic papaya suggests the need for additional management attention. These analyses contribute to the understanding of the community structure of viruses in the agroecological landscape.
Collapse
|
27
|
Rodríguez-Nevado C, G Gavilán R, Pagán I. Host Abundance and Identity Determine the Epidemiology and Evolution of a Generalist Plant Virus in a Wild Ecosystem. PHYTOPATHOLOGY 2020; 110:94-105. [PMID: 31589103 DOI: 10.1094/phyto-07-19-0271-fi] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Increasing evidence indicates that in wild ecosystems plant viruses are important ecological agents, and with potential to jump into crops, but only recently have the diversity and population dynamics of wild plant viruses begun to be explored. Theory proposes that biotic factors (e.g., ecosystem biodiversity, host abundance, and host density) and climatic conditions would determine the epidemiology and evolution of wild plant viruses. However, these predictions seldom have been empirically tested. For 3 years, we analyzed the prevalence and genetic diversity of Potyvirus species in preserved riparian forests of Spain. Results indicated that potyviruses were always present in riparian forests, with a novel generalist potyvirus species provisionally named Iberian hop mosaic virus (IbHMV), explaining the largest fraction of infected plants. Focusing on this potyvirus, we analyzed the biotic and climatic factors affecting virus infection risk and population genetic diversity in its native ecosystem. The main predictors of IbHMV infection risk were host relative abundance and species richness. Virus prevalence and host relative abundance were the major factors determining the genetic diversity and selection pressures in the virus population. These observations support theoretical predictions assigning these ecological factors a key role in parasite epidemiology and evolution. Finally, our phylogenetic analysis indicated that the viral population was genetically structured according to host and location of origin, as expected if speciation is largely sympatric. Thus, this work contributes to characterizing viral diversity and provides novel information on the determinants of plant virus epidemiology and evolution in wild ecosystems.
Collapse
Affiliation(s)
- Cristina Rodríguez-Nevado
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, Madrid, Spain
| | - Rosario G Gavilán
- Facultad de Farmacia, Departamento de Farmacología, Farmacognosia y Botánica, unidad de Botánica, Universidad Complutense de Madrid, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Departamento de Biotecnología-Biología Vegetal, Universidad Politécnica de Madrid, Madrid, Spain
| |
Collapse
|
28
|
Takahashi H, Fukuhara T, Kitazawa H, Kormelink R. Virus Latency and the Impact on Plants. Front Microbiol 2019; 10:2764. [PMID: 31866963 PMCID: PMC6908805 DOI: 10.3389/fmicb.2019.02764] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/12/2019] [Indexed: 11/15/2022] Open
Abstract
Plant viruses are thought to be essentially harmful to the lives of their cultivated crop hosts. In most cases studied, the interaction between viruses and cultivated crop plants negatively affects host morphology and physiology, thereby resulting in disease. Native wild/non-cultivated plants are often latently infected with viruses without any clear symptoms. Although seemingly non-harmful, these viruses pose a threat to cultivated crops because they can be transmitted by vectors and cause disease. Reports are accumulating on infections with latent plant viruses that do not cause disease but rather seem to be beneficial to the lives of wild host plants. In a few cases, viral latency involves the integration of full-length genome copies into the host genome that, in response to environmental stress or during certain developmental stages of host plants, can become activated to generate and replicate episomal copies, a transition from latency to reactivation and causation of disease development. The interaction between viruses and host plants may also lead to the integration of partial-length segments of viral DNA genomes or copy DNA of viral RNA genome sequences into the host genome. Transcripts derived from such integrated viral elements (EVEs) may be beneficial to host plants, for example, by conferring levels of virus resistance and/or causing persistence/latency of viral infections. Studies on viral latency in wild host plants might help us to understand and elucidate the underlying mechanisms of latency and provide insights into the raison d’être for viruses in the lives of plants.
Collapse
Affiliation(s)
- Hideki Takahashi
- Laboratory of Plant Pathology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Plant Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Toshiyuki Fukuhara
- Department of Applied Biological Sciences and Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan.,Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University, Wageningen, Netherlands
| |
Collapse
|
29
|
Claverie S, Ouattara A, Hoareau M, Filloux D, Varsani A, Roumagnac P, Martin DP, Lett JM, Lefeuvre P. Exploring the diversity of Poaceae-infecting mastreviruses on Reunion Island using a viral metagenomics-based approach. Sci Rep 2019; 9:12716. [PMID: 31481704 PMCID: PMC6722101 DOI: 10.1038/s41598-019-49134-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 08/20/2019] [Indexed: 01/22/2023] Open
Abstract
Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.
