Tomato Leaf Curl Palampur Virus Research Articles

Characterization of multiple disease resistance in melons (Cucumis melo L.) against Meloidogyne incognita, Fusarium oxysporum and tomato leaf curl Palampur virus

AbstractMelon is one of the important cucurbitaceous crops being cultivated widely in India and known for its delicious fruits. Crop is threatened by different biotic stresses including nematodes, fungi and viruses. The use of host resistance is the most economical, eco-compatible and long-lasting strategy to combat plant diseases. Keeping in mind this objective, 64 melon genotypes were screened against the prevalent Meloidogyne incognita, Fusarium oxysporum and tomato leaf curl Palampur virus (ToLCPalV) individually as well as with combined inoculations under artificial conditions. Out of 64 genotypes, three genotypes, MCPS, SM2012-1 and WM11 were found moderately resistant to M. incognita, nine genotypes (MM-KP15103, MM327, MM121103, KP4HM15, MM Sel.-103, SM2013-2, SM2012-1, SM2013-9 and WM11) recorded a resistant reaction against Fusarium wilt while four genotypes, WM11, SM2012-1, SM2013-9 and SM2013-2 exhibited a highly resistant reaction against ToLCPalV. A dendrogram constructed based on the resistance response of all the genotypes divided the genotypes into two groups and all resistant genotypes (MM1804, MM120103, SM2012-1, MM121103, SM2013-2, SM2013-9, WM11 and MM Sel.103) clustered in group II. The resistant genotypes when subjected to simultaneous inoculations of all three pathogens showed an increase in disease severity for each pathogen which negatively altered the resistance response of different genotypes. However, the genotypes SM2012-1, SM2013-9, SM2013-2 and WM-11 showing multiple disease resistance exhibited a good level of resistance even after combined inoculations of three pathogens. This study is the first to our knowledge identifying multiple disease resistance against root-knot nematode, Fusarium wilt and tomato leaf curl Palampur virus in muskmelon.

First identification of tomato leaf curl Palampur virus in Oman: detection and characterization

First identification of tomato leaf curl Palampur virus in Oman: detection and characterization

Whole genome characterization, recombination, variation, satellites and phylogeny analyses of Tomato leaf curl Palampur virus infecting courgetti squash (Cucurbita pepo L.) in Iraq

Durning season of 2021-2022, symptoms of leaf curl, yellowing, crumpling and stunting were observed commonly on courgetti crop in Al-Yusufiyah region, Baghdad Province, Iraq. Diseased courgetti leaves were collected randomly and sent for sequencing with Illumina MiSeq. Pairwise nucleotide analysis of the assembled contigs revealed the maximum identity of 98-99% and 95-99% with Tomato leaf curl Palampur virus (ToLCPalV) for DNA-A and DNA-B components, respectively. The DNA-A component (OQ693629.1) contains six main genes encoding six proteins, while DNA-B component (OQ693630.1) comprises only two genes encoding two proteins, with the presence of non-coding regions between genes in both the two segments. Furthermore, the recombination breakpoint analysis shows that ToLCPalV Baghdad-1/Iraq segment DNA-A (OQ693629.1) and ToLCPalV isolate Mosul segment A (OR052249.1) are the parent of the recombinant isolates: ToLCPalV isolate Kufa segment DNA-A (OP810506.1) and ToLCPalV segment A (ON254271.1) from Karbala. However, the ToLCPalV Baghdad-1/Iraq segment DNA-B (OQ693630.1) with ToLCPalV segment DNA-B (OP620406.1) from Kufa are the parent of ToLCPalV isolate Babylon1 segment DNA-B (ON229620.1). As well as, there was no evidence discovered for the association of alpha- and/or beta-satellites with ToLCPalV infecting courgetti crop. Single nucleotide polymorphisms (SNP) analysis indicates a common genetic variation within the current isolate under study and the other Iraqi isolates. Phylogenetic analysis confirms the genetic relationship between the genomics components of Iraqi ToLCPalV and various international isolates of the same virus, especially those distributed in Saudi Arabia and Iran that could be a possible the origin and introduction of ToLCPalV into Iraq.

