Association of tomato leaf curl New Delhi virus DNA-B with bhendi yellow vein mosaic virus in okra showing yellow vein mosaic disease symptoms

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.

Transcriptional Analysis of the Differences between ToLCNDV-India and ToLCNDV-ES Leading to Contrary Symptom Development in Cucumber

Tomato leaf curl New Delhi virus-ES (ToLCNDV-ES), a high threat to cucurbits in the Mediterranean Basin, is listed as a different strain from the Asian ToLCNDV isolates. In this study, the infectivity of two clones previously isolated from Italy and Pakistan were compared in cucumbers, which resulted in the opposite symptom appearance. The swapping subgenome was processed; however, the mechanisms related to the disease phenotype remain unclear. To identify the disease-associated genes that could contribute to symptom development under the two ToLCNDV infections, the transcriptomes of ToLCNDV-infected and mock-inoculated cucumber plants were compared 21 days postinoculation. The number of differentially expressed genes in ToLCNDV-India-infected plants was 10 times higher than in ToLCNDV-ES-infected samples. The gene ontology (GO) and pathway enrichment were analyzed using the Cucurbits Genomics Database. The flavonoid pathway-related genes were upregulated in ToLCNDV-ES, but some were downregulated in ToLCNDV-India infection, suggesting their role in resistance to the two ToLCNDV infections. The relative expression levels of the selected candidate genes were validated by qRT-PCR under two ToLCNDV-infected conditions. Our results reveal the different infectivity of the two ToLCNDVs in cucumber and also provide primary information based on RNA-seq for further analysis related to different ToLCNDV infections.

Copy number variation of two begomovirus acquired and inoculated by different cryptic species of whitefly, Bemisia tabaci in Okra

The whitefly, B.tabaci is a major pest of agricultural crops which transmits begomovirus in a species-specific manner. Yellow vein mosaic disease (YVMD) and okra leaf curl disease (OLCD) caused by distinct begomovirus are a major limitation to production of okra in India. In this framework the present investigation reports, for the first time, comparative study of begomovirus species viz. yellow vein mosaic virus (YVMV) and okra enation leaf curl virus (OELCuV) ingested and egested by two cryptic species (Asia I and Asia II 5) of B.tabaci at different time interval using detached leaf assay. A gradual increase of both virus copies were observed with increased feeding exposure in Asia I and Asia II 5. Both the genetic groups of whitefly could acquire the viruses within just 5 minutes of active feeding however, a significant amount of variation was noted in virus uptake by the both. At 24 hours of active feeding Asia II 5 acquired more of YVMV whereas, Asia I ingested more OELCuV. Similarly, the genetic group acquiring higher titre of virus egested higher amount during inoculation period. On the whole, it can be presumed that Asia I is a more effective transmitter of OELCuV whereas, Asia II 5 of YVMV further suggesting increased risk of virus pandemics (both YVMV and OELCuV) in regions where Asia I and Asia II 5 is dominant.

Two strains of a novel begomovirus encoding Rep proteins with identical β1 strands but different β5 strands are not compatible in replication

Geminiviruses have genomes composed of single-stranded DNA molecules and encode a rolling-circle replication (RCR) initiation protein ("Rep"), which has multiple functions. Rep binds to specific repeated DNA motifs ("iterons"), which are major determinants of virus-specific replication. The particular amino acid (aa) residues that determine the preference of a geminivirus Rep for specific iterons (i.e., the trans-acting replication "specificity determinants", or SPDs) are largely unknown, but diverse lines of evidence indicate that most of them are closely associated with the so-called RCR motif I (FLTYP), located in the first 12-19 aa residues of the protein. In this work, we characterized two strains of a novel begomovirus, rhynchosia golden mosaic Sinaloa virus (RhGMSV), that were incompatible in replication in pseudorecombination experiments. Systematic comparisons of the Rep proteins of both RhGMSV strains in the DNA-binding domain allowed the aa residues at positions 71 and 74 to be identified as the residues most likely to be responsible for differences in replication specificity. Residue 71 is part of the β-5 strand structural element, which was predicted in previous studies to contain Rep SPDs. Since the Rep proteins encoded by both RhGMSV strains are identical in their first 24 aa residues, where other studies have mapped potential SPDs, this is the first study lending direct support to the notion that geminivirus Rep proteins contain separate SPDs in their N-terminal domain.

