1
|
Tripathi JN, Ntui VO, Tripathi L. Precision genetics tools for genetic improvement of banana. THE PLANT GENOME 2024; 17:e20416. [PMID: 38012108 DOI: 10.1002/tpg2.20416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/22/2023] [Accepted: 11/02/2023] [Indexed: 11/29/2023]
Abstract
Banana is an important food security crop for millions of people in the tropics but it faces challenges from diseases and pests. Traditional breeding methods have limitations, prompting the exploration of precision genetic tools like genetic modification and genome editing. Extensive efforts using transgenic approaches have been made to develop improved banana varieties with resistance to banana Xanthomonas wilt, Fusarium wilt, and nematodes. However, these efforts should be extended for other pests, diseases, and abiotic stresses. The commercialization of transgenic crops still faces continuous challenges with regulatory and public acceptance. Genome editing, particularly CRISPR/Cas, offers precise modifications to the banana genome and has been successfully applied in the improvement of banana. Targeting specific genes can contribute to the development of improved banana varieties with enhanced resistance to various biotic and abiotic constraints. This review discusses recent advances in banana improvement achieved through genetic modification and genome editing.
Collapse
Affiliation(s)
| | | | - Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| |
Collapse
|
2
|
Tennant P, Rampersad S, Alleyne A, Johnson L, Tai D, Amarakoon I, Roye M, Pitter P, Chang PG, Myers Morgan L. Viral Threats to Fruit and Vegetable Crops in the Caribbean. Viruses 2024; 16:603. [PMID: 38675944 PMCID: PMC11053604 DOI: 10.3390/v16040603] [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: 01/26/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Viruses pose major global challenges to crop production as infections reduce the yield and quality of harvested products, hinder germplasm exchange, increase financial inputs, and threaten food security. Small island or archipelago habitat conditions such as those in the Caribbean are particularly susceptible as the region is characterized by high rainfall and uniform, warm temperatures throughout the year. Moreover, Caribbean islands are continuously exposed to disease risks because of their location at the intersection of transcontinental trade between North and South America and their role as central hubs for regional and global agricultural commodity trade. This review provides a summary of virus disease epidemics that originated in the Caribbean and those that were introduced and spread throughout the islands. Epidemic-associated factors that impact disease development are also discussed. Understanding virus disease epidemiology, adoption of new diagnostic technologies, implementation of biosafety protocols, and widespread acceptance of biotechnology solutions to counter the effects of cultivar susceptibility remain important challenges to the region. Effective integrated disease management requires a comprehensive approach that should include upgraded phytosanitary measures and continuous surveillance with rapid and appropriate responses.
Collapse
Affiliation(s)
- Paula Tennant
- Department of Life Sciences, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica;
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
| | - Sephra Rampersad
- Department of Life Sciences, The University of the West Indies, St. Augustine 999183, Trinidad and Tobago;
| | - Angela Alleyne
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill, Bridgetown BB11000, Barbados;
| | - Lloyd Johnson
- Department of Life Sciences, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica;
| | - Deiondra Tai
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
| | - Icolyn Amarakoon
- Department of Basic Medical Sciences, Biochemistry Section, Faculty of Medical Sciences Teaching and Research Complex, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica;
| | - Marcia Roye
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
| | - Patrice Pitter
- Biotechnology Centre, The University of the West Indies, Mona, St. Andrew JMAAW07, Jamaica; (D.T.); (M.R.); (P.P.)
- Ministry of Agriculture, Bodles Research Station, Old Harbour, St. Catherine JMACE18, Jamaica; (P.-G.C.); (L.M.M.)
| | - Peta-Gaye Chang
- Ministry of Agriculture, Bodles Research Station, Old Harbour, St. Catherine JMACE18, Jamaica; (P.-G.C.); (L.M.M.)
| | - Lisa Myers Morgan
- Ministry of Agriculture, Bodles Research Station, Old Harbour, St. Catherine JMACE18, Jamaica; (P.-G.C.); (L.M.M.)
| |
Collapse
|
3
|
Fiallo-Olivé E, Navas-Castillo J. The Role of Extensive Recombination in the Evolution of Geminiviruses. Curr Top Microbiol Immunol 2023; 439:139-166. [PMID: 36592245 DOI: 10.1007/978-3-031-15640-3_4] [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: 01/03/2023]
Abstract
Mutation, recombination and pseudo-recombination are the major forces driving the evolution of viruses by the generation of variants upon which natural selection, genetic drift and gene flow can act to shape the genetic structure of viral populations. Recombination between related virus genomes co-infecting the same cell usually occurs via template swapping during the replication process and produces a chimeric genome. The family Geminiviridae shows the highest evolutionary success among plant virus families, and the common presence of recombination signatures in their genomes reveals a key role in their evolution. This review describes the general characteristics of members of the family Geminiviridae and associated DNA satellites, as well as the extensive occurrence of recombination at all taxonomic levels, from strain to family. The review also presents an overview of the recombination patterns observed in nature that provide some clues regarding the mechanisms involved in the generation and emergence of recombinant genomes. Moreover, the results of experimental evolution studies that support some of the conclusions obtained in descriptive or in silico works are summarized. Finally, the review uses a number of case studies to illustrate those recombination events with evolutionary and pathological implications as well as recombination events in which DNA satellites are involved.
Collapse
Affiliation(s)
- Elvira Fiallo-Olivé
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Avenida Dr. Wienberg s/n, 29750, Algarrobo-Costa, Málaga, Spain
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Avenida Dr. Wienberg s/n, 29750, Algarrobo-Costa, Málaga, Spain.
| |
Collapse
|
4
|
Iannella M, De Simone W, D'Alessandro P, Biondi M. Climate change favours connectivity between virus-bearing pest and rice cultivations in sub-Saharan Africa, depressing local economies. PeerJ 2021; 9:e12387. [PMID: 34820174 PMCID: PMC8607929 DOI: 10.7717/peerj.12387] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/04/2021] [Indexed: 12/18/2022] Open
Abstract
Aims Rice is a staple food for many countries, being fundamental for a large part of the worlds’ population. In sub-Saharan Africa, its importance is currently high and is likely to become even more relevant, considering that the number of people and the per-capita consumption are both predicted to increase. The flea beetles belonging to the Chaetocnema pulla species group (pulla group), a harmful rice pest, are an important vector of the Rice Yellow Mottle Virus, a disease which leads even to 80–100% yield losses in rice production. We present a continental-scale study aiming at: (1) locating current and future suitable territories for both pulla group and rice; (2) identifying areas where rice cultivations may occur without suffering the presence of pulla group using an Ecological Niche Modelling (ENM) approach; (3) estimating current and future connectivity among pulla group populations and areas predicted to host rice cultivations, based on the most recent land-use estimates for future agricultural trends; (4) proposing a new connectivity index called “Pest Aggression Index” (PAI) to measure the agricultural susceptibility to the potential future invasions of pests and disease; (5) quantifying losses in terms of production when rice cultivations co‐occur with the pulla group and identifying the SSA countries which, in the future inferred scenarios, will potentially suffer the greatest losses. Location Sub-Saharan Africa. Methods Since the ongoing climate and land-use changes affect species’ distributions, we first assess the impact of these changes through a spatially-jackknifed Maxent-based Ecological Niche Modelling in GIS environment, for both the pulla group and rice, in two climatic/socioeconomic future scenarios (SSP_2.45 and 3.70). We then assess the connectivity potential of the pulla group populations towards rice cultivations, for both current and future predictions, through a circuit theory-based approach (Circuitscape implemented in Julia language). We finally measure the rice production and GPD loss per country through the spatial index named “Pest Aggression Index”, based on the inferred connectivity magnitude. Results The most considerable losses in rice production are observed for Liberia, Sierra Leone and Madagascar in all future scenarios (2030, 2050, 2070). The future economic cost, calculated as USD lost from rice losses/country’s GDP results are high for Central African Republic (−0.6% in SSP_2.45 and −3.0% in SSP_3.70) and Guinea–Bissau (−0.4% in SSP_2.45 and −0.68% in SSP_3.70), with relevant losses also obtained for other countries. Main conclusions Since our results are spatially explicit and focused on each country, we encourage careful land-use planning. Our findings could support best practices to avoid the future settlement of new cultivations in territories where rice would be attacked by pulla group and the virus, bringing economic and biodiversity losses.
Collapse
Affiliation(s)
- Mattia Iannella
- Department of Life, Health & Environmental Sciences, University of L'Aquila, L'Aquila, Abruzzo, Italy
| | - Walter De Simone
- Department of Life, Health & Environmental Sciences, University of L'Aquila, L'Aquila, Abruzzo, Italy
| | - Paola D'Alessandro
- Department of Life, Health & Environmental Sciences, University of L'Aquila, L'Aquila, Abruzzo, Italy
| | - Maurizio Biondi
- Department of Life, Health & Environmental Sciences, University of L'Aquila, L'Aquila, Abruzzo, Italy
| |
Collapse
|
5
|
Bayoumi M, Munir M. Potential Use of CRISPR/Cas13 Machinery in Understanding Virus-Host Interaction. Front Microbiol 2021; 12:743580. [PMID: 34899631 PMCID: PMC8664230 DOI: 10.3389/fmicb.2021.743580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/25/2021] [Indexed: 12/20/2022] Open
Abstract
Prokaryotes have evolutionarily acquired an immune system to fend off invading mobile genetic elements, including viral phages and plasmids. Through recognizing specific sequences of the invading nucleic acid, prokaryotes mediate a subsequent degradation process collectively referred to as the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) (CRISPR-Cas) system. The CRISPR-Cas systems are divided into two main classes depending on the structure of the effector Cas proteins. Class I systems have effector modules consisting of multiple proteins, while class II systems have a single multidomain effector. Additionally, the CRISPR-Cas systems can also be categorized into types depending on the spacer acquisition components and their evolutionary features, namely, types I-VI. Among CRISPR/Cas systems, Cas9 is one of the most common multidomain nucleases that identify, degrade, and modulate DNA. Importantly, variants of Cas proteins have recently been found to target RNA, especially the single-effector Cas13 nucleases. The Cas13 has revolutionized our ability to study and perturb RNAs in endogenous microenvironments. The Cas13 effectors offer an excellent candidate for developing novel research tools in virological and biotechnological fields. Herein, in this review, we aim to provide a comprehensive summary of the recent advances of Cas13s for targeting viral RNA for either RNA-mediated degradation or CRISPR-Cas13-based diagnostics. Additionally, we aim to provide an overview of the proposed applications that could revolutionize our understanding of viral-host interactions using Cas13-mediated approaches.