Geographical distribution of tomato-infecting begomoviruses in major cucurbits in India: a diagnostic analysis using begomovirus species specific PCR.

Cucurbits are an essential summer-season vegetable crops, but they are highly vulnerable from a range of abiotic and biotic factors. One of the significant biotic factors posing a growing menace to the production of major cucurbits in India is the emergence of tomato-infecting begomoviruses. In this study, we utilized PCR-based species-specific primers, developed earlier in our laboratory for the detection of begomoviruses infecting tomato and chilli plants, to identify begomoviruses in cucurbits across various regions of India. Leaf samples from major cucurbits were collected from different regions of Haryana, Delhi, Uttar Pradesh, Chhattisgarh, Maharashtra, Telangana and Karnataka, during the year 2020-2021. Total nucleic acid (TNA) was extracted from the samples and subjected to PCR using a generic primer specific to begomoviruses. The samples that exhibited positive amplification were further tested using six different species-specific primers targeting specific begomovirus species, namely Tomato leaf curl New Delhi virus (ToLCNDV), Tomato leaf curl Palampur virus (ToLCPalV), Tomato leaf curl Bangalore virus (ToLCBV), Tomato leaf curl Joydebpur virus (ToLCJoV), Tomato leaf curl Gujarat virus (ToLCGuV), and Chilli leaf curl virus (ChiLCV). The PCR analysis revealed that among the 551 plant samples tested, a total of 124 samples exhibited positive amplification using the universal begomovirus PCR. Specifically, 47 samples tested positive for ToLCNDV, 73 samples were positive for ToLCPalV and only one sample showed positive amplification for ChiLCV. However, none of the samples tested positive for ToLCJoV, ToLCGuV and ToLCBV. These findings from our study indicate the prevalence of ToLCNDV and ToLCPalV in major cucurbits across India. Furthermore, the study highlights the varied distribution of begomoviruses in major cucurbits between northern and southern regions of India.

Screening for tomato leaf curl Palampur virus resistance in common bean (Phaseolus vulgaris L.) cultivars through phytochemical characterization and enzyme activity analysis

Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide as a major source of protein in the human diet. In the present study, for the first time, tomato leaf curl Palampur virus (ToLCPalV) (Begomovirus, Geminiviridae) was detected in the west of Iran. As it was realized that ToLCPalV was widespread from the east to the west of Iran and the virus-host range was increasing, this study aims to evaluate the twelve popularly grown common bean cultivars in a completely randomized design experiment for their reaction to the virus under greenhouse conditions. According to the biochemical, physiological, and molecular assays, it could be concluded that Dadfar, Ghafar, Ofogh, and Naz cultivars were resistant to ToLCPalV infection. Results showed that peroxidase, polyphenol oxidase, and phenylalanine ammonia-lyase enzymes appear to act as resistance factors because their activities were higher in resistant cultivars compared to susceptible cultivars, and this was proved by hierarchical cluster analysis between the twelve cultivars.

Diversity and phylogeography of begomoviruses and DNA satellites associated with the leaf curl and mosaic disease complex of eggplant

