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Al-Ali E, Al-Hashash H, Akbar A, Al-Aqeel H, Al-Shayji N, Alotaibi M, Ben Hejji A. Genetic recombination among tomato yellow leaf curl virus isolates in commercial tomato crops in Kuwait drives emergence of virus diversity: a comparative genomic analysis. BMC Res Notes 2023; 16:71. [PMID: 37150821 PMCID: PMC10164301 DOI: 10.1186/s13104-023-06319-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 03/30/2023] [Indexed: 05/09/2023] Open
Abstract
OBJECTIVE Whitefly-transmitted tomato yellow leaf curl virus (TYLCV) continues to be a major constraint to tomato production in Kuwait. However, very limited information is available about the population structure and genetic diversity of TYLCV infecting tomato in Kuwait. RESULTS Whole genome sequences of 31 isolates of TYLCV, collected from commercial tomato crops grown in northern (Abdally) and southern (Al Wafra) parts of Kuwait, were deciphered. Eighteen isolates of TYLCV are identified as potential genetic recombinants. The isolates Abdally 6A and Abdally 3B reported in this study were identified to be potential recombinants. Compared to the 15 isolates from the Abdally area, and the three previously reported KISR isolates of Kuwait, six out of sixteen Al Wafra isolates showed an insertion of 19 extra nucleotides near the 5'-end. There are also four nucleotide variations before the 19-extra-nucleotides. The additional 19 nucleotides observed in nine isolates indicate that these isolates might have resulted from a single gene recombination/insertion event. Molecular phylogeny based on complete genome sequences of TYLCV isolates suggests transboundary movement of virus isolates due to geographic proximity. The information presented herein is quite useful for the comprehension of TYLCV biology, epidemiology and would aid in the management of disease in the long run.
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Affiliation(s)
- Ebtisam Al-Ali
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait.
| | - Hanadi Al-Hashash
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
| | - Abrar Akbar
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
| | - Hamed Al-Aqeel
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
| | - Nabila Al-Shayji
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
| | - Mohammed Alotaibi
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
| | - Ahmed Ben Hejji
- Kuwait Institute for Scientific Research, Environmental and Life Science Research Center, Biotechnology Program, 13109, Safat, Kuwait
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Aimone CD, Hoyer JS, Dye AE, Deppong DO, Duffy S, Carbone I, Hanley-Bowdoin L. An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing. J Virol Methods 2021; 300:114405. [PMID: 34896458 DOI: 10.1016/j.jviromet.2021.114405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 08/26/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
The ability of begomoviruses to evolve rapidly threatens many crops and underscores the importance of detecting these viruses quickly and to understand their genome diversity. This study presents an improved protocol for the enhanced amplification and enrichment of begomovirus DNA for use in next generation sequencing of the viral genomes. An enhanced rolling circle amplification (RCA) method using EquiPhi29 polymerase was combined with size selection to generate a cost-effective, short-read sequencing method. This improved short-read sequencing produced at least 50 % of the reads mapping to the target viral reference genomes, African cassava mosaic virus and East African cassava mosaic virus. This study provided other insights into common misconceptions about RCA and lessons that could be learned from the sequencing of single-stranded DNA virus genomes. This protocol can be used to examine the viral DNA as it moves from host to vector, thus producing valuable information for viral DNA population studies, and would likely work well with other circular Rep-encoding ssDNA viruses (CRESS) DNA viruses.
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Affiliation(s)
- Catherine D Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - J Steen Hoyer
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Anna E Dye
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - David O Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
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Abstract
Of the approximately 1,200 plant virus species that have been described to date, nearly one-third are single-stranded DNA (ssDNA) viruses, and all are transmitted by insect vectors. However, most studies of vector transmission of plant viruses have focused on RNA viruses. All known plant ssDNA viruses belong to two economically important families, Geminiviridae and Nanoviridae, and in recent years, there have been increased efforts to understand whether they have evolved similar relationships with their respective insect vectors. This review describes the current understanding of ssDNA virus-vector interactions, including how these viruses cross insect vector cellular barriers, the responses of vectors to virus circulation, the possible existence of viral replication within insect vectors, and the three-way virus-vector-plant interactions. Despite recent breakthroughs in our understanding of these viruses, many aspects of plant ssDNA virus transmission remain elusive. More effort is needed to identify insect proteins that mediate the transmission of plant ssDNA viruses and to understand the complex virus-insect-plant three-way interactions in the field during natural infection.
