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PCR detection of begomovirus using Coat Protein gene specific primers. H: Healthy sample, M: 1 Kb ladder. 1-18 Field collected tomato leaf samples.
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Tomato is known as a highly valuable crop and grown worldwide for various uses. The cultivation and tomato production severely affected globally by several diseases caused by various pathogens. Begomoviruses causes yellow mosaic and leaf curl disease of tomato in the tropical, subtropical, temperate, and semi-arid regions. In Saudi Arabia, the toma...
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Context 1
... begomovirus infection was identified in infected leaf samples from various locations by using specific PCR primers which an amplicon of $750 bp (Fig. 2). Total of seventeen samples was found positive by specific primers. No positive amplification was observed in non-symptomatic samples. Restriction of Rolling Circle Amplified amplicon with EcoRI provided $2.7 kb product and further analyzed by cloning into PUC-18 vector. Total eight full-length and eight betasatellites amplicons were ...
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Citations
... Many monopartite and bipartite begomoviruses have been reported from the Arabian Peninsula, infecting various crops. Among the begomoviruses reported from Saudi Arabia, tomato yellow leaf curl virus (TYLCV) and tomato leaf curl Sudan virus (ToLCSDV) are two important begomoviruses infecting the tomato (Solanum lycopersicum L.) crop [19][20][21]. Similarly, cotton leaf curl Gezira virus (CLCuGeV) has been reported from okra plants in Saudi Arabia [19]. ...
... In Saudi Arabia, tomatoes and cucurbits are cultivated on small farms under natural or protected farming systems, and a significant share goes to local consumption [23]. Two important tomato-infecting begomoviruses in Saudi Arabia are TYLCV and tomato leaf curl Sudan virus (ToLCSDV) [21]. Keeping in view the importance of tomato and muskmelon crops, a detailed study was designed to investigate the suspected begomovirus infection from these crops on a larger scale. ...
... In Saudi Arabia, tomatoes and cucurbits are cultivated on small farms under natural or greenhouse farming systems [23]. Two important begomoviruses, TYLCV and tomato leaf curl Sudan virus (ToLCSDV), are known to affect tomato production in Saudi Arabia [21]. Only a limited number of studies are available on the molecular characterization of begomoviruses in Saudi Arabia; thus, information on economically important geminiviruses is scarce [21,32]. ...
The studies on the prevalence and genetic diversity of begomoviruses in Saudi Arabia are minimal. In this study, field-grown symptomatic tomato and muskmelon plants were collected, and initially, begomovirus infection was confirmed by the core coat protein sequences. Four tomato and two muskmelon plants with viral infections were further evaluated for Illumina MiSeq sequencing, and twelve sequences (2.7–2.8 kb) equivalent to the full-length DNA-A or DNA-B components of begomoviruses were obtained along with eight sequences (~1.3–1.4 kb) equivalent to the begomovirus-associated DNA-satellite components. Four begomovirus sequences obtained from tomato plants were variants of tomato yellow leaf curl virus (TYLCV) with nt sequence identities of 95.3–100%. Additionally, two tomato plants showed a mixed infection of TYLCV and cotton leaf curl Gezira virus (CLCuGeV), okra yellow crinkle Cameroon alphasatellite (OYCrCMA), and okra leaf curl Oman betasatellite (OLCuOMB). Meanwhile, from muskmelon plants, two sequences were closely related (99–99.6%) to the tomato leaf curl Palampur virus (ToLCPalV) DNA-A, whereas two other sequences showed 97.9-100% sequence identities to DNA-B of ToLCPalV, respectively. Complete genome sequences of CLCuGeV and associated DNA-satellites were also obtained from these muskmelon plants. The nt sequence identities of the CLCuGeV, OYCrCMA, and OLCuOMB isolates obtained were 98.3–100%, 99.5–100%, and 95.6–99.7% with their respective available variants. The recombination was only detected in TYLCV and OLCuOMB isolates. To our knowledge, this is the first identification of a mixed infection of bipartite and monopartite begomoviruses associated with DNA-satellites from tomato and muskmelon in Saudi Arabia. The begomovirus variants reported in this study were clustered with Iranian isolates of respective begomovirus components in the phylogenetic dendrogram. Thus, the Iranian agroecological route can be a possible introduction of these begomoviruses and/or their associated DNA-satellites into Saudi Arabia.
