scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Management Strategies ◽  
Purifying Selection ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Virus Population ◽  
Tomato Production ◽  
Tomato Leaf Curl ◽  
Leaf Curl

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.

scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl  Arusha virus affecting tomato plants in Kenya

2020 ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Management Strategies ◽  
Purifying Selection ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Virus Population ◽  
Tomato Production ◽  
Tomato Leaf Curl ◽  
Leaf Curl

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 5 out of the 6 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.

scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl virus complex affecting tomato plants in Kenya

2020 ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Tomato Production ◽  
Coding Regions ◽  
Tomato Leaf Curl Virus ◽  
Tomato Leaf Curl ◽  
Leaf Curl Virus ◽  
Leaf Curl

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 In 2018, we obtained tomato leaf samples with virus-like symptoms from farmers’ fields across Kenya and used Illumina sequencing to identify associated begomoviruses. Using the sequences, we determined the genetic diversity of begomoviruses. Additionally, selection pressure and recombinant isolates within the population were 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. When we analyzed the amino acid sequences, we detected the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and with the C4 gene of ToLCArV (97.1–100%). Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. Recombination analyses identified four putative events (P ≤ 0.05) among the isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in 5 out of the 6 coding regions. Conclusions The begomovirus associated with tomato leaf curl diseases in Kenya is a variant of ToLCArV possibly originating from Tanzania. Recombinant virus strains were detected within the population and there are divergence evolutionary events within the coding regions of the virus in Kenya. This information is useful in the development of appropriate management strategies for the disease.

Emergence of tomato leaf curl New Delhi virus in Italy: estimation of incidence and genetic diversity

2019 ◽  
Vol 68 (3) ◽  
pp. 601-608 ◽  
Author(s):  
S. Panno ◽  
A. G. Caruso ◽  
E. Troiano ◽  
M. Luigi ◽  
A. Manglli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tomato Leaf ◽  
New Delhi ◽  
Tomato Leaf Curl ◽  
Leaf Curl

scholarly journals Natural Hosts and Genetic Diversity of the Emerging Tomato Leaf Curl New Delhi Virus in Spain

2019 ◽  
Vol 10 ◽  
Author(s):  
Miguel Juárez ◽  
María Pilar Rabadán ◽  
Luis Díaz Martínez ◽  
Monia Tayahi ◽  
Ana Grande-Pérez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Tomato Leaf ◽  
New Delhi ◽  
Natural Hosts ◽  
Tomato Leaf Curl ◽  
Leaf Curl

scholarly journals Whitefly Control Strategies against Tomato Leaf Curl New Delhi Virus in Greenhouse Zucchini

2019 ◽  
Vol 16 (15) ◽  
pp. 2673 ◽  
Author(s):  
Estefanía Rodríguez ◽  
Mª Mar Téllez ◽  
Dirk Janssen
Keyword(s):  
Pest Management ◽  
Control Strategies ◽  
Integrated Management ◽  
Management Strategies ◽  
Tomato Leaf ◽  
New Delhi ◽  
Pesticide Reduction ◽  
Virus Suppression ◽  
Tomato Leaf Curl ◽  
Leaf Curl

(1) Background: Tomato leaf curl New Delhi virus (ToLCNDV), transmitted by tobacco whitefly (Bemisia tabaci Gennadius) (Hemiptera: Aleyrodidae), is of major concern in the cultivation of zucchini. The threat of this virus motivates reliance on chemical vector control but European consumers’ demands for vegetables grown free of pesticides provides an important incentive for alternative pest management; (2) Methods: Different whitefly management strategies and ToLCNDV incidences were surveyed in commercial zucchini greenhouses in south-east Spain. In an experimental greenhouse, three different whitefly control strategies, biological, chemical, and integrated (IPM), were evaluated in a replicated trial to determine the most effective strategy for virus suppression (3) Results: Whitefly was present in all commercial zucchini crops surveyed, whereas fewer crops had Amblyseius swirskii or other natural enemies. During three consecutive years, pest management was increasingly based on chemical treatments. Yet, ToLCNDV was widespread in zucchini greenhouses. Experimental results showed that the order of best strategy for virus suppressing was integrated management (73%) > biological control (58%) > chemical control (44%); and (4) Conclusions: IPM was the best strategy for virus suppression. The results can assist in the design of appropriate control strategies for chemical pesticide reduction and decision-making in pest management.