Collapse
Affiliation(s)
- Sohini Claverie
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.,Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, Saint-Pierre, 97410, France
| | - Alassane Ouattara
- INERA, 01 BP 476, Ouagadougou 01, Burkina Faso.,Laboratoire Biosciences, Université Joseph KI-ZERBO, 03 BP 7021, Ouagadougou 03, Burkina Faso
| | | | - Denis Filloux
- CIRAD, UMR BGPI, F-34398, Montpellier, France.,BGPI, Université de Montpellier, INRA, CIRAD, Montpellier SupAgro, F-34398, Montpellier, France
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287-5001, USA.,Structural Biology Research Unit, Departement of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Philippe Roumagnac
- CIRAD, UMR BGPI, F-34398, Montpellier, France.,BGPI, Université de Montpellier, INRA, CIRAD, Montpellier SupAgro, F-34398, Montpellier, France
| | - Darren P Martin
- Computational Biology Division, Departement of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, South Africa
| | | | | |
Collapse
|
30
|
Rodríguez-Negrete EA, Morales-Aguilar JJ, Domínguez-Duran G, Torres-Devora G, Camacho-Beltrán E, Leyva-López NE, Voloudakis AE, Bejarano ER, Méndez-Lozano J. High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico. Viruses 2019; 11:v11070594. [PMID: 31261973 PMCID: PMC6669537 DOI: 10.3390/v11070594] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/28/2019] [Accepted: 06/17/2019] [Indexed: 12/24/2022] Open
Abstract
Plant DNA viruses of the genus Begomovirus have been documented as the most genetically diverse in the family Geminiviridae and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize naturally existing begomoviruses, since viral genetic diversity in non-cultivated plants could lead to future disease epidemics in crops. In this study, high-throughput sequencing (HTS) was employed to determine viral diversity of samples collected in a survey performed during 2012–2016 in seven states of Northern-Pacific Mexico, areas of diverse climatic conditions where different vegetable crops are subject to intensive farming. In total, 132 plant species, belonging to 34 families, were identified and sampled in the natural ecosystems surrounding cultivated areas (agro-ecological interface). HTS analysis and subsequent de novo assembly revealed a number of geminivirus-related DNA signatures with 80 to 100% DNA similarity with begomoviral sequences present in the genome databank. The analysis revealed DNA signatures corresponding to 52 crop-infecting and 35 non-cultivated-infecting geminiviruses that, interestingly, were present in different plant species. Such an analysis deepens our knowledge of geminiviral diversity and could help detecting emerging viruses affecting crops in different agro-climatic regions.
Collapse
Affiliation(s)
- Edgar Antonio Rodríguez-Negrete
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Juan José Morales-Aguilar
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Gustavo Domínguez-Duran
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Gadiela Torres-Devora
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Erika Camacho-Beltrán
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Norma Elena Leyva-López
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
| | - Andreas E Voloudakis
- Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, 75 Iera Odos, Athens 11855, Greece
| | - Eduardo R Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus Teatinos, 29071 Málaga, Spain
| | - Jesús Méndez-Lozano
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico.
| |
Collapse
|
31
|
Shates TM, Sun P, Malmstrom CM, Dominguez C, Mauck KE. Addressing Research Needs in the Field of Plant Virus Ecology by Defining Knowledge Gaps and Developing Wild Dicot Study Systems. Front Microbiol 2019; 9:3305. [PMID: 30687284 PMCID: PMC6333650 DOI: 10.3389/fmicb.2018.03305] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 12/19/2018] [Indexed: 11/30/2022] Open
Abstract
Viruses are ubiquitous within all habitats that support cellular life and represent the most important emerging infectious diseases of plants. Despite this, it is only recently that we have begun to describe the ecological roles of plant viruses in unmanaged systems and the influence of ecosystem properties on virus evolution. We now know that wild plants frequently harbor infections by diverse virus species, but much remains to be learned about how viruses influence host traits and how hosts influence virus evolution and vector interactions. To identify knowledge gaps and suggest avenues for alleviating research deficits, we performed a quantitative synthesis of a representative sample of virus ecology literature, developed criteria for expanding the suite of pathosystems serving as models, and applied these criteria through a case study. We found significant gaps in the types of ecological systems studied, which merit more attention. In particular, there is a strong need for a greater diversity of logistically tractable, wild dicot perennial study systems suitable for experimental manipulations of infection status. Based on criteria developed from our quantitative synthesis, we evaluated three California native dicot perennials typically found in Mediterranean-climate plant communities as candidate models: Cucurbita foetidissima (buffalo gourd), Cucurbita palmata (coyote gourd), and Datura wrightii (sacred thorn-apple). We used Illumina sequencing and network analyses to characterize viromes and viral links among species, using samples taken from multiple individuals at two different reserves. We also compared our Illumina workflow with targeted RT-PCR detection assays of varying costs. To make this process accessible to ecologists looking to incorporate virology into existing studies, we describe our approach in detail and discuss advantages and challenges of different protocols. We also provide a bioinformatics workflow based on open-access tools with graphical user interfaces. Our study provides evidence that dicot perennials in xeric habitats support multiple, asymptomatic infections by viruses known to be pathogenic in related crop hosts. Quantifying the impacts of these interactions on plant performance and virus epidemiology in our logistically tractable host systems will provide fundamental information about plant virus ecology outside of crop environments.