Eggplant is one of the important vegetable crops grown across the world, and its production is threatened by both biotic and abiotic stresses. Diseases caused by viruses are becoming major limiting factors for its successful cultivation. A survey for begomovirus-like symptoms in 72 eggplant fields located in six different Indian states revealed a prevalence of disease ranging from 5.2 to 40.2%, and the symptoms recorded were mosaic, mottling, petiole bending, yellowing, and upward curling, vein thickening, and enation of the leaves, and stunting of plants. The causal agent associated with these plants was transmitted from infected leaf samples to healthy eggplant seedlings via grafting and whiteflies (Bemisia tabaci). The presence of begomovirus was confirmed in 72 infected eggplant samples collected from the surveyed fields exhibiting leaf curl and mosaic disease by PCR using begomovirus specifc primers (DNA-A componet), which resulted in an expected amplicon of 1.2 kb. The partial genome sequence obtained from amplified 1.2 kb from all samples indicated that they are closely related begomovirus species, tomato leaf Karnataka virus (ToLCKV, two samples), tomato leaf curl Palampur virus (ToLCPalV, fifty eggplant samples), and chilli leaf curl virus (ChLCuV, twenty samples). Based on the partial genome sequence analysis, fourteen representative samples were selected for full viral genome amplification by the rolling circle DNA amplification (RCA) technique. Analyses of fourteen eggplant isolates genome sequences using the Sequence Demarcation Tool (SDT) indicated that one isolate had the maximum nucleotide (nt) identity with ToLCKV and eight isolates with ToLCPalV. Whereas, four isolates four isolates (BLC1-CH, BLC2-CH, BLC3-CH, BLC4-CH) are showing nucleotide identity of less than 91% with chilli infecting viruses begomoviruses with chilli infecting begomoviruses and as per the guidelines given by the ICTV study group for the classification of begomoviruses these isolates are considered as one novel begomovirus species, for which name, Eggplant leaf curl Chhattisgarh virus (EgLCuChV) is proposed. For DNA-B component, seven eggplant isolates had the highest nt identity with ToLCPalV infecting other crops. Further, DNA satellites sequence analysis indicated that four betasatellites identified shared maximum nucleotide identity with the tomato leaf curl betasatellite and five alphasatellites shared maximum nucleotide identity with the ageratum enation alphasatellite. Recombination and GC plot analyses indicated that the bulk of begomovirus genome and associated satellites presumably originated from of previously known mono and bipartite begomoviruses and DNA satellites. To the best of our knowledge, this is India's first report of ToLCKV and a noval virus, eggplant leaf curl Chhattisgarh virus associated with eggplant leaf curl disease.

First report of Cucumber vein yellowing virus in Iraq

Courgette (Cucurbita pepo) is one of the main cucurbit crops grown in Iraq for local consumption. Viruses are a major threat to cucurbit production in Iraq, particularly whitefly-transmitted viruses (Mohammed et al., 2021). In the 2022 growing season, courgette plants with extensive leaf vein-yellowing symptoms (Figure 1), associated with whitefly infestation, were observed in fields around Al-Yusufiyah, Baghdad Province, Iraq. The disease incidence was 40–50%. Thirty leaf samples with vein-yellowing symptoms were collected randomly. One sample was sent in RNAprotect Tissue Reagent (Qiagen, Germany) for high throughput RNA sequencing (RNA-seq) at Macrogen Inc. (Seoul, South Korea). Overall, 39,549,599 paired-end reads (151 bp length) were obtained. The reads were first aligned to the complete genome sequence of Cucurbita pepo via Bowtie2 (v. 2.4.5) to deplete host sequence. The Velvet assembler (v. 1.2.10) was operated for de novo assembly of the unmapped reads (Lahuf, 2021). The contigs produced were compared with plant virus sequences retrieved from GenBank (https://www.ncbi.nlm.nih.gov/genome/viruses/) using BLASTn algorithms (Abass & Lahuf, 2023). The BLASTn analysis showed ≥99% pairwise nucleotide identity with the full genomes of five Cucumber vein yellowing virus (CVYV) isolates. Other viruses were also detected including Squash leaf curl virus (SqLCV) and Tomato leaf curl Palampur virus (ToLCPMV). Reference-based genome assembly was conducted using a sequence of CVYV (NC_006941.1). A total of 86,245 reads mapped to NC_006941.1 with 100% coverage and a depth coverage of 1.335× and BLAST analysis showed that the assembled genome of CVYV Iraq-1 shares 99.86% pairwise nucleotide identity with this isolate. The genome sequence of the CVYV isolate Iraq-1 was deposited in GenBank (Accession No. OQ685957.1). A phylogenetic analysis showed a close relationship between CVYV isolate Iraq-1 and isolates from diverse origins, particularly those from Spain (AY578085.1 and MK777994.1) and Portugal (MZ130935.1 and OK181771.1) (Figure 2). Total RNA was extracted from the thirty diseased courgette leaf samples, including the sequenced sample, using a Viral RNA/ Viral Nucleic Acid Mini Kit (Favorgen, Taiwan) and kept at -20°C for further analysis. RT-PCR was done using a OneStep RT-PCR kit (Qiagen, Germany) with CVYV-specific coat protein primers (CV+ and CV-) (Cuadrado et al., 2003). The amplicons were directly sequenced and CVYV infection was confirmed in all thirty leaves. Another fifty diseased leaf samples were collected randomly from different fields of courgette in Baghdad Province to confirm the presence of the virus in the region and 38 also tested positive using the CVYV-specific RT-PCR. This is the first report of CVYV in Iraq. Additional work is needed to reveal the distribution and prevalence of CVYV, SqLCV and ToLCPMV and to determine their role in causing disease in courgette and other curcurbit crops in Iraq. The authors are appreciative of the Plant Protection Department, Agriculture College, University of Kerbala and the Iraqi Ministry of Higher Education and Scientific Research for the facilities and financial support.