Collapse
Affiliation(s)
- Mahmoud Bayoumi
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
- Virology Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
| |
Collapse
|
6
|
Szyniszewska AM, Chikoti PC, Tembo M, Mulenga R, Gilligan CA, van den Bosch F, McQuaid CF. Smallholder Cassava Planting Material Movement and Grower Behavior in Zambia: Implications for the Management of Cassava Virus Diseases. PHYTOPATHOLOGY 2021; 111:1952-1962. [PMID: 33856231 DOI: 10.1094/phyto-06-20-0215-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cassava (Manihot esculenta) is an important food crop across sub-Saharan Africa, where production is severely inhibited by two viral diseases, cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), both propagated by a whitefly vector and via human-mediated movement of infected cassava stems. There is limited information on growers' behavior related to movement of planting material, as well as growers' perception and awareness of cassava diseases, despite the importance of these factors for disease control. This study surveyed a total of 96 cassava subsistence growers and their fields across five provinces in Zambia between 2015 and 2017 to address these knowledge gaps. CMD symptoms were observed in 81.6% of the fields, with an average incidence of 52% across the infected fields. No CBSD symptoms were observed. Most growers used planting materials from their own (94%) or nearby (<10 km) fields of family and friends, although several large transactions over longer distances (10 to 350 km) occurred with friends (15 transactions), markets (1), middlemen (5), and nongovernmental organizations (6). Information related to cassava diseases and certified clean (disease-free) seed reached only 48% of growers. The most frequent sources of information related to cassava diseases included nearby friends, family, and neighbors, while extension workers were the most highly preferred source of information. These data provide a benchmark on which to plan management approaches to controlling CMD and CBSD, which should include clean propagation material, increasing growers' awareness of the diseases, and increasing information provided to farmers (specifically disease symptom recognition and disease management options).[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
| | - Patrick Chiza Chikoti
- Zambia Agriculture Research Institute, Plant Protection and Quarantine Division, Mt. Makulu Research Station, Chilanga, Zambia
| | - Mathias Tembo
- Zambia Agriculture Research Institute, Plant Protection and Quarantine Division, Mt. Makulu Research Station, Chilanga, Zambia
| | - Rabson Mulenga
- Zambia Agriculture Research Institute, Plant Protection and Quarantine Division, Mt. Makulu Research Station, Chilanga, Zambia
| | | | - Frank van den Bosch
- Department of Environment & Agriculture, Centre for Crop and Disease Management, Curtin University, Bentley, Perth, WA 6102, Australia
| | - Christopher Finn McQuaid
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, WC1E 7HT London, United Kingdom
| |
Collapse
|
7
|
Cassava mosaic virus in Africa: Functional analysis of virus coat proteins based on evolutionary processes and protein structure. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
8
|
Odongo PJ, Onaga G, Ricardo O, Natsuaki KT, Alicai T, Geuten K. Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:671355. [PMID: 34267770 PMCID: PMC8276079 DOI: 10.3389/fpls.2021.671355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Rice is the main food crop for people in low- and lower-middle-income countries in Asia and sub-Saharan Africa (SSA). Since 1982, there has been a significant increase in the demand for rice in SSA, and its growing importance is reflected in the national strategic food security plans of several countries in the region. However, several abiotic and biotic factors undermine efforts to meet this demand. Rice yellow mottle virus (RYMV) caused by Solemoviridae is a major biotic factor affecting rice production and continues to be an important pathogen in SSA. To date, six pathogenic strains have been reported. RYMV infects rice plants through wounds and rice feeding vectors. Once inside the plant cells, viral genome-linked protein is required to bind to the rice translation initiation factor [eIF(iso)4G1] for a compatible interaction. The development of resistant cultivars that can interrupt this interaction is the most effective method to manage this disease. Three resistance genes are recognized to limit RYMV virulence in rice, some of which have nonsynonymous single mutations or short deletions in the core domain of eIF(iso)4G1 that impair viral host interaction. However, deployment of these resistance genes using conventional methods has proved slow and tedious. Molecular approaches are expected to be an alternative to facilitate gene introgression and/or pyramiding and rapid deployment of these resistance genes into elite cultivars. In this review, we summarize the knowledge on molecular genetics of RYMV-rice interaction, with emphasis on host plant resistance. In addition, we provide strategies for sustainable utilization of the novel resistant sources. This knowledge is expected to guide breeding programs in the development and deployment of RYMV resistant rice varieties.
Collapse
Affiliation(s)
- Patrick J. Odongo
- Molecular Biotechnology of Plants and Micro-Organisms, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
| | - Geoffrey Onaga
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
- M’bé Research Station, Africa Rice Center (AfricaRice), Bouaké, Côte d’Ivoire
| | - Oliver Ricardo
- Breeding Innovations Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Keiko T. Natsuaki
- Graduate School of Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Titus Alicai
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
| | - Koen Geuten
- Molecular Biotechnology of Plants and Micro-Organisms, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
| |
Collapse
|
9
|
Mubarik MS, Wang X, Khan SH, Ahmad A, Khan Z, Amjid MW, Razzaq MK, Ali Z, Azhar MT. Engineering broad-spectrum resistance to cotton leaf curl disease by CRISPR-Cas9 based multiplex editing in plants. GM CROPS & FOOD 2021; 12:647-658. [PMID: 34124996 PMCID: PMC9208622 DOI: 10.1080/21645698.2021.1938488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Advances in genome editing technologies have tremendous potential to address the limitations of classical resistance breeding. CRISPR-Cas9 based gene editing has been applied successfully in plants to tolerate virus infections. In this study, we successfully tested CRISPR-Cas9 system to counteract cotton leaf curl disease (CLCuD) caused by whitefly transmitted cotton leaf curl viruses (CLCuVs). We also analyzed the ability of CLCuV to escape the Cas9 endonuclease activity. Targeting overlapping genes of most prevalent CLCuVs with three gRNAs resulted in virus interference, as validated by low virus titer. Furthermore, multiplex CRISPR-Cas9 construct simultaneously targeting six genes of CLCuV, was found more effective to interfere with virus proliferation compared to targeting single region individually. Additionally, transgenic N. benthamiana plants expressing multiple gRNAs simultaneously showed enhanced tolerance against CLCuV infection when compared to wild-type plants. T7 Endonuclease-I (T7EI) assay, showing indels in the CLCuV genome, confirmed the occurrence of double strand breaks (DSBs) in DNA at target sequence induced by Cas9 endonuclease. We observed that targeting CLCuV genome at multiple sites simultaneously resulted in better interference, also with inefficient recovery of altered virus molecules. Next, we tested multiplex construct in cotton to interfere CLCuV infection. We found significant decrease in virus accumulation in cotton leaves co-infiltrated with multiplex cassette and virus compared to cotton leaves infiltrated with virus only. The results demonstrate future use of CRISPR-Cas9 system for engineering virus resistance in crops. Moreover, our results also advocate that resistance to mixed virus infections can be engineered using multiplex genome editing.
Collapse
Affiliation(s)
- Muhammad Salman Mubarik
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi, China
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Aftab Ahmad
- Department of Biochemistry, University of Agriculture, Faisalabad, Pakistan
| | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology (IPBB), MNS University of Agriculture, Multan, Pakistan
| | - Muhammad Waqas Amjid
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Khuram Razzaq
- Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology (IPBB), MNS University of Agriculture, Multan, Pakistan
| | - Muhammad Tehseen Azhar
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan.,School of Agriculture Sciences Zhengzhou University, Zhengzhou, China
| |
Collapse
|
10
|
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]
|
11
|
Daugrois JH, Filloux D, Julian C, Claude L, Ferdinand R, Fernandez E, Fontes H, Rott PC, Roumagnac P. Comparison of the Virome of Quarantined Sugarcane Varieties and the Virome of Grasses Growing near the Quarantine Station. Viruses 2021; 13:922. [PMID: 34065683 PMCID: PMC8157134 DOI: 10.3390/v13050922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/28/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
Visacane is a sugarcane quarantine station located in the South of France, far away from sugarcane growing areas. Visacane imports up to 100 sugarcane varieties per year, using safe control and confinement measures of plants and their wastes to prevent any risk of pathogen spread outside of the facilities. Viruses hosted by the imported material are either known or unknown to cause disease in cultivated sugarcane. Poaceae viruses occurring in plants surrounding the quarantine glasshouse are currently unknown. These viruses could be considered as a source of new sugarcane infections and potentially cause new sugarcane diseases in cases of confinement barrier failure. The aim of this study was to compare the plant virome inside and outside of the quarantine station to identify potential confinement failures and risks of cross infections. Leaves from quarantined sugarcane varieties and from wild Poaceae growing near the quarantine were collected and processed by a metagenomics approach based on virion-associated nucleic acids extraction and library preparation for Illumina sequencing. While viruses belonging to the same virus genus or family were identified in the sugarcane quarantine and its surroundings, no virus species was detected in both environments. Based on the data obtained in this study, no virus movement between quarantined sugarcane and nearby grassland has occurred so far, and the confinement procedures of Visacane appear to be properly implemented.