scholarly journals A Distinct Strain of Tomato leaf curl Sudan virus Causes Tomato Leaf Curl Disease in Oman

Plant Disease ◽  
2013 ◽  
Vol 97 (11) ◽  
pp. 1396-1402 ◽  
Author(s):  
A. J. Khan ◽  
S. Akhtar ◽  
A. K. Singh ◽  
R. W. Briddon
Keyword(s):  
Monopartite Begomoviruses ◽  
Tomato Leaf ◽  
Tomato Production ◽  
Tomato Leaf Curl Disease ◽  
The North ◽  
Distinct Strain ◽  
Tomato Leaf Curl ◽  
Leaf Curl Virus ◽  
Leaf Curl Disease ◽  
Leaf Curl

Tomato leaf curl disease (ToLCD) is a significant constraint for tomato production in the Sultanate of Oman. The disease in the north of the country has previously been shown to be caused by the monopartite begomoviruses (family Geminiviridae) Tomato yellow leaf curl virus and Tomato leaf curl Oman virus. Many tomato plants infected with these two viruses were also found to harbor a symptom enhancing betasatellite. Here an analysis of a virus isolated from tomato exhibiting ToLCD symptoms originating from south and central Oman is reported. Three clones of a monopartite begomovirus were obtained. One of the clones was shown to be infectious to tomato and Nicotiana benthamiana and to induce symptoms typical of ToLCD. Analysis of the cloned sequences show them to correspond to isolates of Tomato leaf curl Sudan virus (ToLCSDV), a virus that occurs in Sudan and Yemen. However, the sequences showed less than 93% nucleotide sequence identity to previously characterized ToLCSDV isolates, indicating that the viruses represent a distinct strain of the species, for which we propose the name “Oman” strain (ToLCSDV-OM). Closer analysis of the sequences showed them to differ from their closest relative, the “Tobacco” strain of ToLCSDV originating from Yemen, in three regions of the genome. This suggests that the divergence of the “Oman” and “Tobacco” strains has occurred due to recombination. Surprisingly, ToLCSDV-OM was not found to be associated with a betasatellite, even though the isolates of the other ToLCSDV strains have been shown to be. The significance of these findings and the possible reasons for the distinct geographic distributions of the tomato-infecting begomoviruses within Oman are discussed.

scholarly journals Non chemical management strategies for control of tomato leaf curl virus

2017 ◽  
Vol 12 (Special-5) ◽  
pp. 1430-1435
Author(s):  
NAGAMANDLA RAMYA SRI ◽  
NAGULAPALLY SNEHA LATHA ◽  
SHANTANU JHA
Keyword(s):  
Management Strategies ◽  
Tomato Leaf ◽  
Chemical Management ◽  
Tomato Leaf Curl Virus ◽  
Tomato Leaf Curl ◽  
Leaf Curl Virus ◽  
Leaf Curl

scholarly journals Identification of Begomoviruses from Three Cryptic Species of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) in Nepal

Agronomy ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 2032
Author(s):  
Rajendra Acharya ◽  
Yam Kumar Shrestha ◽  
Mst Fatema Khatun ◽  
Kyeong-Yeoll Lee
Keyword(s):  
Cryptic Species ◽  
Bemisia Tabaci ◽  
Management Strategies ◽  
Plant Viruses ◽  
Tomato Leaf ◽  
Begomovirus Species ◽  
Tomato Leaf Curl ◽  
Leaf Curl Virus ◽  
Asia Ii 1 ◽  
Leaf Curl