Collapse
Affiliation(s)
- Tessa M. Shates
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| | - Penglin Sun
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| | - Carolyn M. Malmstrom
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Graduate Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, United States
| | - Chrysalyn Dominguez
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| | - Kerry E. Mauck
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| |
Collapse
|
32
|
Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
Collapse
|
33
|
Pagán I. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view. INFECTION GENETICS AND EVOLUTION 2018; 65:187-199. [PMID: 30055330 DOI: 10.1016/j.meegid.2018.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
During the past four decades, the scientific community has seen an exponential advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of plant virus populations. Predating these advances, the field of Phylogenetics has significantly contributed to understand important aspects of plant virus evolution. This review aims at summarizing the impact of Phylogenetics in the current knowledge on three major aspects of plant virus evolution that have benefited from the development of phylogenetic inference: (1) The identification and classification of plant virus diversity. (2) The mechanisms and forces shaping the evolution of plant virus populations. (3) The understanding of the interaction between plant virus evolution, epidemiology and ecology. The work discussed here highlights the important role of phylogenetic approaches in the study of the dynamics of plant virus populations.
Collapse
Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28223, Spain.
| |
Collapse
|
34
|
From Spatial Metagenomics to Molecular Characterization of Plant Viruses: A Geminivirus Case Study. Adv Virus Res 2018; 101:55-83. [PMID: 29908594 DOI: 10.1016/bs.aivir.2018.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The number of plant viruses that are known likely remains only a vanishingly small fraction of all extant plant virus species. Consequently, the distribution and population dynamics of plant viruses within even the best-studied ecosystems have only ever been studied for small groups of virus species. Even for the best studied of these groups very little is known about virus diversity at spatial scales ranging from an individual host, through individual local host populations to global host populations. To date, metagenomics studies that have assessed the collective or metagenomes of viruses at the ecosystem scale have revealed many previously unrecognized viral species. More recently, novel georeferenced metagenomics approaches have been devised that can precisely link individual sequence reads to both the plant hosts from which they were obtained, and the spatial arrangements of these hosts. Besides illuminating the diversity and the distribution of plant viruses at the ecosystem scale, application of these "geometagenomics" approaches has enabled the direct testing of hypotheses relating to the impacts of host diversity, host spatial variations, and environmental conditions on plant virus diversity and prevalence. To exemplify how such top-down approaches can provide a far deeper understanding of host-virus associations, we provide a case-study focusing on geminiviruses within two complex ecosystems containing both cultivated and uncultivated areas. Geminiviruses are a highly relevant model for studying the evolutionary and ecological aspects of viral emergence because the family Geminiviridae includes many of the most important crop pathogens that have emerged over the past century. In addition to revealing unprecedented degrees of geminivirus diversity within the analyzed ecosystems, the geometagenomics-based approach enabled the focused in-depth analysis of the complex evolutionary dynamics of some of the highly divergent geminivirus species that were discovered.
Collapse
|
35
|
Ghorbani A, Izadpanah K, Dietzgen RG. Changes in maize transcriptome in response to maize Iranian mosaic virus infection. PLoS One 2018; 13:e0194592. [PMID: 29634778 PMCID: PMC5892904 DOI: 10.1371/journal.pone.0194592] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 03/06/2018] [Indexed: 12/14/2022] Open
Abstract
Background Maize Iranian mosaic virus (MIMV, genus Nucleorhabdovirus, family Rhabdoviridae) causes an economically important disease in maize and other gramineous crops in Iran. MIMV negative-sense RNA genome sequence of 12,426 nucleotides has recently been completed. Maize Genetics and Genomics database shows that 39,498 coding genes and 4,976 non-coding genes of maize have been determined, but still some transcripts could not be annotated. The molecular host cell responses of maize to MIMV infection including differential gene expression have so far not been elucidated. Methodology/Principal findings Complementary DNA libraries were prepared from total RNA of MIMV-infected and mock-inoculated maize leaves and sequenced using Illumina HiSeq 2500. Cleaned raw transcript reads from MIMV-infected maize were mapped to reads from uninfected maize and to a maize reference genome. Differentially expressed transcripts were characterized by gene ontology and biochemical pathway analyses. Transcriptome data for selected genes were validated by real-time quantitative PCR. Conclusion/Significance Approximately 42 million clean reads for each treatment were obtained. In MIMV-infected maize compared to uninfected plants, 1689 transcripts were up-regulated and 213 transcripts were down-regulated. In response to MIMV infection, several pathways were activated in maize including immune receptor signaling, metabolic pathways, RNA silencing, hormone-mediated pathways, protein degradation, protein kinase and ATP binding activity, and fatty acid metabolism. Also, several transcripts including those encoding hydrophobic protein RCI2B, adenosylmethionine decarboxylase NAC transcription factor and nucleic acid binding, leucine-rich repeat, heat shock protein, 26S proteasome, oxidoreductases and endonuclease activity protein were up-regulated. These data will contribute to the identification of genes and pathways involved in plant-virus interactions that may serve as future targets for improved disease control.