Occurrence and variability of begomoviruses associated with bhendi yellow vein mosaic and okra enation leaf curl diseases in south-western India

Bhendi yellow vein mosaic disease (BYVMD) and Okra enation leaf curl disease (OELCuD) are common diseases of okra/bhendi [Abelmoschus esculentus (L.) Moench] affecting both pod yield and quality in the Indian subcontinent. BYVMD is caused by the infection of a begomovirus and associated betasatellite. In this study, we have made an attempt to investigate the diversity of begomoviral and the satellite sequences in okra samples showing BYVMD and OELCuD, by using a rapid PCR-based approach on 46 samples collected from 23 locations of Southern and Western India. We have also analyzed nine RCA-generated full-length begomoviral clones, some generated from the above samples displaying BYVMD and some OELCuD. By the PCR approach, we find the presence of begomovirus okra enation leaf curl virus (OELCuV) in most samples, irrespective of the disease being displayed (BYVMD or OELCuD). The nine apparently full-length sequences also show high identities with OELCuV and show instances of both intra-specific as well as intra-strainal recombination. We have also analyzed the begomoviral sequences associated with BYVMD and OELCuD from publicly available nucleotide sequence databases and show much higher sequence diversity amongst BYVMV, as compared to OELCuV. This is the first study which comprehensively demonstrates the presence of OELCuV in okra samples showing BYVMD and those showing OELCuD.

World Management of Geminiviruses

Management of geminiviruses is a worldwide challenge because of the widespread distribution of economically important diseases caused by these viruses. Regardless of the type of agriculture, management is most effective with an integrated pest management (IPM) approach that involves measures before, during, and after the growing season. This includes starting with resistant cultivars and virus- and vector-free transplants and propagative plants. For high value vegetables, protected culture (e.g., greenhouses and screenhouses) allows for effective management but is limited owing to high cost. Protection of young plants in open fields is provided by row covers, but other measures are typically required. Measures that are used for crops in open fields include roguing infected plants and insect vector management. Application of insecticide to manage vectors (whiteflies and leafhoppers) is the most widely used measure but can cause undesirable environmental and human health issues. For annual crops, these measures can be more effective when combined with host-free periods of two to three months. Finally, given the great diversity of the viruses, their insect vectors, and the crops affected, IPM approaches need to be based on the biology and ecology of the virus and vector and the crop production system. Here, we present the general measures that can be used in an IPM program for geminivirus diseases, specific case studies, and future challenges.

Absolute Quantification of Tomato leaf curl New Delhi virus Spain strain, ToLCNDV-ES: Virus Accumulation in a Host-Specific Manner

Tomato leaf curl New Delhi virus (ToLCNDV) (family Geminiviridae, genus Begomovirus) has recently been introduced in western Mediterranean countries. Isolates in Spain constitute a new strain, denominated ToLCNDV-ES, that is causing losses in commercial zucchini and melon crops; however, it is also, although less often, detected in commercial tomato crops. We developed a tissue-print hybridization test to detect the two genomic components of the virus and a TaqMan quantitative polymerase chain reaction (qPCR) test to estimate the number of genome copies in plants. qPCR was approximately 10⁴ to 10⁶ times more sensitive than tissue-print hybridization to detect viral genomic DNA-A and DNA-B, respectively. It also detected the virus in more experimentally and naturally ToLCNDV-ES-infected zucchini squash and tomato plants. ToLCNDV-ES DNA-A titers were significantly lower in tomato than in zucchini plants, often falling below the detection limits in the hybridization test. In addition, the DNA-B accumulation was impaired in tomato when compared with zucchini. According to the data obtained in this study, the differences in viral titers of both plant species contribute to explain the dissimilarities in symptom expression, capability of detection, and transmission of the virus.

Identification of a new begomovirus infecting Duranta repens in Pakistan

Ornamental perennial plants may serve as reservoirs for viruses that infect field crops. Duranta repens is an ornamental shrub that frequently exhibits leaf curl symptoms typical of begomoviral infection. Two begomoviruses or DNA-A components (isolates 57SA and 58SA) along with a DNA-B component (31SA) were identified in a symptomatic D. repens plant. Isolates 57SA and 58SA showed the highest nucleotide sequence identity of 90% and 92.2% to catharanthus yellow mosaic virus (CaYMV) and chilli leaf curl India virus (ChiLCINV), respectively, whereas 31SA shared the highest nucleotide sequence identity of 95.2% with the DNA-B component of tomato leaf curl New Delhi Virus (ToLCNDV). Isolate 57SA (showing < 91% highest nucleotide sequence identity) may thus be considered a member of a distinct species, and we propose the name "duranta leaf curl virus" (DLCV) for this virus. In addition, isolate 58SA (showing highest nucleotide sequence identity < 94%) is a newly identified strain of ChiLCINV for which the name "Duranta" strain is proposed. Further analysis showed that 57SA, 58SA and 31SA are recombinant, again highlighting the importance of recombination in begomovirus evolution. This is the first identification of DLCV. Also, a mixed infection with two viruses (or DNA-A components) and one DNA-B is reported.