Collapse
Affiliation(s)
- Jean H. Daugrois
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Charlotte Julian
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Lisa Claude
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Romain Ferdinand
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Emmanuel Fernandez
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Hugo Fontes
- Tour du Valat, Research Institute for the Conservation of Mediterranean Wetlands, 13200 Arles, France;
- Institut Méditerranéen de Biodiversité et Ecologie, UMR CNRS-IRD, Avignon Université, Aix-Marseille Université, IUT d’Avignon, 337 chemin des Meinajariés, Site Agroparc BP 61207, 84911 Avignon, France
| | - Philippe C. Rott
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090 Montpellier, France; (J.H.D.); (D.F.); (C.J.); (L.C.); (R.F.); (E.F.); (P.C.R.)
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090 Montpellier, France
| |
Collapse
|
12
|
Uhls A, Petersen S, Keith C, Howard S, Bao X, Qiu W. Grapevine vein clearing virus Is Prevalent and Genetically Variable in Grape Aphid ( Aphis illinoisensis Shimer) Populations. PLANT DISEASE 2021; 105:1531-1538. [PMID: 33174799 DOI: 10.1094/pdis-10-20-2176-re] [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: 06/11/2023]
Abstract
Grapevine vein clearing virus (GVCV) causes severe stunting and death of cultivated grapevines and is prevalent in native Vitis spp. and Ampelopsis cordata in the Midwest region of the United States. GVCV can be transmitted from wild A. cordata to Vitis spp. by grape aphid (Aphis illinoisensis) under greenhouse conditions, but its prevalence, genetic composition, and genome number in native grape aphids are unknown. In this study, we collected grape aphids from native Vitaceae across the state of Missouri in 2018 and 2019, and conducted diagnostic, genetic, and quantitative analyses. GVCV was detected in 91 of the 105 randomly sampled communities on 71 Vitaceae plants (87%). It was present in 211 of 525 single grape aphids (40%). Diverse GVCV variants from aphids were present on both GVCV-negative and GVCV-positive plants. Identical GVCV variants were found in grape aphids sampled from wild and cultivated Vitaceae, indicating that viruliferous aphids likely migrate and disperse GVCV variants among wild and cultivated Vitaceae. In addition, we found that the number of GVCV genomes varies largely in the stylet and body of individual aphids. Our study provides a snapshot of GVCV epidemics and genetic structure in its mobile vector and sessile hosts. This presents a good model for studying the epidemiology, ecology, and evolution of a plant virus.
Collapse
Affiliation(s)
- Adam Uhls
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Sylvia Petersen
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Cory Keith
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Susanne Howard
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Xiaokai Bao
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| | - Wenping Qiu
- Center for Grapevine Biotechnology, W. H. Darr College of Agriculture, Missouri State University, Springfield, MO 65897
| |
Collapse
|
13
|
Emerging infectious diseases threatening food security and economies in Africa. GLOBAL FOOD SECURITY 2021. [DOI: 10.1016/j.gfs.2020.100479] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
14
|
Dash SP, Dipankar P, Burange PS, Rouse BT, Sarangi PP. Climate change: how it impacts the emergence, transmission, resistance and consequences of viral infections in animals and plants. Crit Rev Microbiol 2021; 47:307-322. [PMID: 33570448 DOI: 10.1080/1040841x.2021.1879006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The ongoing COVID-19 pandemic has made us wonder what led to its occurrence and what can be done to avoid such events in the future. As we document, one changing circumstance that is resulting in the emergence and changing the expression of viral diseases in both plants and animals is climate change. Of note, the rapidly changing environment and weather conditions such as excessive flooding, droughts, and forest fires have raised concerns about the global ecosystem's security, sustainability, and balance. In this review, we discuss the main consequences of climate change and link these to how they impact the appearance of new viral pathogens, how they may facilitate transmission between usual and novel hosts, and how they may also affect the host's ability to manage the infection. We emphasize how changes in temperature and humidity and other events associated with climate change influence the reservoirs of viral infections, their transmission by insects and other intermediates, their survival outside the host as well the success of infection in plants and animals. We conclude that climate change has mainly detrimental consequences for the emergence, transmission, and outcome of viral infections and plead the case for halting and hopefully reversing this dangerous event.
Collapse
Affiliation(s)
- Shiba Prasad Dash
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pankaj Dipankar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Prasad S Burange
- Department of Entomology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Barry T Rouse
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Sciences, The University of Tennessee Knoxville, Knoxville, TN, USA
| | - Pranita P Sarangi
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| |
Collapse
|
15
|
Tripathi L, Ntui VO, Tripathi JN, Kumar PL. Application of CRISPR/Cas for Diagnosis and Management of Viral Diseases of Banana. Front Microbiol 2021; 11:609784. [PMID: 33584573 PMCID: PMC7873300 DOI: 10.3389/fmicb.2020.609784] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/29/2020] [Indexed: 12/26/2022] Open
Abstract
Viral diseases are significant biotic constraints for banana (Musa spp.) production as they affect the yield and limit the international movement of germplasm. Among all the viruses known to infect banana, the banana bunchy top virus and banana streak viruses are widespread and economically damaging. The use of virus-resistant bananas is the most cost-effective option to minimize the negative impacts of viral-diseases on banana production. CRISPR/Cas-based genome editing is emerging as the most powerful tool for developing virus-resistant crop varieties in several crops, including the banana. The availability of a vigorous genetic transformation and regeneration system and a well-annotated whole-genome sequence of banana makes it a compelling candidate for genome editing. A robust CRISPR/Cas9-based genome editing of the banana has recently been established, which can be applied in developing disease-resistant varieties. Recently, the CRISPR system was exploited to detect target gene sequences using Cas9, Cas12, Cas13, and Cas14 enzymes, thereby unveiling the use of this technology for virus diagnosis. This article presents a synopsis of recent advancements and perspectives on the application of CRISPR/Cas-based genome editing for diagnosing and developing resistance against banana viruses and challenges in genome-editing of banana.
Collapse
Affiliation(s)
- Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | | | | | - P. Lava Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| |
Collapse
|
16
|
Jones RAC. Global Plant Virus Disease Pandemics and Epidemics. PLANTS (BASEL, SWITZERLAND) 2021; 10:233. [PMID: 33504044 PMCID: PMC7911862 DOI: 10.3390/plants10020233] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/18/2022]
Abstract
The world's staple food crops, and other food crops that optimize human nutrition, suffer from global virus disease pandemics and epidemics that greatly diminish their yields and/or produce quality. This situation is becoming increasingly serious because of the human population's growing food requirements and increasing difficulties in managing virus diseases effectively arising from global warming. This review provides historical and recent information about virus disease pandemics and major epidemics that originated within different world regions, spread to other continents, and now have very wide distributions. Because they threaten food security, all are cause for considerable concern for humanity. The pandemic disease examples described are six (maize lethal necrosis, rice tungro, sweet potato virus, banana bunchy top, citrus tristeza, plum pox). The major epidemic disease examples described are seven (wheat yellow dwarf, wheat streak mosaic, potato tuber necrotic ringspot, faba bean necrotic yellows, pepino mosaic, tomato brown rugose fruit, and cucumber green mottle mosaic). Most examples involve long-distance virus dispersal, albeit inadvertent, by international trade in seed or planting material. With every example, the factors responsible for its development, geographical distribution and global importance are explained. Finally, an overall explanation is given of how to manage global virus disease pandemics and epidemics effectively.
Collapse
Affiliation(s)
- Roger A C Jones
- The UWA Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| |
Collapse
|
17
|
Disease Pandemics and Major Epidemics Arising from New Encounters between Indigenous Viruses and Introduced Crops. Viruses 2020; 12:v12121388. [PMID: 33291635 PMCID: PMC7761969 DOI: 10.3390/v12121388] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 01/13/2023] Open
Abstract
Virus disease pandemics and epidemics that occur in the world’s staple food crops pose a major threat to global food security, especially in developing countries with tropical or subtropical climates. Moreover, this threat is escalating rapidly due to increasing difficulties in controlling virus diseases as climate change accelerates and the need to feed the burgeoning global population escalates. One of the main causes of these pandemics and epidemics is the introduction to a new continent of food crops domesticated elsewhere, and their subsequent invasion by damaging virus diseases they never encountered before. This review focusses on providing historical and up-to-date information about pandemics and major epidemics initiated by spillover of indigenous viruses from infected alternative hosts into introduced crops. This spillover requires new encounters at the managed and natural vegetation interface. The principal virus disease pandemic examples described are two (cassava mosaic, cassava brown streak) that threaten food security in sub-Saharan Africa (SSA), and one (tomato yellow leaf curl) doing so globally. A further example describes a virus disease pandemic threatening a major plantation crop producing a vital food export for West Africa (cacao swollen shoot). Also described are two examples of major virus disease epidemics that threaten SSA’s food security (rice yellow mottle, groundnut rosette). In addition, brief accounts are provided of two major maize virus disease epidemics (maize streak in SSA, maize rough dwarf in Mediterranean and Middle Eastern regions), a major rice disease epidemic (rice hoja blanca in the Americas), and damaging tomato tospovirus and begomovirus disease epidemics of tomato that impair food security in different world regions. For each pandemic or major epidemic, the factors involved in driving its initial emergence, and its subsequent increase in importance and geographical distribution, are explained. Finally, clarification is provided over what needs to be done globally to achieve effective management of severe virus disease pandemics and epidemics initiated by spillover events.