Collapse
Affiliation(s)
- Abozar Ghorbani
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, Iran
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
| | | | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
- * E-mail:
| |
Collapse
|
36
|
Gupta N, Zahra S, Singh A, Kumar S. PVsiRNAdb: a database for plant exclusive virus-derived small interfering RNAs. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5126495. [PMID: 30307523 PMCID: PMC6181178 DOI: 10.1093/database/bay105] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/14/2018] [Indexed: 11/13/2022]
Abstract
Ribonucleic acids (RNA) interference mechanism has been proved to be an important regulator of both transcriptional and post-transcription controls of gene expression during biotic and abiotic stresses in plants. Virus-derived small interfering RNAs (vsiRNAs) are established components of the RNA silencing mechanism for incurring anti-viral resistance in plants. Some databases like siRNAdb, HIVsirDB and VIRsiRNAdb are available online pertaining to siRNAs as well as vsiRNAs generated during viral infection in humans; however, currently there is a lack of repository for plant exclusive vsiRNAs. We have developed `PVsiRNAdb (http://www.nipgr.res.in/PVsiRNAdb)', a manually curated plant-exclusive database harboring information related to vsiRNAs found in different virus-infected plants collected by exhaustive data mining of published literature so far. This database contains a total of 322 214 entries and 282 549 unique sequences of vsiRNAs. In PVsiRNAdb, detailed and comprehensive information is available for each vsiRNA sequence. Apart from the core information consisting of plant, tissue, virus name and vsiRNA sequence, additional information of each vsiRNAs (map position, length, coordinates, strand information and predicted structure) may be of high utility to the user. Different types of search and browse modules with three different tools namely BLAST, Smith-Waterman Align and Mapping are provided at PVsiRNAdb. Thus, this database being one of its kind will surely be of much use to molecular biologists for exploring the complex viral genetics and genomics, viral-host interactions and beneficial to the scientific community and can prove to be very advantageous in the field of agriculture for producing viral resistance transgenic crops.
Collapse
Affiliation(s)
- Nikita Gupta
- Bioinformatics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Shafaque Zahra
- Bioinformatics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Ajeet Singh
- Bioinformatics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| |
Collapse
|
37
|
Rodríguez-Nevado C, Montes N, Pagán I. Ecological Factors Affecting Infection Risk and Population Genetic Diversity of a Novel Potyvirus in Its Native Wild Ecosystem. FRONTIERS IN PLANT SCIENCE 2017; 8:1958. [PMID: 29184567 PMCID: PMC5694492 DOI: 10.3389/fpls.2017.01958] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
Increasing evidence indicates that there is ample diversity of plant virus species in wild ecosystems. The vast majority of this diversity, however, remains uncharacterized. Moreover, in these ecosystems the factors affecting plant virus infection risk and population genetic diversity, two traits intrinsically linked to virus emergence, are largely unknown. Along 3 years, we have analyzed the prevalence and diversity of plant virus species from the genus Potyvirus in evergreen oak forests of the Iberian Peninsula, the main wild ecosystem in this geographic region and in the entire Mediterranean basin. During this period, we have also measured plant species diversity, host density, plant biomass, temperature, relative humidity, and rainfall. Results indicated that potyviruses were always present in evergreen oak forests, with a novel virus species explaining the largest fraction of potyvirus-infected plants. We determined the genomic sequence of this novel virus and we explored its host range in natural and greenhouse conditions. Natural host range was limited to the perennial plant mountain rue (Ruta montana), commonly found in evergreen oak forests of the Iberian Peninsula. In this host, the virus was highly prevalent and was therefore provisionally named mediterranean ruda virus (MeRV). Focusing in this natural host-virus interaction, we analyzed the ecological factors affecting MeRV infection risk and population genetic diversity in its native wild ecosystem. The main predictor of virus infection risk was the host density. MeRV prevalence was the major factor determining genetic diversity and selection pressures in the virus populations. This observation supports theoretical predictions assigning these two traits a key role in parasite epidemiology and evolution. Thus, our analyses contribute both to characterize viral diversity and to understand the ecological determinants of virus population dynamics in wild ecosystems.