The Bemisia tabaci species complex consists of at least 44 cryptic species, which are potential vectors of approximately 320 begomovirus species, most of which are significant plant viruses. However, the relationship of begomovirus transmission through vectors at the cryptic species level is uncertain. In our previous study, three cryptic species (Asia I, Asia II 1, and Asia II 5) of B. tabaci were identified from 76 B. tabaci samples collected across 23 districts in Nepal. Using the same individuals we identified seven different begomovirus species (Squash leaf curl China virus [SLCCNV], Tomato leaf curl New Delhi virus [ToLCNDV], Okra enation leaf curl virus [OELCuV], Synedrella leaf curl virus [SyLCV], Tomato leaf curl Kerala virus [ToLCKeV], Ageratum enation virus [AEV], and Tomato leaf curl Karnataka virus [ToLCKV]) by PCR using universal begomovirus primers. The begomoviruses were detected in 55.26% of whitefly samples, and SLCCNV was the most prevalent species (27.63%). Among the three cryptic species of B. tabaci, the virus detection rate was highest in Asia I (60%), followed by Asia II 1 (58.82%) and Asia II 5 (53.06%). Most viruses were detected in all three species, but AEV and ToLCKV were found only in Asia I and Asia II 1, respectively. Geographic analysis showed that SLCCNV was distributed in the whole country, which is similar to the distribution of the Asia II 5 species, but OELCuV and SyLCV were detected only in the middle region of Nepal. Our results provide important information on the begomovirus profile in Nepal which can be beneficial for plant virus risk assessment and develop the management strategies to reduce the damage of whitefly transmitted viruses.

scholarly journals A BRIEF DESCRIPTION OF TOMATO LEAF CURL VIRUS AND ITS MANAGEMENT

2020 ◽  
Vol 4 (3) ◽  
pp. 137-147
Author(s):  
Mustansar Mubeen ◽  
Yasir Iftikhar ◽  
Qaiser Shakeel ◽  
Farazia Hassan ◽  
Aqleem Abbas ◽  
...  
Keyword(s):  
Abiotic Factors ◽  
Management Strategies ◽  
Tomato Leaf ◽  
Biochemical Changes ◽  
Economic Losses ◽  
Tomato Crop ◽  
Tomato Leaf Curl Virus ◽  
Tomato Leaf Curl ◽  
Leaf Curl Virus ◽  
Leaf Curl

The tomato crop is affected by various biotic and abiotic factors. Among the biotic factors, Tomato Leaf Curl Virus (TLCV) is one of the most devastating viruses of tomato. The virus belongs to Begomovirus and family Gemniniviridae. The genome of virus is single-stranded-DNA. It is naturally transmitted through whitefly (Bemisia tabaci). The virus is responsible for causing severe economic losses up to 80% in tomato crop-growing regions and continuously threatening the tomato crops. The increasing severity of TLCV has compelled plant virologists to develop accurate detection and identification of the virus. TLCV is responsible for certain biochemical changes and considerably affecting the plant growth. Tomato Leaf Curl Virus is significantly influenced physiological parameters and metabolic activities of all tomato varieties. The biochemical changes of cellular components are caused due to morphological deviation of infected virus plants, and symptoms expressed by the plants can determine the magnitude of the vegetable losses. It is evident from the previous reports, that nutrients were effective in reducing TLCV from a tomato plant. Moreover, the usage of resistant varieties and controlling of whitefly population and management of TLCV by different nutrients are some of the economical and recommendable ways to manage TLCV. Among the organic management strategies, the compost is also considered best in suppressing disease severity. Moreover, epidemiology plays a vital role in the spread and progress of the disease. Keeping in view the importance of TLCV and its effects on tomato crop, the present review will highlight the etiology, physiology and management of TLCV.

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