... In addition to analytical applications, RCA is used for the high-performance amplification of large CTs during the creation of libraries for sequencing [33] and for the genetic analysis of bacterial symbionts by the generation of products of the amplification of their specific plasmids during RCA [130]. As in the case of plasmids, the amplification and subsequent sequencing of the mitochondrial genome [131] and circular viral genomes are possible [132]. RCA is a more convenient alternative to PCR for the production of large amounts of candidate sequences during the selection of aptamers using the SELEX strategy [133]. ...
Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.
... All the Kenyan ToLArV-like sequences obtained in this study, shared very high nucleotide and amino acid sequence similarities, indicating low intra-population genetic diversity. Similar conclusions have been reached in other studies on tomato begomoviruses [51,52]. Curiously, we observed that the nucleotide sequences of the 12 ToLCArV-like isolates shared high identities among themselves but shared lower sequence identities with other begomoviruses. ...
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.
... So far, viral diseases including begomovirus on various crops have been identified from the Arabian region and neighboring countries like; Nile Basin, Oman, Yemen, and Iran (Al-Shahwan et al., 1997;Ghanem et al., 2003;Ajlan et al., 2007;Idris et al., 2012Idris et al., , 2014Khan et al., 2013;Hosseinzadeh et al., 2014;Al-Saleh et al., 2014;Sohrab, 2016;Khan and Khan, 2017;Shahid et al., 2019). The begomovirus and their associated satellites infecting other crops like Amaranthus, Beans, Cucurbits, Corchorus, Mentha, Tomato and weeds have been identified earlier from the Arabian region (Al-Shahwan et al., 1997;Ghanem et al., 2003;Ajlan et al., 2007;Idris et al., 2012Idris et al., , 2014;Hosseinzadeh et al., 2014;Al-Saleh et al., 2014;Sohrab, 2016Sohrab, , 2017aSohrab, , 2017bSohrab, , 2020;Sohrab et al., 2016;Daur, 2018a, 2018b). ...
... The genetic diversity of and variability of TYLCV and Chilli leaf curl virus from Solanaceous crops have been reported earlier from the Kingdom of Saudi Arabia, Arabian Peninsula and South East Asia (Idris et al., 2012;Khan et al., 2013;Hosseinzadeh et al., 2014;Kenyon et al., 2014). So far, only a few begomoviruses in the Kingdom such as TYLCV and ToLCSDV causing disease in Tomato, Cucumber, Sponge gourd, Squash, Mentha, Corchorus, Amaranthus, and Okra have been reported (Idris et al., 2012;Al-Saleh et al., 2014;Sohrab, 2016Sohrab, , 2017aSohrab, , 2017bSohrab, , 2020;Sohrab et al., 2016;Daur, 2018a, 2018b). The Association of ChiLCV and betasatellite infecting crops has been reported from Oman (Khan et al., 2013;Shahid et al., 2019). ...
... The transmission and spread of TYLCV from tomato to Chilli crops shows an alarming situation for vegetable growers in the kingdom of Saudi Arabia. It is well reported that the weeds and whiteflies play an important role as an alternative host and to spread of begomovirus from one region to others with extended hosts range (Sohrab, 2017a(Sohrab, , 2017b(Sohrab, , 2020;Sohrab and Daur, 2018a). The genetic diversity is a common phenomenon in both plants and humans and favors the emergence of new virus strains/ species and causing diseases in both plants and humans (Ahmad et al., 2009(Ahmad et al., , 2018. ...