Collapse
Affiliation(s)
- Cristina Rodríguez-Nevado
- Centro de Biotecnología y Genómica de Plantas – Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Nuria Montes
- Plant Physiology, Pharmaceutical and Health Sciences Department, Faculty of Pharmacy, CEU-San Pablo University, Madrid, Spain
- Rheumatology Service, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas – Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| |
Collapse
|
38
|
Tugume AK, Mukasa SB, Valkonen JPT. Mixed Infections of Four Viruses, the Incidence and Phylogenetic Relationships of Sweet Potato Chlorotic Fleck Virus (Betaflexiviridae) Isolates in Wild Species and Sweetpotatoes in Uganda and Evidence of Distinct Isolates in East Africa. PLoS One 2016; 11:e0167769. [PMID: 28005969 PMCID: PMC5179071 DOI: 10.1371/journal.pone.0167769] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/18/2016] [Indexed: 01/05/2023] Open
Abstract
Viruses infecting wild flora may have a significant negative impact on nearby crops, and vice-versa. Only limited information is available on wild species able to host economically important viruses that infect sweetpotatoes (Ipomoea batatas). In this study, Sweet potato chlorotic fleck virus (SPCFV; Carlavirus, Betaflexiviridae) and Sweet potato chlorotic stunt virus (SPCSV; Crinivirus, Closteroviridae) were surveyed in wild plants of family Convolvulaceae (genera Astripomoea, Ipomoea, Hewittia and Lepistemon) in Uganda. Plants belonging to 26 wild species, including annuals, biannuals and perennials from four agro-ecological zones, were observed for virus-like symptoms in 2004 and 2007 and sampled for virus testing. SPCFV was detected in 84 (2.9%) of 2864 plants tested from 17 species. SPCSV was detected in 66 (5.4%) of the 1224 plants from 12 species sampled in 2007. Some SPCSV-infected plants were also infected with Sweet potato feathery mottle virus (SPFMV; Potyvirus, Potyviridae; 1.3%), Sweet potato mild mottle virus (SPMMV; Ipomovirus, Potyviridae; 0.5%) or both (0.4%), but none of these three viruses were detected in SPCFV-infected plants. Co-infection of SPFMV with SPMMV was detected in 1.2% of plants sampled. Virus-like symptoms were observed in 367 wild plants (12.8%), of which 42 plants (11.4%) were negative for the viruses tested. Almost all (92.4%) the 419 sweetpotato plants sampled from fields close to the tested wild plants displayed virus-like symptoms, and 87.1% were infected with one or more of the four viruses. Phylogenetic and evolutionary analyses of the 3'-proximal genomic region of SPCFV, including the silencing suppressor (NaBP)- and coat protein (CP)-coding regions implicated strong purifying selection on the CP and NaBP, and that the SPCFV strains from East Africa are distinguishable from those from other continents. However, the strains from wild species and sweetpotato were indistinguishable, suggesting reciprocal movement of SPCFV between wild and cultivated Convolvulaceae plants in the field.
Collapse
Affiliation(s)
- Arthur K. Tugume
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
- Department of Plant Sciences, Microbiology and Biotechnology, School of Biosciences, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Settumba B. Mukasa
- Department of Agricultural Production, School of Agricultural Sciences, College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | - Jari P. T. Valkonen
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| |
Collapse
|
39
|
Kamitani M, Nagano AJ, Honjo MN, Kudoh H. RNA-Seq reveals virus-virus and virus-plant interactions in nature. FEMS Microbiol Ecol 2016; 92:fiw176. [PMID: 27549115 PMCID: PMC5854034 DOI: 10.1093/femsec/fiw176] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/10/2016] [Accepted: 08/16/2016] [Indexed: 11/17/2022] Open
Abstract
As research on plant viruses has focused mainly on crop diseases, little is known about these viruses in natural environments. To understand the ecology of viruses in natural systems, comprehensive information on virus-virus and virus-host interactions is required. We applied RNA-Seq to plants from a natural population of Arabidopsis halleri subsp. gemmifera to simultaneously determine the presence/absence of all sequence-reported viruses, identify novel viruses and quantify the host transcriptome. By introducing the criteria of read number and genome coverage, we detected infections by Turnip mosaic virus (TuMV), Cucumber mosaic virus and Brassica yellows virus Active TuMV replication was observed by ultramicroscopy. De novo assembly further identified a novel partitivirus, Arabidopsis halleri partitivirus 1 Interestingly, virus reads reached a maximum level that was equivalent to that of the host's total mRNA, although asymptomatic infection was common. AhgAGO2, a key gene in host defence systems, was upregulated in TuMV-infected plants. Multiple infection was frequent in TuMV-infected leaves, suggesting that TuMV facilitates multiple infection, probably by suppressing host RNA silencing. Revealing hidden plant-virus interactions in nature can enhance our understanding of biological interactions and may have agricultural applications.
Collapse
Affiliation(s)
- Mari Kamitani
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2914, Japan JST PRESTO, Japan Science and Technology Agency, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113, Japan
| |
Collapse
|
40
|
Mascia T, Gallitelli D. Synergies and antagonisms in virus interactions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:176-192. [PMID: 27717453 DOI: 10.1016/j.plantsci.2016.07.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/22/2016] [Accepted: 07/27/2016] [Indexed: 05/25/2023]
Abstract
Metagenomic surveys and data from next generation sequencing revealed that mixed infections among plant viruses are probably a rule rather than an exception in natural pathosystems. The documented cases may range from synergism to antagonism, which may depend from the spatiotemporal order of arrival of the viruses on the host and upon the host itself. In synergistic interactions, the measurable differences in replication, phenotypic and cytopathological changes, cellular tropism, within host movement, and transmission rate of one of the two viruses or both are increased. Conversely, a decrease in replication, or inhibition of one or more of the above functions by one virus against the other, leads to an antagonistic interaction. Viruses may interact directly and by transcomplementation of defective functions or indirectly, through responses mediated by the host like the defense mechanism based on RNA silencing. Outcomes of these interactions can be applied to the risk assessment of transgenic crops expressing viral proteins, or cross-protected crops for the identification of potential hazards. Prior to experimental evidence, mathematical models may help in forecasting challenges deriving from the great variety of pathways of synergistic and antagonistic interactions. Actually, it seems that such predictions do not receive sufficient credit in the framework of agriculture.