Detecting Tomato Leaf Curl New Delhi Virus Causing Ridge Gourd Yellow Mosaic Disease, and Other Begomoviruses by Antibody-Based Methods.

The incidence and severity of begomovirus diseases have been increasing around the world recently, and the ridge gourd [Luffa acutangula (Roxb.) L.] is the latest example of a crop that has become highly susceptible to the outbreak of the tomato leaf curl New Delhi virus (ToLCNDV, genus Begomovirus) in India. Accurate diagnosis of causal agents is important in designing disease management strategies. In this study the coat protein (CP) gene from a ToLCNDV-Rg ridge gourd isolate was used to produce polyclonal antibodies (ToLCNDV-Rg-CP-PAb) in a rabbit. The antibodies successfully detected a 30.5 kDa ToLCNDV-Rg-CP in extracts of symptomatic ridge gourd leaf samples by several assays, such as Western Blotting (WB), Dot Immuno Binding Assay (DIBA), Direct Antigen Coating Enzyme Linked Immuno Sorbent Assay (DAC-ELISA), Immuno Capture Polymerase Chain Reaction (IC-PCR), and Immuno Capture Loop-Mediated Isothermal Amplification (IC-LAMP) assays. However, none of the negative samples tested positive in either of the detection methods. Among all the methods tested, the immunocapture assay, IC-LAMP, was the most sensitive in detecting ToLCNDV-Rg. Furthermore, antibodies generated in this study also detected other commonly occurring begomoviruses in South India, such as tomato leaf curl Palampur virus and squash leaf curl China virus in cucurbits. Together, ToLCNDV-Rg-CP-PAb can be used for detecting at least three species of begomoviruses infecting cucurbits. The obtained antibodies will contribute to monitoring disease outbreaks in multiple crops.

Unraveling different begomoviruses, DNA satellites and cryptic species of Bemisia tabaci and their endosymbionts in vegetable ecosystem.