Collapse
|
18
|
Krüger K, van der Waals JE. Potato virus Y and Potato leafroll virus management under climate change in sub-Saharan Africa. S AFR J SCI 2020. [DOI: 10.17159/sajs.2020/8579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Potato has increased in importance as a staple food in sub-Saharan Africa, where its production is faced with a multitude of challenges, including plant disease development and spread under changing climatic conditions. The economically most important plant viruses affecting potatoes globally are Potato virus Y (PVY) and Potato leafroll virus (PLRV). Disease management relies mostly on the use of insecticides, cultural control and seed certification schemes. A major obstacle in many sub-Saharan Africa countries is the availability of disease-free quality seed potatoes. Establishment and implementation of quality control through specialised seed production systems and certification schemes is critical to improve seed potato quality and reduce PVY and PLRV sources. Seed could be further improved by breeding virus-resistant varieties adapted to different environmental conditions combined with management measures tailored for smallholder or commercial farmers to specific agricultural requirements. Innovative technologies – including more sensitive testing, remote sensing, machine learning and predictive models – provide new tools for the management of PVY and PLRV, but require support for adoption and implementation in sub-Saharan Africa.
Collapse
Affiliation(s)
- Kerstin Krüger
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jacquie E. van der Waals
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| |
Collapse
|
19
|
Kojima K, Juma KM, Akagi S, Hayashi K, Takita T, O'Sullivan CK, Fujiwara S, Nakura Y, Yanagihara I, Yasukawa K. Solvent engineering studies on recombinase polymerase amplification. J Biosci Bioeng 2020; 131:219-224. [PMID: 33177003 DOI: 10.1016/j.jbiosc.2020.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 11/24/2022]
Abstract
Recombinase polymerase amplification (RPA) is a technique that is used to specifically amplify a target nucleic acid sequence. Unlike the polymerase chain reaction (PCR), RPA is performed at a constant temperature between 37 and 42°C. Therefore, it can be potentially used for the onsite detection of various pathogens when combined with DNA extraction and amplicon detection techniques. In this study, we prepared recombinant recombinase and single-stranded DNA-binding protein from T4 phage and used them to examine the effects of reaction conditions and additives on the efficiency of RPA. The results revealed that the optimal pH was 7.5-8.0, optimal potassium acetate concentration was 40-80 mM, and optimal reaction temperature was 37-45°C although dimethyl sulfoxide at 5% v/v and formamide at 5% v/v inhibited the reaction. Our results suggest that RPA could be conducted using a wider range of optimal reaction conditions than those required for PCR and that RPA is highly suitable for point-of-care use.
Collapse
Affiliation(s)
- Kenji Kojima
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kevin Maafu Juma
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Shihomi Akagi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kaichi Hayashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Teisuke Takita
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Shinsuke Fujiwara
- Department of Bioscience, School of Science and Technology, Kwansei-Gakuin University, Hyogo 669-1337, Japan
| | - Yukiko Nakura
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Osaka 594-1101, Japan
| | - Itaru Yanagihara
- Department of Developmental Medicine, Research Institute, Osaka Women's and Children's Hospital, Osaka 594-1101, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| |
Collapse
|
20
|
Savary S, Willocquet L. Modeling the Impact of Crop Diseases on Global Food Security. ANNUAL REVIEW OF PHYTOPATHOLOGY 2020; 58:313-341. [PMID: 32511041 DOI: 10.1146/annurev-phyto-010820-012856] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Plant pathology must contribute to improving food security in a safe operating space, which is shrinking as a result of declining natural resources, climate change, and the growing world population. This review analyzes the position of plant pathology in a nexus of relationships, which is mapped and where the coupled dynamics of crop growth, disease, and yield losses are modeled. We derive a hierarchy of pathogens, whereby pathogens reducing radiation interception (RI), radiation use efficiency (RUE), and harvest index increasingly impact crop yields in the approximate proportions: 1:4.5:4,700. Since the dawn of agriculture, plant breeding has targeted the harvest index as a main objective for domesticated plants. Surprisingly, the literature suggests that pathogens that reduce yields by directly damaging harvestable plant tissues have received much less attention than those that reduce RI or RUE. Ecological disease management needs to target diverse production situations and therefore must consider variation in attainable yields; this can be achieved through the reengineering of agrosystems to incorporate built-in dynamic diversity of genes, plants, and crop stands.
Collapse
Affiliation(s)
- Serge Savary
- INRAE, Université de Toulouse, UMR AGIR, F-31320, Castanet-Tolosan, France;
| | | |
Collapse
|
21
|
Huang X, Chen S, Yang X, Yang X, Zhang T, Zhou G. Friend or Enemy: A Dual Role of Autophagy in Plant Virus Infection. Front Microbiol 2020; 11:736. [PMID: 32373106 PMCID: PMC7186577 DOI: 10.3389/fmicb.2020.00736] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/30/2020] [Indexed: 11/20/2022] Open
Abstract
Autophagy is a primary protective process that involves removing damaged organelles or dysfunctional proteins in eukaryotes. The autophagy pathway not only maintains cellular homeostasis, but also modulates the host's cellular response to pathogen infection. Several studies proved that autophagy plays a dominant role in plant fitness and immunity. As intracellular parasites, the replication and spread of viruses entirely rely upon the molecular machinery of the host cell, including the autophagy process. Plant viruses severely affect crop yields and quality. During infection, complex interactions occur between viral proteins and host factors in relation to plant defense and virus counter-defense. An increasing number of studies demonstrated that plants use autophagy to eliminate and inhibit viruses; some viruses were shown to manipulate the process of autophagy to promote their own replication and survival in plant cells. In this review, we summarize recent advances in plant autophagy, with an emphasis on the role of autophagy in plant virus infection.
Collapse
Affiliation(s)
- Xiuqin Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Siping Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiaorong Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Xin Yang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Tong Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Guohui Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| |
Collapse
|
22
|
Lefeuvre P, Martin DP, Elena SF, Shepherd DN, Roumagnac P, Varsani A. Evolution and ecology of plant viruses. Nat Rev Microbiol 2019; 17:632-644. [PMID: 31312033 DOI: 10.1038/s41579-019-0232-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2019] [Indexed: 02/07/2023]
Abstract
The discovery of the first non-cellular infectious agent, later determined to be tobacco mosaic virus, paved the way for the field of virology. In the ensuing decades, research focused on discovering and eliminating viral threats to plant and animal health. However, recent conceptual and methodological revolutions have made it clear that viruses are not merely agents of destruction but essential components of global ecosystems. As plants make up over 80% of the biomass on Earth, plant viruses likely have a larger impact on ecosystem stability and function than viruses of other kingdoms. Besides preventing overgrowth of genetically homogeneous plant populations such as crop plants, some plant viruses might also promote the adaptation of their hosts to changing environments. However, estimates of the extent and frequencies of such mutualistic interactions remain controversial. In this Review, we focus on the origins of plant viruses and the evolution of interactions between these viruses and both their hosts and transmission vectors. We also identify currently unknown aspects of plant virus ecology and evolution that are of practical importance and that should be resolvable in the near future through viral metagenomics.
Collapse
Affiliation(s)
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-UV, Paterna, València, Spain.,The Santa Fe Institute, Santa Fe, NM, USA
| | | | - Philippe Roumagnac
- CIRAD, UMR BGPI, Montpellier, France.,BGPI, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, 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, USA. .,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
| |
Collapse
|
23
|
Abstract
Viral diseases provide a major challenge to twenty-first century agriculture worldwide. Climate change and human population pressures are driving rapid alterations in agricultural practices and cropping systems that favor destructive viral disease outbreaks. Such outbreaks are strikingly apparent in subsistence agriculture in food-insecure regions. Agricultural globalization and international trade are spreading viruses and their vectors to new geographical regions with unexpected consequences for food production and natural ecosystems. Due to the varying epidemiological characteristics of diverent viral pathosystems, there is no one-size-fits-all approach toward mitigating negative viral disease impacts on diverse agroecological production systems. Advances in scientific understanding of virus pathosystems, rapid technological innovation, innovative communication strategies, and global scientific networks provide opportunities to build epidemiologic intelligence of virus threats to crop production and global food security. A paradigm shift toward deploying integrated, smart, and eco-friendly strategies is required to advance virus disease management in diverse agricultural cropping systems.