Chilli (Capsicum annum L.) is well known as ‘wonder spice’. This is a very valuable cash crop grown as a vegetable globally. Chilli leaf curl disease is a major threat and global concern for the cultivation of Chilli by farmers and growers. In this work, the molecular diagnosis, genetic diversity, phylogenetic relationship, and begomovirus association with Chilli leaf curl disease have been discussed. The infected leaves were randomly harvested from the Chilli field, at Jeddah, Saudi Arabia. A group of begomovirus vector, whiteflies were also observed on the Chilli crop and infected weeds growing in the neighboring field. The begomovirus was confirmed by coat protein gene specific primer, dot blot hybridization, sequencing and sequence analysis. The full coat protein gene was found to have 774 nucleotides. The nucleotide sequences analysis shared the highest identity with Tomato yellow leaf curl virus reported earlier infecting tomato from Saudi Arabia, and the lowest identity was observed with Tomato yellow leaf curl virus Oman isolate. The overall sequence identity ranged from more than ninety percent among the analyzed sequences. The phylogenetic relationship analysis formed the major three clusters and showed the closed clustering with Tomato yellow leaf curl virus isolates. The natural spread of the Tomato yellow leaf curl virus on the Chilli crop from other crops poses an important and serious threat to Chili cultivation in the Kingdom of Saudi Arabia. Based on the literature review and current evidence, this is the first report of leaf curl disease of Chilli from Saudi Arabia.
... All the Kenyan ToLArV-like sequences obtained in this study, shared very high nucleotide and amino acid sequence similarities, indicating low intrapopulation genetic diversity. Similar conclusions have been reached in other studies on tomato begomoviruses [51,52]. Curiously, we observed that the nucleotide sequences of the 12 ToLCArV-like isolates shared high identities among themselves but shared lower sequence identities with other begomoviruses. ...
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.
... All the Kenyan ToLArV-like sequences obtained in this study shared very high nucleotide and amino acid sequence similarities, indicating low intra-population genetic diversity. Similar conclusions have been reached in other studies on tomato begomoviruses [61,62]. Curiously, we observed that the nucleotide sequences of the 12 ToLCArV-like isolates shared high identities among themselves but shared lower sequence identities with other begomoviruses (Table 3). ...
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.
Tomato leaf curl New Delhi virus (ToLCNDV) is a whitefly-transmitted bipartite ssDNA virus causing worldwide havoc to the tomato production. The present study addresses first report for the existence of ToLCNDV at Manipur region of North East India. Sequence comparison of DNA A (MG649330) and DNA B (OM752176) genomes showed close homogeneity of about 98% and 100% with Bangladesh isolates, but revealed only 84–96% (DNA A) and 81–100% (DNA B) similarity with other isolates of ToLCNDV. Phylogenetic relationship of global ToLCV species showed interchangeable results, substantiating that the isolate belonged to the old world bipartite group. Significant recombination events were ascertained around the intergenic region and the 5’end of the AC1 gene implicating a constant driving force for evolution and emergence of the strain. Population dynamics of global ToLCNDV isolates and other dominant ToLCV species within India were determined based upon several parameters i.e. genetic diversity, historic demographic events including neutrality test, Fst distance, Mismatch distribution plot, Haplotype network yielding significant results. Population genetics analysis overall showed low nucleotide diversity indicating recent population expansion. The dominant species of ToLCV in India also reinforced similar results where all the population showed diversifying selection constraint for the coat protein genes. Population dynamics of these viruses portrays Indian subcontinent as the possible hotspot for rapid demographic expansion from a small virus population size, indicating probability for rapid spread and emergence of distinct strains which may assist in future to signal the emergence of new threats to tomato production.
Tomato (Solanum lycopersicum Mill.), belonging to the family Solanaceae, is an extensively grown vegetable crop including both tropical and subtropical areas in the world. Among the begomovirus infecting tomato, Tomato leaf curl virus and Tomato yellow leaf curl virus cause major devastation in terms of quality and quantity. These viruses are transmitted by whiteflies. Significant research has been conducted regarding begomovirus infection causing impactful diseases in tomato crop. Still, there is more yet to be reported and characterized due to the wide evolutionary drive for the occurrence of novel strains and recombination with other begomovirus strains. Recent advances in the detection and diagnosis techniques will help to resolve the problem and decrease the spread of the infection and prevent the formation of new strains. Hence the focus is made on the detection and genome characterization of the novel strains of the virus infecting tomatoes so that resistance-breaking strategies and genetic engineering technologies can be developed for the future.