Collapse
Affiliation(s)
- Tiziana Mascia
- Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; Istituto del CNR per la Protezione sostenibile delle Piante, Unità Operativa di Supporto di Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - Donato Gallitelli
- Dipartimento di Scienze del Suolo della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; Istituto del CNR per la Protezione sostenibile delle Piante, Unità Operativa di Supporto di Bari, Via Amendola 165/A, 70126 Bari, Italy.
| |
Collapse
|
41
|
Hadidi A, Flores R, Candresse T, Barba M. Next-Generation Sequencing and Genome Editing in Plant Virology. Front Microbiol 2016; 7:1325. [PMID: 27617007 PMCID: PMC4999435 DOI: 10.3389/fmicb.2016.01325] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/11/2016] [Indexed: 01/18/2023] Open
Abstract
Next-generation sequencing (NGS) has been applied to plant virology since 2009. NGS provides highly efficient, rapid, low cost DNA, or RNA high-throughput sequencing of the genomes of plant viruses and viroids and of the specific small RNAs generated during the infection process. These small RNAs, which cover frequently the whole genome of the infectious agent, are 21-24 nt long and are known as vsRNAs for viruses and vd-sRNAs for viroids. NGS has been used in a number of studies in plant virology including, but not limited to, discovery of novel viruses and viroids as well as detection and identification of those pathogens already known, analysis of genome diversity and evolution, and study of pathogen epidemiology. The genome engineering editing method, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been successfully used recently to engineer resistance to DNA geminiviruses (family, Geminiviridae) by targeting different viral genome sequences in infected Nicotiana benthamiana or Arabidopsis plants. The DNA viruses targeted include tomato yellow leaf curl virus and merremia mosaic virus (begomovirus); beet curly top virus and beet severe curly top virus (curtovirus); and bean yellow dwarf virus (mastrevirus). The technique has also been used against the RNA viruses zucchini yellow mosaic virus, papaya ringspot virus and turnip mosaic virus (potyvirus) and cucumber vein yellowing virus (ipomovirus, family, Potyviridae) by targeting the translation initiation genes eIF4E in cucumber or Arabidopsis plants. From these recent advances of major importance, it is expected that NGS and CRISPR-Cas technologies will play a significant role in the very near future in advancing the field of plant virology and connecting it with other related fields of biology.
Collapse
Affiliation(s)
- Ahmed Hadidi
- United States Department of Agriculture – Agricultural Research ServiceBeltsville, MD, USA
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia–Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, Institut National de la Recherche Agronomique, Université de BordeauxBordeaux, France
| | - Marina Barba
- Consiglio per la Ricerca in Agricoltura e l’analisi dell’Economia Agraria, Centro di Ricerca per la Patologia VegetaleRome, Italy
| |
Collapse
|
42
|
Martin RR, Constable F, Tzanetakis IE. Quarantine Regulations and the Impact of Modern Detection Methods. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:189-205. [PMID: 27491434 DOI: 10.1146/annurev-phyto-080615-100105] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Producers worldwide need access to the best plant varieties and cultivars available to be competitive in global markets. This often means moving plants across international borders as soon as they are available. At the same time, quarantine agencies are tasked with minimizing the risk of introducing exotic pests and pathogens along with imported plant material, with the goal to protect domestic agriculture and native fauna and flora. These two drivers, the movement of more plant material and reduced risk of pathogen introduction, are at odds. Improvements in large-scale or next-generation sequencing (NGS) and bioinformatics for data analysis have resulted in improved speed and accuracy of pathogen detection that could facilitate plant trade with reduced risk of pathogen movement. There are concerns to be addressed before NGS can replace existing tools used for pathogen detection in plant quarantine and certification programs. Here, we discuss the advantages and possible pitfalls of this technology for meeting the needs of plant quarantine and certification.
Collapse
Affiliation(s)
- Robert R Martin
- Horticultural Crops Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Corvallis, Oregon 97330;
| | - Fiona Constable
- Department of Economic Development, Jobs, Transport and Resources, AgriBio, Bundoora, Victoria, Australia 3083:
| | - Ioannis E Tzanetakis
- Department of Plant Pathology, Division of Agriculture, University of Arkansas, Fayetteville, Arkansas 72701;
| |
Collapse
|
43
|
Characterization of Five Novel Mitoviruses in the White Pine Blister Rust Fungus Cronartium ribicola. PLoS One 2016; 11:e0154267. [PMID: 27196406 PMCID: PMC4873031 DOI: 10.1371/journal.pone.0154267] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/11/2016] [Indexed: 11/19/2022] Open
Abstract
The white pine blister rust (WPBR) fungus Cronartium ribicola (J.C. Fisch.) is an exotic invasive forest pathogen causing severe stem canker disease of native white pine trees (subgenus Strobus) in North America. The present study reports discovery of five novel mitoviruses in C. ribicola by deep RNA sequencing. The complete genome of each mitovirus was determined by rapid amplification of cDNA ends (RACE) and reverse transcriptase-polymerase chain reaction (RT-PCR). A single open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) was detected in each of the viral genomes using mitochondrial genetic codes. Phylogenetic analysis indicated that the C. ribicola mitoviruses (CrMV1 to CrMV5) are new putative species of the genus Mitovirus. qRT-PCR and RNA-Seq analyses revealed that viral RNAs were significantly increased in fungal mycelia in cankered pine stems compared to expression during two different stages of spore development, suggesting that viral genome replication and transcription benefit from active growth of the host fungus. CrMVs were widespread with relatively high levels of minor allele frequency (MAF) in western North America. As the first report of mitoviruses in the Class Pucciniomycetes, this work allows further investigation of the dynamics of a viral community in the WPBR pathosystem, including potential impacts that may affect pathogenicity and virulence of the host fungus.