Collapse
Affiliation(s)
- Roger A C Jones
- Institute of Agriculture, University of Western Australia, Crawley, Western Australia 6009, Australia; .,Department of Primary Industries and Regional Development, South Perth, Western Australia 6151, Australia
| | - Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, Washington 99350, USA;
| |
Collapse
|
24
|
Wainaina JM, Ateka E, Makori T, Kehoe MA, Boykin LM. A metagenomic study of DNA viruses from samples of local varieties of common bean in Kenya. PeerJ 2019; 7:e6465. [PMID: 30891366 PMCID: PMC6422016 DOI: 10.7717/peerj.6465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/16/2019] [Indexed: 11/20/2022] Open
Abstract
Common bean (Phaseolus vulgaris L.) is the primary source of protein and nutrients in the majority of households in sub-Saharan Africa. However, pests and viral diseases are key drivers in the reduction of bean production. To date, the majority of viruses reported in beans have been RNA viruses. In this study, we carried out a viral metagenomic analysis on virus symptomatic bean plants. Our virus detection pipeline identified three viral fragments of the double-stranded DNA virus Pelargonium vein banding virus (PVBV) (family, Caulimoviridae, genus Badnavirus). This is the first report of the dsDNA virus and specifically PVBV in legumes to our knowledge. In addition two previously reported +ssRNA viruses the bean common mosaic necrosis virus (BCMNVA) (Potyviridae) and aphid lethal paralysis virus (ALPV) (Dicistroviridae) were identified. Bayesian phylogenetic analysis of the Badnavirus (PVBV) using amino acid sequences of the RT/RNA-dependent DNA polymerase region showed the Kenyan sequence (SRF019_MK014483) was closely matched with two Badnavirus viruses: Dracaena mottle virus (DrMV) (YP_610965) and Lucky bamboo bacilliform virus (ABR01170). Phylogenetic analysis of BCMNVA was based on amino acid sequences of the Nib region. The BCMNVA phylogenetic tree resolved two clades identified as clade (I and II). Sequence from this study SRF35_MK014482, clustered within clade I with other Kenyan sequences. Conversely, Bayesian phylogenetic analysis of ALPV was based on nucleotide sequences of the hypothetical protein gene 1 and 2. Three main clades were resolved and identified as clades I-III. The Kenyan sequence from this study (SRF35_MK014481) clustered within clade II, and nested within a sub-clade; comprising of sequences from China and an earlier ALPV sequences from Kenya isolated from maize (MF458892). Our findings support the use of viral metagenomics to reveal the nascent viruses, their viral diversity and evolutionary history of these viruses. The detection of ALPV and PVBV indicate that these viruses have likely been underreported due to the unavailability of diagnostic tools.
Collapse
Affiliation(s)
- James M Wainaina
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Elijah Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Timothy Makori
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Monica A Kehoe
- Diagnostic Laboratory Service, Plant Pathology, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Laura M Boykin
- School of Molecular Sciences and Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| |
Collapse
|
25
|
Minato N, Sok S, Chen S, Delaquis E, Phirun I, Le VX, Burra DD, Newby JC, Wyckhuys KAG, de Haan S. Surveillance for Sri Lankan cassava mosaic virus (SLCMV) in Cambodia and Vietnam one year after its initial detection in a single plantation in 2015. PLoS One 2019; 14:e0212780. [PMID: 30794679 PMCID: PMC6386488 DOI: 10.1371/journal.pone.0212780] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 02/08/2019] [Indexed: 11/18/2022] Open
Abstract
Cassava mosaic disease, one of the ten most economically important crop viral diseases in the world, was first reported in Southeast Asia from a single plantation in Cambodia in 2015. To determine the presence and incidence of Sri Lankan cassava mosaic virus (SLCMV) one year after first detection, a total of 6,480 samples from 419 fields were systematically collected from cassava production areas across Cambodia (3,840 samples; 240 fields) and Vietnam (2,640samples; 179 fields) in the 2016 cropping season. Using PCR-based diagnostics, we identified 49 SLCMV-infected plants from nine fields, representing 2% of the total number of fields sampled. Infected fields were geographically restricted to two provinces of Eastern Cambodia, while no infection was detected from any of the other sampled sites in either country. Symptom expression patterns in infected plants suggested that SLCMV may have been transmitted both through infected planting materials, and by Bemisia tabaci, the known whitefly vector of SLCMV. In addition, 14% of virus infected plants did not express typical symptoms of cassava mosaic disease on their leaves, highlighting that molecular-based validation is needed to confirm the presence of SLCMV in the field. None of the owners of the SLCMV-infected fields indicated acquired planting materials from the plantation in Ratanakiri where SLCMV was first reported. The surveillance baseline data generated for both countries is discussed in light of future options to control and manage cassava mosaic disease.
Collapse
Affiliation(s)
- Nami Minato
- Agrobiodiversity Research Area, Asia Regional Office, International Center for Tropical Agriculture (CIAT), CGIAR Research Program on Roots Tubers and Bananas, Hanoi, Vietnam
| | - Sophearith Sok
- Agrobiodiversity Research Area, Asia Regional Office, International Center for Tropical Agriculture (CIAT), CGIAR Research Program on Roots Tubers and Bananas, Hanoi, Vietnam
| | - Songbi Chen
- Tropical Crops Genetic Resources Institute (TCGRI), Chinese Academy of Tropical Agricultural Sciences (CATAS), Danzhou, Hainan, China
| | - Erik Delaquis
- Agrobiodiversity Research Area, Asia Regional Office, International Center for Tropical Agriculture (CIAT), CGIAR Research Program on Roots Tubers and Bananas, Hanoi, Vietnam
| | - Iv Phirun
- Department of Industrial Crops, General Directorate of Agriculture (GDA), Phnom Penh, Cambodia
| | - Vi Xuan Le
- Plant Protection Research Institute (PPRI), Vietnam Academy of Agricultural Sciences, Hanoi, Vietnam
| | - Dharani D. Burra
- Decision and Policy Analysis Research Area, Asia Regional Office, International Center for Tropical Agriculture (CIAT), Hanoi, Vietnam
| | - Jonathan C. Newby
- Agrobiodiversity Research Area, Asia Regional Office, International Center for Tropical Agriculture (CIAT), CGIAR Research Program on Roots Tubers and Bananas, Hanoi, Vietnam
| | - Kris A. G. Wyckhuys
- International Joint Research Laboratory on Ecological Pest Management, Fuzhou, China
| | - Stef de Haan
- Agrobiodiversity Research Area, Asia Regional Office, International Center for Tropical Agriculture (CIAT), CGIAR Research Program on Roots Tubers and Bananas, Hanoi, Vietnam
- * E-mail:
| |
Collapse
|
26
|
Tripathi JN, Ntui VO, Ron M, Muiruri SK, Britt A, Tripathi L. CRISPR/Cas9 editing of endogenous banana streak virus in the B genome of Musa spp. overcomes a major challenge in banana breeding. Commun Biol 2019; 2:46. [PMID: 30729184 PMCID: PMC6355771 DOI: 10.1038/s42003-019-0288-7] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/21/2018] [Indexed: 12/19/2022] Open
Abstract
Presence of the integrated endogenous banana streak virus (eBSV) in the B genome of plantain (AAB) is a major challenge for breeding and dissemination of hybrids. As the eBSV activates into infectious viral particles under stress, the progenitor Musa balbisiana and its derivants, having at least one B genome, cannot be used as parents for crop improvement. Here, we report a strategy to inactivate the eBSV by editing the virus sequences. The regenerated genome-edited events of Gonja Manjaya showed mutations in the targeted sites with the potential to prevent proper transcription or/and translational into functional viral proteins. Seventy-five percent of the edited events remained asymptomatic in comparison to the non-edited control plants under water stress conditions, confirming inactivation of eBSV into infectious viral particles. This study paves the way for the improvement of B genome germplasm and its use in breeding programs to produce hybrids that can be globally disseminated.
Collapse
Affiliation(s)
| | - Valentine O. Ntui
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Mily Ron
- Department of Plant Biology, University of California, Davis, CA USA
| | - Samwel K. Muiruri
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Anne Britt
- Department of Plant Biology, University of California, Davis, CA USA
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| |
Collapse
|
27
|
Díaz-Pendón JA, Sánchez-Campos S, Fortes IM, Moriones E. Tomato Yellow Leaf Curl Sardinia Virus, a Begomovirus Species Evolving by Mutation and Recombination: A Challenge for Virus Control. Viruses 2019; 11:E45. [PMID: 30634476 PMCID: PMC6356960 DOI: 10.3390/v11010045] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/28/2018] [Accepted: 01/08/2019] [Indexed: 12/12/2022] Open
Abstract
The tomato leaf curl disease (TYLCD) is associated with infections of several species of begomoviruses (genus Begomovirus, family Geminiviridae) and causes severe damage to tomatoes throughout tropical and sub-tropical regions of the world. Among others, the Tomato yellow leaf curl Sardinia virus (TYLCSV) species causes damage in the Mediterranean Basin since early outbreaks occurred. Nevertheless, scarce information is available about the diversity of TYLCSV. Here, we study this aspect based on the sequence information accessible in databases. Isolates of two taxonomically differentiated TYLCSV strains can be found in natural epidemics. Their evolution is mostly associated with mutation combined with selection and random genetic drift and also with inter-species recombination which is frequent in begomoviruses. Moreover, a novel putative inter-strain recombinant is reported. Although no significantly new biological behaviour was observed for this latter recombinant, its occurrence supports that as shown for other related begomoviruses, recombination continues to play a central role in the evolution of TYLCD-associated viruses and the dynamism of their populations. The confrontation of resistant tomatoes with isolates of different TYLCD-associated viruses including the novel recombinant demonstrates the existence of a variable virus x plant genotype interaction. This has already been observed for other TYLCD-associated viruses and is a challenge for the control of their impact on tomato production.