Bemisia tabaci species complex contains more than 46 cryptic species. It has emerged as an important pest causing significant yield loss in many cultivated crops. This pest is also a vector for more than 100 species of begomoviruses, that are a major threat for the cultivation of many crops in different regions of the world. The relation between cryptic species of the B. tabaci species complex and associated begomoviruses that infect different crops remains unclear. In the present study, four cryptic species (Asia I, China 3, Asia II 5 and Asia II-1) of B. tabaci and four associated endosymbionts (Arsenophonus, Cardinium, Rickettsia and Wolbachia) were identified in different vegetable crops. The vector-based PCR detection revealed five different begomoviruses such as okra enation leaf curl virus (OELCuV), tomato leaf curl Palampur virus (ToLCPalV), squash leaf curl China virus (SLCCNV), chilli leaf curl virus (ChiLCuV), and tomato leaf curl New Delhi virus (ToLCNDV). Of these begomoviruses, the maximum infection rate was observed (9.1%) for OELCuV, followed by 7.3% for ToLCNDV. The infection rate of the other three viruses (SLCCNV, ChiLCuV, ToLCPalV) ranged from 0.9 to 2.7% in cryptic species of B. tabaci. Further, each cryptic species was infected with multiple virus species and the virus infection rate of Asia I, Asia II-5, China 3 and Asia II-1 was 21.2%, 15.1%, 15.1% and 0.6% respectively. Similarly, in case of betasatellites the highest infection rate was 12% for ToLCBDB, followed by 6% for OLCuB and PaLCB. With regard to alphasatellites, the highest infection rate was 18.2% for AEV and 3% for CLCuMuA. This study demonstrates the distribution of cryptic species of whitefly and their endosymbionts, and associated begomoviruses and DNA satellites in vegetable ecosystem. We believe that the information generated here is useful for evolving an effective pest management strategies for vegetable production.

First report of tomato leaf curl Palampur virus infecting tomato in Iraq

First report of tomato leaf curl Palampur virus infecting tomato in Iraq

High-Throughput Sequencing Identified Distinct Bipartite and Monopartite Begomovirus Variants Associated with DNA-Satellites from Tomato and Muskmelon Plants in Saudi Arabia.

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.

Characterization of tomato leaf curl Palampur virus naturally infecting wild melon in Oman

Characterization of tomato leaf curl Palampur virus naturally infecting wild melon in Oman

Identification and estimation of sequence variation dynamics of Tomato Leaf curl Palampur virus and betasatellite complex infecting a new weed host

Leaf samples from the symptomatic Solanum nigrum plants showing curling on leaf margins, leaf chlorosis, leaf crumpling and stunting in growth were collected during spring 2018. Subsequently, the standard procedures of total genomic DNA isolation, enrichment via rolling circle amplification, polymerase chain reaction, cloning and complete genome sequencing were performed. Pairwise nucleotide (nt) sequence comparison and phylogenetic studies of the inferred genome sequences confirmed the identity of a bipartite begomovirus Tomato leaf curl Palampur virus (ToLCPalV) in the symptomatic plant samples sharing 97.6 and 95.5% nt identity with ToLCPalV isolates identified from Pakistan and India. In the phylogenetic analysis, ToLCPalV grouped with ToLCPalV isolates previously described from Pakistan and India. Additional attempts to identify any putative DNA-satellites in S. nigrum plant samples revealed an associated betasatellite component, cotton leaf curl Multan betasatellite (CLCuMuB). This is the first identification of cotton leaf curl disease-associated betasatellite with ToLCPalV in this region. The nt diversity analysis showed that ToLCPalV populations have a high mutation rate and evolve independently under strong purifying selection, but not via recombination.

Relative consequences of interaction among Meloidogyne incognita, Fusarium oxysporum and tomato leaf curl Palampur virus on disease severity and growth of muskmelon

Relative consequences of interaction among Meloidogyne incognita, Fusarium oxysporum and tomato leaf curl Palampur virus on disease severity and growth of muskmelon

Identification of resistance sources and monogenic dominant nature of resistance to tomato leaf curl Palampur virus in melons

Identification of resistance sources and monogenic dominant nature of resistance to tomato leaf curl Palampur virus in melons

Tomato leaf curl Palampur virus

This datasheet on Tomato leaf curl Palampur virus covers Identity, Distribution, Hosts/Species Affected, Further Information.