Collapse
|
44
|
Fraile A, García-Arenal F. Environment and evolution modulate plant virus pathogenesis. Curr Opin Virol 2016; 17:50-56. [DOI: 10.1016/j.coviro.2016.01.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/07/2016] [Accepted: 01/14/2016] [Indexed: 12/17/2022]
|
45
|
Plant Virus Diversity and Evolution. CURRENT RESEARCH TOPICS IN PLANT VIROLOGY 2016. [PMCID: PMC7123681 DOI: 10.1007/978-3-319-32919-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Historically, the majority of plant virology focused on agricultural systems. Recent efforts have expanded our knowledge of the true diversity of plant viruses by studying those viruses that infect wild, undomesticated plants. Those efforts have provided answers to basic ecological questions regarding viruses in the wild, and insights into evolutionary questions, regarding the origins of viruses. While much work has been done, we have merely scratched the surface of the diversity that is estimated to exist. In this chapter we discuss the state of our knowledge of virus diversity, both in agricultural systems as well as in native wild systems, the border between these two systems and how viruses adapt and move across this border into an artificial, domesticated environment. We look at how this diversity has affected our outlook on viruses as a whole, shifting our past view of viruses as purely antagonistic entities of destruction to one where viruses are in a mutually beneficial relationship with their hosts. Additionally, we discuss the current work that plant virology has put forth regarding the evolutionary mechanisms, the life histories, and the deep evolution of viruses.
Collapse
|
46
|
Hily JM, Poulicard N, Mora MÁ, Pagán I, García-Arenal F. Environment and host genotype determine the outcome of a plant-virus interaction: from antagonism to mutualism. THE NEW PHYTOLOGIST 2016; 209:812-22. [PMID: 26365599 DOI: 10.1111/nph.13631] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 07/31/2015] [Indexed: 05/21/2023]
Abstract
It has been hypothesized that plant-virus interactions vary between antagonism and conditional mutualism according to environmental conditions. This hypothesis is based on scant experimental evidence, and to test it we examined the effect of abiotic factors on the Arabidopsis thaliana-Cucumber mosaic virus (CMV) interaction. Four Arabidopsis genotypes clustering into two allometric groups were grown under six environments defined by three temperature and two light-intensity conditions. Plants were either CMV-infected or mock-inoculated, and the effects of environment and infection on temporal and resource allocation life-history traits were quantified. Life-history traits significantly differed between allometric groups over all environments, with group 1 plants tolerating abiotic stress better than those of group 2. The effect of CMV infection on host fitness (virulence) differed between genotypes, being lower in group 1 genotypes. Tolerance to abiotic stress and to infection was similarly achieved through life-history trait responses, which resulted in resource reallocation from growth to reproduction. Effects of infection varied according to plant genotype and environment from detrimental to beneficial for host fitness. These results are highly relevant and demonstrate that plant viruses can be pleiotropic parasites along the antagonism-mutualism continuum, which should be considered in analyses of the evolution of plant-virus interactions.
Collapse
Affiliation(s)
- Jean-Michel Hily
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) & Escuela Técnica Superior de Ingenieros (ETSI) Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Nils Poulicard
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) & Escuela Técnica Superior de Ingenieros (ETSI) Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Miguel-Ángel Mora
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) & Escuela Técnica Superior de Ingenieros (ETSI) Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) & Escuela Técnica Superior de Ingenieros (ETSI) Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) & Escuela Técnica Superior de Ingenieros (ETSI) Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón (Madrid), 28223, Spain
| |
Collapse
|
47
|
Gorni C, Allemand D, Rossi D, Mariani P. Microbiome profiling in fresh-cut products. Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2015.10.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
48
|
Zhang C, Wu Z, Li Y, Wu J. Biogenesis, Function, and Applications of Virus-Derived Small RNAs in Plants. Front Microbiol 2015; 6:1237. [PMID: 26617580 PMCID: PMC4637412 DOI: 10.3389/fmicb.2015.01237] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
RNA silencing, an evolutionarily conserved and sequence-specific gene-inactivation system, has a pivotal role in antiviral defense in most eukaryotic organisms. In plants, a class of exogenous small RNAs (sRNAs) originating from the infecting virus called virus-derived small interfering RNAs (vsiRNAs) are predominantly responsible for RNA silencing-mediated antiviral immunity. Nowadays, the process of vsiRNA formation and the role of vsiRNAs in plant viral defense have been revealed through deep sequencing of sRNAs and diverse genetic analysis. The biogenesis of vsiRNAs is analogous to that of endogenous sRNAs, which require diverse essential components including dicer-like (DCL), argonaute (AGO), and RNA-dependent RNA polymerase (RDR) proteins. vsiRNAs trigger antiviral defense through post-transcriptional gene silencing (PTGS) or transcriptional gene silencing (TGS) of viral RNA, and they hijack the host RNA silencing system to target complementary host transcripts. Additionally, several applications that take advantage of the current knowledge of vsiRNAs research are being used, such as breeding antiviral plants through genetic engineering technology, reconstructing of viral genomes, and surveying viral ecology and populations. Here, we will provide an overview of vsiRNA pathways, with a primary focus on the advances in vsiRNA biogenesis and function, and discuss their potential applications as well as the future challenges in vsiRNAs research.