Collapse
Affiliation(s)
- Juan A Díaz-Pendón
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora". Av. Dr. Wienberg s/n, Algarrobo-Costa, 29750 Málaga, Spain.
| | - Sonia Sánchez-Campos
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora". Av. Dr. Wienberg s/n, Algarrobo-Costa, 29750 Málaga, Spain.
| | - Isabel María Fortes
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora". Av. Dr. Wienberg s/n, Algarrobo-Costa, 29750 Málaga, Spain.
| | - Enrique Moriones
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC), Consejo Superior de Investigaciones Científicas, Estación Experimental "La Mayora". Av. Dr. Wienberg s/n, Algarrobo-Costa, 29750 Málaga, Spain.
| |
Collapse
|
28
|
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
|
29
|
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
|
30
|
Jeger MJ, Madden LV, van den Bosch F. Plant Virus Epidemiology: Applications and Prospects for Mathematical Modeling and Analysis to Improve Understanding and Disease Control. PLANT DISEASE 2018; 102:837-854. [PMID: 30673389 DOI: 10.1094/pdis-04-17-0612-fe] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In recent years, mathematical modeling has increasingly been used to complement experimental and observational studies of biological phenomena across different levels of organization. In this article, we consider the contribution of mathematical models developed using a wide range of techniques and uses to the study of plant virus disease epidemics. Our emphasis is on the extent to which models have contributed to answering biological questions and indeed raised questions related to the epidemiology and ecology of plant viruses and the diseases caused. In some cases, models have led to direct applications in disease control, but arguably their impact is better judged through their influence in guiding research direction and improving understanding across the characteristic spatiotemporal scales of plant virus epidemics. We restrict this article to plant virus diseases for reasons of length and to maintain focus even though we recognize that modeling has played a major and perhaps greater part in the epidemiology of other plant pathogen taxa, including vector-borne bacteria and phytoplasmas.
Collapse
Affiliation(s)
- M J Jeger
- Centre for Environmental Policy, Imperial College London, Silwood Park, Ascot SL5 7PY, United Kingdom
| | - L V Madden
- Department of Plant Pathology, Ohio State University, Wooster, OH 44691
| | - F van den Bosch
- Computational and Systems Biology, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| |
Collapse
|
31
|
Hébrard E, Pinel-Galzi A, Oludare A, Poulicard N, Aribi J, Fabre S, Issaka S, Mariac C, Dereeper A, Albar L, Silué D, Fargette D. Identification of a Hypervirulent Pathotype of Rice yellow mottle virus: A Threat to Genetic Resistance Deployment in West-Central Africa. PHYTOPATHOLOGY 2018; 108:299-307. [PMID: 28990483 DOI: 10.1094/phyto-05-17-0190-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Rice yellow mottle virus (RYMV) causes high losses to rice production in Africa. Several sources of varietal high resistance are available but the emergence of virulent pathotypes that are able to overcome one or two resistance alleles can sometimes occur. Both resistance spectra and viral adaptability have to be taken into account to develop sustainable rice breeding strategies against RYMV. In this study, we extended previous resistance spectrum analyses by testing the rymv1-4 and rymv1-5 alleles that are carried by the rice accessions Tog5438 and Tog5674, respectively, against isolates that are representative of RYMV genetic and pathogenic diversity. Our study revealed a hypervirulent pathotype, named thereafter pathotype T', that is able to overcome all known sources of high resistance. This pathotype, which is spatially localized in West-Central Africa, appears to be more abundant than previously suspected. To better understand the adaptive processes of pathotype T', molecular determinants of resistance breakdown were identified via Sanger sequencing and validated through directed mutagenesis of an infectious clone. These analyses confirmed the key role of convergent nonsynonymous substitutions in the central part of the viral genome-linked protein to overcome RYMV1-mediated resistance. In addition, deep-sequencing analyses revealed that resistance breakdown does not always coincide with fixed mutations. Actually, virulence mutations that are present in a small proportion of the virus population can be sufficient for resistance breakdown. Considering the spatial distribution of RYMV strains in Africa and their ability to overcome the RYMV resistance genes and alleles, we established a resistance-breaking risk map to optimize strategies for the deployment of sustainable and resistant rice lines in Africa.
Collapse
Affiliation(s)
- Eugénie Hébrard
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Agnès Pinel-Galzi
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Aderonke Oludare
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Nils Poulicard
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Jamel Aribi
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Sandrine Fabre
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Souley Issaka
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Cédric Mariac
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Alexis Dereeper
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Laurence Albar
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Drissa Silué
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Denis Fargette
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| |
Collapse
|
32
|
Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol 2018; 19:1. [PMID: 29301551 PMCID: PMC5755456 DOI: 10.1186/s13059-017-1381-1] [Citation(s) in RCA: 372] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/13/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleaving single-stranded RNA (ssRNA) molecules of the phage genome. Here, we employ CRISPR/Cas13a to engineer interference with an RNA virus, Turnip Mosaic Virus (TuMV), in plants. RESULTS CRISPR/Cas13a produces interference against green fluorescent protein (GFP)-expressing TuMV in transient assays and stable overexpression lines of Nicotiana benthamiana. CRISPR RNA (crRNAs) targeting the HC-Pro and GFP sequences exhibit better interference than those targeting other regions such as coat protein (CP) sequence. Cas13a can also process pre-crRNAs into functional crRNAs. CONCLUSIONS Our data indicate that CRISPR/Cas13a can be used for engineering interference against RNA viruses, providing a potential novel mechanism for RNA-guided immunity against RNA viruses and for other RNA manipulations in plants.
Collapse
Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Fatimah Aljedaani
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Zuhaib Khan
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shouwei Ding
- Center for Plant Cell Biology, Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
| |
Collapse
|
33
|
Kreuze JF, Valkonen JP. Utilization of engineered resistance to viruses in crops of the developing world, with emphasis on sub-Saharan Africa. Curr Opin Virol 2017; 26:90-97. [PMID: 28800552 PMCID: PMC5669357 DOI: 10.1016/j.coviro.2017.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 02/08/2023]
Abstract
Viral diseases in crop plants constitute a major obstacle to food security in the developing world. Subsistence crops, including cassava, sweetpotato, potato, banana, papaya, common bean, rice and maize are often infected with RNA and/or DNA viruses that cannot be controlled with pesticides. Hence, healthy planting materials and virus-resistant cultivars are essential for high yields of good quality. However, resistance genes are not available for all viral diseases of crop plants. Therefore, virus resistance engineered in plants using modern biotechnology methods is an important addition to the crop production toolbox.
Collapse
Affiliation(s)
| | - Jari Pt Valkonen
- Department of Agricultural Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
| |
Collapse
|
34
|
Picard C, Dallot S, Brunker K, Berthier K, Roumagnac P, Soubeyrand S, Jacquot E, Thébaud G. Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:139-160. [PMID: 28525307 DOI: 10.1146/annurev-phyto-080516-035616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.
Collapse
Affiliation(s)
- Coralie Picard
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Sylvie Dallot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | - Philippe Roumagnac
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | | | - Emmanuel Jacquot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Gaël Thébaud
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| |
Collapse
|
35
|
Abstract
Cassava is the fourth largest source of calories in the world but is subject to economically important yield losses due to viral diseases, including cassava brown streak disease and cassava mosaic disease. Cassava mosaic disease occurs in sub-Saharan Africa and the Asian subcontinent and is associated with nine begomovirus species, whereas cassava brown streak disease has to date been reported only in sub-Saharan Africa and is caused by two distinct ipomovirus species. We present an overview of key milestones and their significance in the understanding and characterization of these two major diseases as well as their associated viruses and whitefly vector. New biotechnologies offer a wide range of opportunities to reduce virus-associated yield losses in cassava for farmers and can additionally enable the exploitation of this valuable crop for industrial purposes. This review explores established and new technologies for genetic manipulation to achieve desired traits such as virus resistance.
Collapse
Affiliation(s)
- Chrissie Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg 2000, South Africa;
| | - Hervé Vanderschuren
- AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium;
| |
Collapse
|
36
|
Jang C, Wang R, Wells J, Leon F, Farman M, Hammond J, Goodin MM. Genome sequence variation in the constricta strain dramatically alters the protein interaction and localization map of Potato yellow dwarf virus. J Gen Virol 2017; 98:1526-1536. [PMID: 28635588 PMCID: PMC5656794 DOI: 10.1099/jgv.0.000771] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/10/2017] [Indexed: 12/19/2022] Open
Abstract
The genome sequence of the constricta strain of Potato yellow dwarf virus (CYDV) was determined to be 12 792 nt long and organized into seven ORFs with the gene order 3'-N-X-P-Y-M-G-L-5', which encodes the nucleocapsid, phospho, movement, matrix, glyco, and RNA-dependent RNA polymerase proteins, respectively, except for X, which is of unknown function. Cloned ORFs for each gene, except L, were used to construct a protein interaction and localization map (PILM) for this virus, which shares greater than 80 % amino acid similarity in all ORFs except X and P with the sanguinolenta strain of this species (SYDV). Protein localization patterns and interactions unique to each viral strain were identified, resulting in strain-specific PILMs. Localization of CYDV and SYDV proteins in virus-infected cells mapped subcellular loci likely to be sites of replication, morphogenesis and movement.