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Affiliation(s)
- Xiao-Wei Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Stéphane Blanc
- Plant Health Institute of Montpellier, Univ Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France;
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Avedi EK, Adediji AO, Kilalo DC, Olubayo FM, Macharia I, Ateka EM, Machuka EM, Mutuku JM. Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya. Virol J 2021; 18:2. [PMID: 33407584 PMCID: PMC7789182 DOI: 10.1186/s12985-020-01466-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. METHODS Tomato leaf samples with virus-like symptoms were obtained from farmers' field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. RESULTS Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7-99.7% identity among each other and 95.9-98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5-100%) within the isolates, and 97.1-100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. CONCLUSIONS The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.
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Affiliation(s)
- Edith Khamonya Avedi
- Department of Phytosanitary Services and Biosafety, Kenya Plant Health Inspectorate Service, Nairobi, Kenya. .,Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya. .,Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya.
| | - Adedapo Olutola Adediji
- Department of Crop Protection and Environmental Biology, Faculty of Agriculture, University of Ibadan, Ibadan, Nigeria.
| | - Dora Chao Kilalo
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | | | - Isaac Macharia
- Department of Phytosanitary Services and Biosafety, Kenya Plant Health Inspectorate Service, Nairobi, Kenya
| | - Elijah Miinda Ateka
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Eunice Magoma Machuka
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - Josiah Musembi Mutuku
- Biosciences Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya.,Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.,The Central and West African Virus Epidemiology (WAVE), Pôle Scientifique et d'Innovation de Bingerville, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire
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Prasad A, Sharma N, Hari-Gowthem G, Muthamilarasan M, Prasad M. Tomato Yellow Leaf Curl Virus: Impact, Challenges, and Management. TRENDS IN PLANT SCIENCE 2020; 25:897-911. [PMID: 32371058 DOI: 10.1016/j.tplants.2020.03.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 05/26/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV) is one of the most studied plant viral pathogens because it is the most damaging virus for global tomato production. In order to combat this global threat, it is important that we understand the biology of TYLCV and devise management approaches. The prime objective of this review is to highlight management strategies for efficiently tackling TYLCV epidemics and global spread. For that purpose, we focus on the impact TYLCV has on worldwide agriculture and the role of recent advances for our understanding of TYLCV interaction with its host and vector. Another important focus is the role of recombination and mutations in shaping the evolution of TYLCV genome and geographical distribution.
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Affiliation(s)
- Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | | | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Pan LL, Chi Y, Liu C, Fan YY, Liu SS. Mutations in the coat protein of a begomovirus result in altered transmission by different species of whitefly vectors. Virus Evol 2020; 6:veaa014. [PMID: 32153997 PMCID: PMC7055206 DOI: 10.1093/ve/veaa014] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
For many crop pathogens including viruses, high genetic variation provides them with potential to adapt to and prevail in a changing environment. Understanding genetic variation in viruses and their significance is a key to elaborate virus epidemiology and evolution. While genetic variation of plant viruses has been documented to impact virus–host interactions, how it affects virus–insect vector interactions remains elusive. Here, we report the impact of mutations in the coat protein of squash leaf curl China virus (SLCCNV), a begomovirus, on the interaction between the virus and its whitefly vectors. We characterized mutations in the coat protein of SLCCNV and found that some residues exhibited higher mutation frequency than the others. We assayed the impact of mutation on infectivity using agroinoculation and found these mutations marginally affect virus infectivity. We further analyze their functions using virus acquisition and transmission trials and found some of mutations resulted in altered transmission of SLCCNV by different species of the whitefly Bemisia tabaci complex. We then identified the key amino acid residue(s) involved by constructing several mutant viruses and found that a single-residue mutation in the coat protein of SLCCNV was sufficient to significantly alter the whitefly transmission characteristics of SLCCNV. We examined the competition between different genotypes of SLCCNV in plant infection and whitefly transmission. We found that mutations in the coat protein did not alter the fitness of SLCCNV in plants, but they rendered the virus more competitive in transmission by certain species of whiteflies. Our findings indicate that mutations in the coat protein may play a key role in both the adaptation of begomoviruses to the changing vector populations and the evolution of begomoviruses.
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Affiliation(s)
- Li-Long Pan
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yao Chi
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chao Liu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yun-Yun Fan
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
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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.
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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.
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