Collapse
Affiliation(s)
- Chao Zhang
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zujian Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Yi Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, China
| | - Jianguo Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China ; Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, China
| |
Collapse
|
49
|
Rosario K, Seah YM, Marr C, Varsani A, Kraberger S, Stainton D, Moriones E, Polston JE, Duffy S, Breitbart M. Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) Reveal Novel Begomovirus Species in the New and Old Worlds. Viruses 2015; 7:5553-70. [PMID: 26516898 PMCID: PMC4632403 DOI: 10.3390/v7102895] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 01/16/2023] Open
Abstract
Whitefly-transmitted viruses belonging to the genus Begomovirus (family Geminiviridae) represent a substantial threat to agricultural food production. The rapid evolutionary potential of these single-stranded DNA viruses combined with the polyphagous feeding behavior of their whitefly vector (Bemisia tabaci) can lead to the emergence of damaging viral strains. Therefore, it is crucial to characterize begomoviruses circulating in different regions and crops globally. This study utilized vector-enabled metagenomics (VEM) coupled with high-throughput sequencing to survey begomoviruses directly from whiteflies collected in various locations (California (USA), Guatemala, Israel, Puerto Rico, and Spain). Begomoviruses were detected in all locations, with the highest diversity identified in Guatemala where up to seven different species were identified in a single field. Both bipartite and monopartite viruses were detected, including seven new begomovirus species from Guatemala, Puerto Rico, and Spain. This begomovirus survey extends the known diversity of these highly damaging plant viruses. However, the new genomes described here and in the recent literature appear to reflect the outcome of interactions between closely-related species, often resulting from recombination, instead of unique, highly divergent species.
Collapse
Affiliation(s)
- Karyna Rosario
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Yee Mey Seah
- Microbiology and Molecular Genetics, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Christian Marr
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.
| | - Simona Kraberger
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Daisy Stainton
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch 8041, New Zealand.
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora", Algarrobo-Costa, Málaga 29750, Spain.
| | - Jane E Polston
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA.
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
| | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA.
| |
Collapse
|
50
|
Ma J, Pallett D, Jiang H, Hou Y, Wang H. Mutational bias of Turnip Yellow Mosaic Virus in the context of host anti-viral gene silencing. Virology 2015; 486:2-6. [PMID: 26379088 DOI: 10.1016/j.virol.2015.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 05/01/2015] [Accepted: 08/21/2015] [Indexed: 01/04/2023]
Abstract
Plant Dicer-like (DCL) enzymes exhibit a GC-preference during anti-viral post-transcriptional gene silencing (PTGS), delivering an evolutionary selection pressure resulting in plant viruses with GC-poor genomes. However, some viruses, e.g. Turnip Yellow Mosaic Virus (TYMV, genus Tymovirus) have GC-rich genomes, raising the question as to whether or not DCL derived selection pressure affects these viruses. In this study we analyzed the virus-derived small interfering RNAs from TYMV-infected leaves of Brassica juncea showed that the TYMV population accumulated a mutational bias with AU replacing GC (GC-AU), demonstrating PTGS pressure. Interestingly, at the highly polymorphic sites the GC-AU bias was no longer observed. This suggests the presence of an unknown mechanism preventing mutational drift of the viral population and maintaining viral genome stability, despite the host PTGS pressure.
Collapse
Affiliation(s)
- Jinmin Ma
- BGI-shenzhen, Beishan Road, Yantian, Shenzhen 518083, China
| | - Denise Pallett
- NERC/Centre for Ecology & Hydrology, Benson Lane, Wallingford, Oxfordshire OX10 8BB, UK
| | - Hui Jiang
- BGI-shenzhen, Beishan Road, Yantian, Shenzhen 518083, China
| | - Yong Hou
- BGI-shenzhen, Beishan Road, Yantian, Shenzhen 518083, China
| | - Hui Wang
- BGI-shenzhen, Beishan Road, Yantian, Shenzhen 518083, China; NERC/Centre for Ecology & Hydrology, Benson Lane, Wallingford, Oxfordshire OX10 8BB, UK; Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| |
Collapse
|