Collapse
Affiliation(s)
- Chanyong Jang
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - Renyuan Wang
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - Joseph Wells
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - Fabian Leon
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| | - John Hammond
- USDA-ARS, United States National Arboretum, Beltsville, MD, USA
| | - Michael M. Goodin
- Department of Plant Pathology, University of Kentucky, Lexington, KY, USA
| |
Collapse
|
37
|
Wang IN, Yeh WB, Lin NS. Phylogeography and Coevolution of Bamboo Mosaic Virus and Its Associated Satellite RNA. Front Microbiol 2017; 8:886. [PMID: 28588562 PMCID: PMC5440514 DOI: 10.3389/fmicb.2017.00886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/02/2017] [Indexed: 11/17/2022] Open
Abstract
Bamboo mosaic virus (BaMV), a plant potexvirus, has been found only in infected bamboo species. It is frequently associated with a large, linear single-stranded satellite RNA (satBaMV) that encodes a non-structural protein. Decades of collecting across a wide geographic area in Asia have accumulated a sizable number of BaMV and satBaMV isolates. In this study, we reconstructed the BaMV phylogeny and satBaMV phylogeny with partial coat protein gene sequences and partial genomic sequences, respectively. The evolutionary relationships allowed us to infer the phylogeography of BaMV and satBaMV on the Asian continent and its outlying islands. The BaMV phylogeny suggests that the BaMV isolates from Taiwan, unsurprisingly, are most likely derived from China. Interestingly, the newly available satBaMV isolates from China were found to be most closely related to the previously established Clade III, which is found in India. The general pattern of clustering along the China/India and Taiwan divide led us to hypothesize that the Taiwan Strait has been a physical barrier to gene flow in the past evolutionary history of both BaMV and satBaMV. Lastly, cophylogeny analyses revealed a complex association pattern between BaMV and satBaMV isolates from China. In general, closely related BaMV sequences tend to carry closely related satBaMV sequences as well; but instances of mismatching with distantly related satBaMV isolates were also found. We hypothesize plausible scenarios of infection and superinfection of bamboo hosts that may be responsible for the observed association pattern. However, a more systematic sampling throughout the geographic distribution of various bamboo species is needed to unambiguously establish the origin, movement, and evolution of BaMV and satBaMV.
Collapse
Affiliation(s)
- Ing-Nang Wang
- Department of Biological Sciences, University at Albany, AlbanyNY, United States
| | - Wen-Bin Yeh
- Department of Entomology, National Chung Hsin UniversityTaichung, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
| |
Collapse
|
38
|
Beach S, Kovens M, Hubbert L, Honesty S, Guo Q, Pap D, Dai R, Kovacs L, Qiu W. Genetic and Phenotypic Characterization of Grapevine vein clearing virus from Wild Vitis rupestris. PHYTOPATHOLOGY 2017; 107:138-144. [PMID: 27577962 DOI: 10.1094/phyto-04-16-0173-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Grapevine vein clearing virus (GVCV), a new member of the genus Badnavirus in the family Caulimoviridae, is associated with a vein clearing and vine decline disease that severely affects grape production and berry quality in commercial vineyards in the Midwest region of the United States. In this paper, the genetic and phenotypic characteristics of GVCV-VRU1 and GVCV-VRU2, two isolates from wild Vitis rupestris grapevines in their native habitat, are described. The GVCV-VRU1 genome is 7,755 bp long while the GVCV-VRU2 genome consists of 7,725 bp, both of which are different from the genome of the GVCV-CHA isolate (7,753 bp), which was originally discovered in the grape cultivar 'Chardonel'. The nucleotide sequence identity among GVCV-VRU1, GVCV-VRU2, and GVCV-CHA ranges from 91.6 to 93.4%, and open reading frame (ORF) II is the most divergent ORF with only 83.3 to 88.5% identity. Sequence analysis of the ORF II indicated that GVCV isolates genetically similar to GVCV-VRU1 and GVCV-VRU2 also are present in commercial vineyards. Symptoms of GVCV-VRU1- or GVCV-VRU2-infected wild V. rupestris grapevine appeared initially as translucent vein clearing on young leaves and progressed to vein necrosis on mature leaves. Inoculation of GVCV-VRU1 or GVCV-VRU2 by grafting onto grape cultivar Chardonel resulted in mild mottle and leaf distortion. The natural range of wild V. rupestris grapevines overlaps with commercial vineyards in the Midwestern United States. Therefore, the discovery of GVCV isolates in wild V. rupestris grapevines has important implications for epidemics and management of the GVCV-associated disease.
Collapse
Affiliation(s)
- Steven Beach
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Michael Kovens
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - LeAnn Hubbert
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Shae Honesty
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Qiang Guo
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Daniel Pap
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Ru Dai
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Laszlo Kovacs
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| | - Wenping Qiu
- First, second, third, fourth, fifth, sixth, seventh, and ninth authors: Center for Grapevine Biotechnology, Darr School of Agriculture, Missouri State University, Mountain Grove, MO 65711; and eighth author: Department of Biology, Missouri State University, Springfield, MO 65897
| |
Collapse
|
39
|
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
|
40
|
Zhang J, Borth WB, Lin B, Dey KK, Melzer MJ, Shen H, Pu X, Sun D, Hu JS. Deep sequencing of banana bract mosaic virus from flowering ginger (Alpinia purpurata) and development of an immunocapture RT-LAMP detection assay. Arch Virol 2016; 161:1783-95. [PMID: 27038825 DOI: 10.1007/s00705-016-2830-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/14/2016] [Indexed: 10/22/2022]
Abstract
Banana bract mosaic virus (BBrMV) has never been reported in banana plants in Hawaii. In 2010, however, it was detected in a new host, flowering ginger (Alpinia purpurata). In this study, we characterize the A. purpurata isolate and study its spread in flowering ginger in Hawaii. A laboratory study demonstrated that BBrMV could be transmitted from flowering ginger to its natural host, banana, therefore raising a serious concern about the potential risk to the rapidly growing banana industry of Hawaii. To quickly monitor this virus in the field, we developed a robust immunocapture reverse transcription loop-mediated isothermal amplification (IC-RT-LAMP) assay. Deep sequencing of the BBrMV isolate from A. purpurata revealed a single-stranded RNA virus with a genome of 9,713 nt potentially encoding a polyprotein of 3,124 aa, and another predicted protein, PIPO, in the +2 reading-frame shift. Most of the functional motifs in the Hawaiian isolate were conserved among the genomes of isolates from one found in the Philippines and India. However, the A. purpurata isolate had an amino acid deletion in the Pl protein that was most similar to the Philippine isolate. Phylogenetic analysis of an eastern Pacific subpopulation that included A. purpurata was closest in genetic distance to a Southeast Asian subpopulation, suggesting frequent gene flow and supporting the hypothesis that the A. purpurata isolate arrived in Hawaii from Southeast Asia.
Collapse
Affiliation(s)
- Jingxin Zhang
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, USA
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Wayne B Borth
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, USA
| | - Birun Lin
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Kishore K Dey
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, USA
| | - Michael J Melzer
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, USA
| | - Huifang Shen
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoming Pu
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Dayuan Sun
- Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - John S Hu
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, USA.
| |
Collapse
|
41
|
Jones RAC, Kehoe MA. A proposal to rationalize within-species plant virus nomenclature: benefits and implications of inaction. Arch Virol 2016; 161:2051-7. [PMID: 27101071 DOI: 10.1007/s00705-016-2848-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/29/2016] [Indexed: 01/13/2023]
Abstract
Current approaches used to name within-species, plant virus phylogenetic groups are often misleading and illogical. They involve names based on biological properties, sequence differences and geographical, country or place-association designations, or any combination of these. This type of nomenclature is becoming increasingly unsustainable as numbers of sequences of the same virus from new host species and different parts of the world increase. Moreover, this increase is accelerating as world trade and agriculture expand, and climate change progresses. Serious consequences for virus research and disease management might arise from incorrect assumptions made when current within-species phylogenetic group names incorrectly identify properties of group members. This could result in development of molecular tools that incorrectly target dangerous virus strains, potentially leading to unjustified impediments to international trade or failure to prevent such strains being introduced to countries, regions or continents formerly free of them. Dangerous strains might be missed or misdiagnosed by diagnostic laboratories and monitoring programs, and new cultivars with incorrect strain-specific resistances released. Incorrect deductions are possible during phylogenetic analysis of plant virus sequences and errors from strain misidentification during molecular and biological virus research activities. A nomenclature system for within-species plant virus phylogenetic group names is needed which avoids such problems. We suggest replacing all other naming approaches with Latinized numerals, restricting biologically based names only to biological strains and removing geographically based names altogether. Our recommendations have implications for biosecurity authorities, diagnostic laboratories, disease-management programs, plant breeders and researchers.
Collapse
Affiliation(s)
- Roger A C Jones
- Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia. .,Department of Agriculture and Food, Locked Bag No. 4, Bentley Delivery Centre, Perth, WA, 6983, Australia.