Characterization of Tomato leaf curl Palampur virus associated with leaf curl and yellowing disease of watermelon from India

Characterization of Tomato leaf curl Palampur virus associated with leaf curl and yellowing disease of watermelon from India

Molecular characterization of recombinant Bipartite begomovirus associated with mosaic and leaf curl disease of Cucumber and Muskmelon

Muskmelon and cucumber are important vegetables grown in different parts of India. Leaf curl and mosaic diseases caused by begomovirus are economically important on these crops. Survey during 2012–2015 to assess the incidence of both leaf curl and mosaic in Mirzapur and Varanasi Districts of Eastern Uttar Pradesh, India revealed incidence of leaf curl up to 30–40% and mosaic disease up to 50–60% in both the crops. Totally, 103 leaf samples of muskmelon (58) and cucumber (45) were collected from the plants showing viral disease symptoms. These samples were tested for infection by different viruses using DAC-ELISA and PCR. A total of ten samples reacted for CGMMV, nine for PRSV-W, 25 for GBNV, 21 for CMV, 7 for ZYMV and 21 for DNA virus. Together, ELISA and PCR detected mixed infection of RNA viruses (CGMMV, CMV, PRSV-W and GBNV) and DNA virus in different combination in ten samples. The partial DNA virus genome (1.2 kb fragment) sequencing performed on samples indicated possible infection by a known bipartite begomovirus (Tomato leaf curl Palampur virus, ToLCPalV) in 21 samples. Therefore, one sample each from muskmelon (Mm-1) and cucumber (Cb-1) were used for full-length genome amplification of begomovirus genome using RCA method. Sequencing of the full-length viral genome (DNA A) and subsequent analysis using SDT program revealed that Mm-1 and Cb-1 isolates share a nucleotide (nt) identity of 90.4–92.2% and 95.9–99.1%, respectively with ToLCPalV infecting tomato and cucurbits. Similarly, analysis of full-length DNA B of Mm-1 and Cb-1 isolates indicated that they shared genome identity of 88.4–94.0% with tomato infecting ToLCPalV. Further, recombination breakpoint analysis of the viral genome indicated the recombinant nature of the virus isolates. The significance of ToLCPalV strains/variants as an emerging threat in the production of cucurbits in India is discussed.

Molecular characterization of viruses associated to leaf curl disease complex on zucchini squash in Iraq reveals Deng primer set could distinguish between New and Old World Begomoviruses.

The emergence of begomoviruses has led to significant losses in vegetable production in the recent years. Squash leaf curl disease (SqLCD) is caused by begomoviruses, and the infected plants show leaf curl symptoms on zucchini squash. In this study, we characterized the begomoviruses responsible for SqLCD symptoms and economic losses in zucchini major growing area near Baghdad and Babylon provinces. PCR amplification was performed to screen for begomovirus infection using Deng (a begomovirus specific) primer set. Sequence comparison confirmed the detection of two begomoviruses; Tomato leaf curl Palampur virus (ToLCPMV) and Squash leaf curl virus (SLCuV), in symptomatic zucchini samples when shared 99.14 and 99.50% maximum nucleotide (nt) identities with coat protein CP gene, respectively. All samples collected from Baghdad/Al-Jadriya were ToLCPMV infected while those collected from Babylon/Jibela were SLCuV infected. Moreover, mixed infection of the two viruses was detected in all zucchini squash samples collected from Baghdad/Yusufiyah. Evidence is provided here of the relevance of the wild species Malva neglecta and Datura stramonium as reservoir of begomoviruses that cause epedemics of leaf curl disease in zucchini squash in Iraq. Neighbor joining (NJ) Phylogenetic analysis confirmed the relatedness when diverged virus sequences in separated groups based on CP gene. The high nt identity suggests the two begomoviruses may recently be introduced to Iraq and could be a serious threatening to squash cultivation.

First report of tomato leaf curl Palampur virus infecting muskmelon in India

First report of tomato leaf curl Palampur virus infecting muskmelon in India