Comparative transmission of Bhendi yellow vein mosaic virus by two cryptic species of the whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae)

The leaf sample from okra plants showing prominent yellow vein mosaic symptoms and healthy plant without any virus symptoms were collected from farmer's field. The presence of begomovirus in the infected sample was confirmed by polymerase chain reaction (PCR) and the amplicons were cloned and sequenced. The genome analysis showed that the isolate in the present study had 99% nucleotide identity with Bhendi yellow vein mosaic virus (BYVMV) revealing it as BYVMV variant. The genetic species of Bemisia tabaci collected from fields were identified as Asia-1 and MEAM-1 genetic species based on silver leaf assay, sequence characterized amplified region marker, and mtCOI gene sequence. The comparative virus-vector relationship of both genetic species of B. tabaci indicates a minimum of two and three B. tabaci in MEAM-1 and Asia-1 genetic species, respectively, per plant were required to transmit the disease. The minimum acquisition access period and inoculation access period of 15 (MEAM-1) and 20 min (Asia-1) were required to transmit the YVMD; it was further confirmed by nucleic acid hybridization using coat protein gene-specific probe of BYVMV. With respect to the sex, the female B. tabaci were more efficient in transmitting the disease as compared to male ones in both the genetic species of B. tabaci. The MEAM-1 to transmit the BYVMV more efficiently than Asia-1 genetic species of B. tabaci.

Tomato Leaf Curl New Delhi Virus: An Emerging Virus Complex Threatening Vegetable and Fiber Crops

The tomato leaf curl New Delhi virus (ToLCNDV) (genus Begomovirus, family Geminiviridae) represents an important constraint to tomato production, as it causes the most predominant and economically important disease affecting tomato in the Indian sub-continent. However, in recent years, ToLCNDV has been fast extending its host range and spreading to new geographical regions, including the Middle East and the western Mediterranean Basin. Extensive research on the genome structure, protein functions, molecular biology, and plant-virus interactions of ToLCNDV has been conducted in the last decade. Special emphasis has been given to gene silencing suppression ability in order to counteract host plant defense responses. The importance of the interaction with DNA alphasatellites and betasatellites in the biology of the virus has been demonstrated. ToLCNDV genetic variability has been analyzed, providing new insights into the taxonomy, host adaptation, and evolution of this virus. Recombination and pseudorecombination have been shown as motors of diversification and adaptive evolution. Important progress has also been made in control strategies to reduce disease damage. This review highlights these various achievements in the context of the previous knowledge of begomoviruses and their interactions with plants.

Tomato leaf curl New Delhi virus: a widespread bipartite begomovirus in the territory of monopartite begomoviruses

Tomato leaf curl New Delhi virus (ToLCNDV) is an exceptional Old World bipartite begomovirus. On the Indian subcontinent, a region in which monopartite DNA satellite-associated begomoviruses with mostly narrow geographical ranges predominate, it is widespread, with a geographical range also including the Far East, Middle East, North Africa and Europe. The success of ToLCNDV probably derives from its broad host range and highly flexible genomic configuration: its DNA-A component is capable of productively interacting with, and trans-replicating, diverse DNA-B components and betasatellites. An understanding of the capacity of ToLCNDV to infect a variety of hosts and spread across a broad and ecologically variable geographical range could illuminate the potential economic threats associated with similar begomoviral invasions. Towards this end, we used available ToLCNDV sequences to reconstruct the history of ToLCNDV spread.

TAXONOMY

Family Geminiviridae, Genus Begomovirus. ToLCNDV is a bipartite begomovirus. Following the revised begomovirus taxonomic criteria of 91% and 94% nucleotide identity for species and strain demarcation, respectively, ToLCNDV is a distinct species with two strains: ToLCNDV and ToLCNDV-Spain.

HOST RANGE

The primary cultivated host of ToLCNDV is tomato (Solanum lycopersicum), but the virus is also known to infect 43 other plant species from a range of families, including Cucurbitaceae, Euphorbiaceae, Solanaceae, Malvaceae and Fabaceae.

DISEASE SYMPTOMS

Typical symptoms of ToLCNDV infection in its various hosts include leaf curling, vein thickening, puckering, purpling/darkening of leaf margins, leaf area reduction, internode shortening and severe stunting.

Biotechnological Advancements and Begomovirus Management in Okra (Abelmoschus esculentus L.): Status and Perspectives

Despite the importance of okra, as one of the important vegetable crop, very little attention has been paid to its genetic improvement using advanced biotechnological tools. The exploitation of marker assisted breeding in okra is often limited due to the availability of a few molecular markers, the absence of molecular genetic-map(s), and other molecular tools. Chromosome linkage-groups were not yet constructed for this crop and reports on marker development are very scanty and mostly hovering around cultivar characterization. Besides, very little progress has been observed for transgenic development. However, high throughput biotechnological tools like chromosome engineering, RNA interference (RNAi), marker-assisted recurrent selection (MARS), genome-wide selection (GWS), targeted gene replacement, next generation sequencing (NGS), and nanobiotechnology can provide a rapid way for okra improvement. Further, the etiology of many deadly viral diseases like the yellow vein mosaic virus (YVMV) and okra enation leaf curl virus (OELCV) in okra is broadly indistinct and has been shown to be caused by various begomovirus species. These diseases cause systemic infections and have a very effective mode of transmission; thus, preventing their spread has been very complicated. Biotechnological interventions have the potential to enhance okra production even under different viral-stress conditions. In this background, this review deals with the biotechnological advancements in okra per se along with the begomoviruses infecting okra, and special emphasis has been laid on the exploitation of advanced genomic tools for the development of resistant varieties.