| | - Monica A Kehoe
- Department of Agriculture and Food, Locked Bag No. 4, Bentley Delivery Centre, Perth, WA, 6983, Australia
| |
Collapse
|
42
|
Ndunguru J, De León L, Doyle CD, Sseruwagi P, Plata G, Legg JP, Thompson G, Tohme J, Aveling T, Ascencio-Ibáñez JT, Hanley-Bowdoin L. Two Novel DNAs That Enhance Symptoms and Overcome CMD2 Resistance to Cassava Mosaic Disease. J Virol 2016; 90:4160-4173. [PMID: 26865712 PMCID: PMC4810563 DOI: 10.1128/jvi.02834-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/03/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Cassava mosaic begomoviruses (CMBs) cause cassava mosaic disease (CMD) across Africa and the Indian subcontinent. Like all members of the geminivirus family, CMBs have small, circular single-stranded DNA genomes. We report here the discovery of two novel DNA sequences, designated SEGS-1 and SEGS-2 (forsequencesenhancinggeminivirussymptoms), that enhance symptoms and break resistance to CMD. The SEGS are characterized by GC-rich regions and the absence of long open reading frames. Both SEGS enhanced CMD symptoms in cassava (Manihot esculentaCrantz) when coinoculated withAfrican cassava mosaic virus(ACMV),East African cassava mosaic Cameroon virus(EACMCV), orEast African cassava mosaic virus-Uganda(EACMV-UG). SEGS-1 also overcame resistance of a cassava landrace carrying the CMD2 resistance locus when coinoculated with EACMV-UG. Episomal forms of both SEGS were detected in CMB-infected cassava but not in healthy cassava. SEGS-2 episomes were also found in virions and whiteflies. SEGS-1 has no homology to geminiviruses or their associated satellites, but the cassava genome contains a sequence that is 99% identical to full-length SEGS-1. The cassava genome also includes three sequences with 84 to 89% identity to SEGS-2 that together encompass all of SEGS-2 except for a 52-bp region, which includes the episomal junction and a 26-bp sequence related to alphasatellite replication origins. These results suggest that SEGS-1 is derived from the cassava genome and facilitates CMB infection as an integrated copy and/or an episome, while SEGS-2 was originally from the cassava genome but now is encapsidated into virions and transmitted as an episome by whiteflies. IMPORTANCE Cassava is a major crop in the developing world, with its production in Africa being second only to maize. CMD is one of the most important diseases of cassava and a serious constraint to production across Africa. CMD2 is a major CMD resistance locus that has been deployed in many cassava cultivars through large-scale breeding programs. In recent years, severe, atypical CMD symptoms have been observed occasionally on resistant cultivars, some of which carry the CMD2 locus, in African fields. In this report, we identified and characterized two DNA sequences, SEGS-1 and SEGS-2, which produce similar symptoms when coinoculated with cassava mosaic begomoviruses onto a susceptible cultivar or a CMD2-resistant landrace. The ability of SEGS-1 to overcome CMD2 resistance and the transmission of SEGS-2 by whiteflies has major implications for the long-term durability of CMD2 resistance and underscore the need for alternative sources of resistance in cassava.
Collapse
Affiliation(s)
- Joseph Ndunguru
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | - Leandro De León
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Catherine D Doyle
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | - German Plata
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA
| | - James P Legg
- International Institute of Tropical Agriculture-Tanzania, Dar es Salaam, Tanzania
| | - Graham Thompson
- ARC-Institute for Industrial Crops, Rusternburg, South Africa
| | - Joe Tohme
- International Center for Tropical Agriculture, Cali, Colombia
| | - Theresa Aveling
- University of Pretoria, Department of Microbiology and Plant Pathology, Pretoria, South Africa
| | - Jose T Ascencio-Ibáñez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| |
Collapse
|
43
|
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
|
44
|
Trovão NS, Baele G, Vrancken B, Bielejec F, Suchard MA, Fargette D, Lemey P. Host ecology determines the dispersal patterns of a plant virus. Virus Evol 2015; 1:vev016. [PMID: 27774287 PMCID: PMC5014491 DOI: 10.1093/ve/vev016] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Since its isolation in 1966 in Kenya, rice yellow mottle virus (RYMV) has been reported throughout Africa resulting in one of the economically most important tropical plant emerging diseases. A thorough understanding of RYMV evolution and dispersal is critical to manage viral spread in tropical areas that heavily rely on agriculture for subsistence. Phylogenetic analyses have suggested a relatively recent expansion, perhaps driven by the intensification of agricultural practices, but this has not yet been examined in a coherent statistical framework. To gain insight into the historical spread of RYMV within Africa rice cultivations, we analyse a dataset of 300 coat protein gene sequences, sampled from East to West Africa over a 46-year period, using Bayesian evolutionary inference. Spatiotemporal reconstructions date the origin of RMYV back to 1852 (1791-1903) and confirm Tanzania as the most likely geographic origin. Following a single long-distance transmission event from East to West Africa, separate viral populations have been maintained for about a century. To identify the factors that shaped the RYMV distribution, we apply a generalised linear model (GLM) extension of discrete phylogenetic diffusion and provide strong support for distances measured on a rice connectivity landscape as the major determinant of RYMV spread. Phylogeographic estimates in continuous space further complement this by demonstrating more pronounced expansion dynamics in West Africa that are consistent with agricultural intensification and extensification. Taken together, our principled phylogeographic inference approach shows for the first time that host ecology dynamics have shaped the historical spread of a plant virus.
Collapse
Affiliation(s)
- Nídia Sequeira Trovão
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Filip Bielejec
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Marc A. Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 0095-1766, USA
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 0095-1766, USA and
| | - Denis Fargette
- Institut de Recherches pour le Développement (IRD), UMR IPME (IRD, CIRAD, Université de Montpellier), 34394 Montpellier, France
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| |
Collapse
|
45
|
Random Plant Viral Variants Attain Temporal Advantages During Systemic Infections and in Turn Resist other Variants of the Same Virus. Sci Rep 2015; 5:15346. [PMID: 26481091 PMCID: PMC4612314 DOI: 10.1038/srep15346] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/22/2015] [Indexed: 01/19/2023] Open
Abstract
Infection of plants with viruses containing multiple variants frequently leads to dominance by a few random variants in the systemically infected leaves (SLs), for which a plausible explanation is lacking. We show here that SL dominance by a given viral variant is adequately explained by its fortuitous lead in systemic spread, coupled with its resistance to superinfection by other variants. We analyzed the fate of a multi-variant turnip crinkle virus (TCV) population in Arabidopsis and N. benthamiana plants. Both wild-type and RNA silencing-defective plants displayed a similar pattern of random dominance by a few variant genotypes, thus discounting a prominent role for RNA silencing. When introduced to plants sequentially as two subpopulations, a twelve-hour head-start was sufficient for the first set to dominate. Finally, SLs of TCV-infected plants became highly resistant to secondary invasions of another TCV variant. We propose that random distribution of variant foci on inoculated leaves allows different variants to lead systemic movement in different plants. The leading variants then colonize large areas of SLs, and resist the superinfection of lagging variants in the same areas. In conclusion, superinfection resistance is the primary driver of random enrichment of viral variants in systemically infected plants.
Collapse
|
46
|
Variability in yellow leaf symptom expression caused by the Sugarcane yellow leaf virus and its seasonal influence in sugarcane. PHYTOPARASITICA 2015. [DOI: 10.1007/s12600-015-0468-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
47
|
Affiliation(s)
- Antoine Gessain
- Unit of Epidemiology and Physiopathology of Oncogenic Viruses, Institut Pasteur, and Centre National de la Recherche Scientifique, UMR 356928 rue du Docteur Roux, F75015 Paris, France.
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, Campus de Montegancedo, and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Madrid, Spain.
| |
Collapse
|
48
|
Sharma SK, Vignesh Kumar P, Geetanjali AS, Pun KB, Baranwal VK. Subpopulation level variation of banana streak viruses in India and common evolution of banana and sugarcane badnaviruses. Virus Genes 2015; 50:450-65. [PMID: 25672291 DOI: 10.1007/s11262-015-1179-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 01/31/2015] [Indexed: 01/21/2023]
Abstract
Genome sequences of three episomal Banana streak MY virus (BSMYV) isolates sampled from triploid banana hybrids (Chini Champa: AAB; Malbhog: AAB and Monthan: ABB), grown in North-East and South India are reported in this study by sequence-independent improved rolling circle amplification (RCA). RCA coupled with restriction fragment length polymorphism revealed diverse restriction profiles of five BSMYV isolates. Nucleotide substitution rates of BSMYV subpopulation and Banana streak OL virus subpopulation was 7.13 × 10(-3) to 1.59 × 10(-2) and 2.65 × 10(-3) to 5.49 × 10(-3), respectively, for the different coding regions. Analysis of the genetic diversity of banana and sugarcane badnaviruses revealed a total of 32 unique recombination events among banana and sugarcane badnaviruses (inter BSV-SCBV), in addition to the extensive recombination with in banana streak viruses and sugarcane bacilliform viruses (intra-BSV and intra-SCBV). Many unique fragments were shown to contain similar ruminant sequence fragments which indicated the possibility that the two groups of badnaviruses or their ancestors to colonise same host before making the host shift. The distribution of recombination events, hot-spots (intergenic region and C-terminal of ORF3) as well as cold-spots (distributed in ORF3) displayed the mirroring of recombination traces in both group of badnaviruses. These results support the hypothesis of relatedness of banana and sugarcane badnaviruses and the host and geographical shifts that followed the fixation of the species complex appear to be a recent event.
Collapse
Affiliation(s)
- Susheel Kumar Sharma
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | | | | | | |
Collapse
|
49
|
Lefeuvre P, Moriones E. Recombination as a motor of host switches and virus emergence: geminiviruses as case studies. Curr Opin Virol 2015; 10:14-9. [DOI: 10.1016/j.coviro.2014.12.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/26/2014] [Accepted: 12/03/2014] [Indexed: 10/24/2022]
|
50
|
Roossinck MJ, García-Arenal F. Ecosystem simplification, biodiversity loss and plant virus emergence. Curr Opin Virol 2015; 10:56-62. [PMID: 25638504 PMCID: PMC7102708 DOI: 10.1016/j.coviro.2015.01.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 01/08/2015] [Accepted: 01/14/2015] [Indexed: 01/02/2023]
Abstract
Plant viruses can emerge into crops from wild plant hosts, or conversely from domestic (crop) plants into wild hosts. Changes in ecosystems, including loss of biodiversity and increases in managed croplands, can impact the emergence of plant virus disease. Although data are limited, in general the loss of biodiversity is thought to contribute to disease emergence. More in-depth studies have been done for human viruses, but studies with plant viruses suggest similar patterns, and indicate that simplification of ecosystems through increased human management may increase the emergence of viral diseases in crops.
Collapse
Affiliation(s)
- Marilyn J Roossinck
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, USA; Murdoch University, Perth, Australia.
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Spain
| |
Collapse
|