Begomoviruses (Geminiviridae) cause severe diseases in several crops, often causing significant losses due to reduced yield and quality. These viruses are easily transmitted by the whitefly (Bemisia tabaci) vector. Begomovirus-like symptoms were observed in wild poinsettia (Euphorbia cyathophora) and cultivated papaya (Carica papaya) plants in the Nizwa, Al-Dakhliya and Al-Batinah regions of Oman, where papaya is grown extensively. The aim of this study was to identify the suspected viral causal agent associated with yellow mosaic and leaf curl symptoms in the poinsettia and papaya plants. Symptomatic leaf samples were collected and subjected to DNA isolation followed by PCR amplification with begomovirus-coat protein specic primers. An amplicon of betasatellites was also amplified using betasatellite-specific primers. The amplicons were cloned and sequenced bi-directionally. The full-length begomoviral genome was determined to be 2766 and 2752 bp in length for the wild poinsettia and papaya isolates, respectively. The respective betasatellites were found to be 1354 and 1370 bp. Sequence analysis indicated that the papaya isolate, herein tomato yellow leaf curl virus (TYLCV)-Pap-Oman, shared 95.0% nucleotide identity with the wild poinsettia isolate, herein TYLCV-Poin-Oman, followed by 93.5% identity with TYLCV-Iran (GU076448). Phylogenetic analysis grouped TYLCV-Pap-Oman and TYLCV-Poin-Oman with TYLCV isolates previously reported from Iran, Saudi Arabia and Sudan, whereas the two betasatellites grouped them with TYLCB isolates previously reported from Oman. Based on the nucleotide sequence identity and phylogenetic tree analysis, the Begomovirus identified from papaya and wild poinsettia is considered an isolate of TYLCV from plant host species previously reported in the Arabian Peninsula.
Okra [Abelmoschus esculentus (L.) Moench] is an essential vegetable cultivated primarily for its delicious green pods. Whitefly, Bemisia tabaci (Genn.) attacks it and damages the foliage by sap-sucking, and also, it transmits Phyto-viruses like Okra Yellow Vein Mosaic Virus and Okra Leaf Curl Virus. The okra production losses due to Whitefly and transmitted viruses are prodigious. This research investigated the population fluctuations of whitefly and the Begomoviruses Percent Disease incidence (PDI) and Disease Severity Index (DSI) in different okra varieties. The Whitefly population's first incidence was recorded in early May, while it peaked in July and vanished in August. The highly susceptible variety was the native Peshawar-local (3.37 Whitefly/ 3 leaf), and the most resistant variety was Sabz-Pari (1.00 Whitefly/3 leaf). The highest disease incidence and severity were recorded on Peshawar-Local (PDI = 72.6, DSI = 69.0), followed by Ganga (PDI = 66.0, DSI = 54.8), while the most resistant variety against the virus infection was Sabz-Pari having lower PDI = 6.00 and DSI = 1.20. The viral infection is characterized by Polymerase Chain Reaction (PCR) through specific primers. Okra Yellow Vein Mosiac Virus was found to be the most prevailing and was amplified (800 bp) in all varieties apart from two resistant one’s, Peshawar-Local and Swat-Green, while Okra Leaf Curl Virus found to be the milder strain, and infection amplified (1600 bp) only in two varieties (Rama-Krishna and Peshawar-Local). The current finding insinuates that due to frequent use of the Peshawar-Local variety, it becomes susceptible to the whitefly and associated viruses; thus, this variety cultivation should be replaced by a resistant variety Sabz-Pari alongside proper monitoring of whitefly masses for expedient management.
