Sequence variability and phylogenetic relationship of betasatellite isolates associated with yellow vein mosaic disease of mesta in India

A novel monopartite begomovirus and satellites associated with yellow mosaic disease of Sida spp. in India

Begomoviruses (family Geminiviridae) cause severe diseases in many economically important crops and non-cultivated plants in the warmer regions of the world. Non-cultivated weeds have been reported to act as natural virus reservoirs. In January 2016, Sida plants with yellow mosaic symptoms were found at the edge of an agricultural field in Gujarat, India. Sequence analysis of the viral genomic components cloned from a diseased Sida plant indicated the presence of a distinct monopartite begomovirus (proposed as sida yellow mosaic Gujarat virus) along with a betasatellite (ludwigia leaf distortion betasatellite) and an alphasatellite (malvastrum yellow mosaic alphasatellite). Our results emphasize that this weed may harbor a begomovirus-alphasatellite-betasatellite complex. This host serves as a potential source of virus inoculum, which can be transmitted by whiteflies to other cultivated crops.

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.

Detection of Mesta yellow vein mosaic virus (MeYVMV) in field samples by a loop-mediated isothermal amplification reaction

A loop-mediated isothermal amplification (LAMP) assay was optimized for the detection of Mesta yellow vein mosaic virus (MeYVMV) in diseased plants of mesta (Hibiscus sabdariffa L.& H. cannabinus L.). The LAMP assay was optimized using a set of six primers targeting the MeYVMV genome and could be completed in 30-60 min at 63 °C. The LAMP amplification results were visualized by adding 1 μl of hydroxy naphthol blue (HNB) dye in a 25 μl LAMP reaction mixture prior to amplification as well as by electrophoresis. The LAMP assay, which detected MeYVMV in a 10^-5-fold diluted total DNA, was more sensitive than the PCR assay (10^-4-fold dilution). The optimized LAMP assay was able to detect MeYVMV in different parts of the kenaf and roselle plants. Similarly, the optimized PCR assay was also capable of detecting MeYVMV in all the different parts of the kenaf plant but failed to detect the virus in the stem and flower buds of the roselle plant. Validation of the LAMP and LAMP with HNB dye assays revealed that the optimized reactions can be used successfully for the in-situ detection of MeYVMV in field samples and in virus quarantine programs. This is the first report of the detection of the begomovirus species, MeYVMV, in the mucilaginous plant species, kenaf and roselle, using a LAMP assay.

Begomovirus research in India: a critical appraisal and the way ahead

Begomoviruses are a large group of whitefly-transmitted plant viruses containing single-stranded circular DNA encapsidated in geminate particles. They are responsible for significant yield losses in a wide variety of crops in India. Research on begomoviruses has focussed on the molecular characterization of the viruses, their phylogenetic analyses, infectivities on host plants, DNA replication, transgenic resistance, promoter analysis and development of virus-based gene silencing vectors. There have been a number of reports of satellite molecules associated with begomoviruses. This article aims to summarize the major developments in begomoviral research in India in the last approximately 15 years and identifies future areas that need more attention.

Advances in understanding begomovirus satellites

Begomoviruses are numerous and geographically widespread viruses that cause devastating diseases in many crops. Monopartite begomoviruses are frequently associated with betasatellites or alphasatellites. Both betasatellite and alphasatellite DNA genomes are approximately half the size of begomovirus DNA genomes. Betasatellites are essential for induction of typical disease symptoms. The βC1 genes encoded by the betasatellites have important roles in symptom induction, in suppression of transcriptional and posttranscriptional gene silencing, and they can affect jasmonic acid responsive genes. Host plants of begomoviruses have evolved diverse innate defense mechanisms against the βC1 protein to counter these challenges. Alphasatellites have been identified mainly in monopartite begomoviruses that associate with betasatellites and have no known contributions to pathogenesis of begomovirus-betasatellite disease complexes. Applications of current molecular tools are facilitating viral diagnosis and the discovery of novel species of geminiviruses and satellite DNAs and are also advancing our understanding of the global diversity and evolution of satellite DNAs.

A melting pot of Old World begomoviruses and their satellites infecting a collection of Gossypium species in Pakistan

CLCuD in southern Asia is caused by a complex of multiple begomoviruses (whitefly transmitted, single-stranded [ss]DNA viruses) in association with a specific ssDNA satellite; Cotton leaf curl Multan betasatellite (CLCuMuB). A further single ssDNA molecule, for which the collective name alphasatellites has been proposed, is also frequently associated with begomovirus-betasatellite complexes. Multan is in the center of the cotton growing area of Pakistan and has seen some of the worst problems caused by CLCuD. An exhaustive analysis of the diversity of begomoviruses and their satellites occurring in 15 Gossypium species (including G. hirsutum, the mainstay of Pakistan's cotton production) that are maintained in an orchard in the vicinity of Multan has been conducted using φ29 DNA polymerase-mediated rolling-circle amplification, cloning and sequence analysis. The non-cultivated Gossypium species, including non-symptomatic plants, were found to harbor a much greater diversity of begomoviruses and satellites than found in the cultivated G. hirsutum. Furthermore an African cassava mosaic virus (a virus previously only identified in Africa) DNA-A component and a Jatropha curcas mosaic virus (a virus occurring only in southern India) DNA-B component were identified. Consistent with earlier studies of cotton in southern Asia, only a single species of betasatellite, CLCuMuB, was identified. The diversity of alphasatellites was much greater, with many previously unknown species, in the non-cultivated cotton species than in G. hirsutum. Inoculation of newly identified components showed them to be competent for symptomatic infection of Nicotiana benthamiana plants. The significance of the findings with respect to our understanding of the role of host selection in virus diversity in crops and the geographical spread of viruses by human activity are discussed.

Biochemical characterization of compatible plant-viral interaction: a case study with a begomovirus-kenaf host-pathosystem

Yellow vein mosaic disease of mesta, a compatible plant virus interaction poses a serious threat to mesta cultivation in India. Plants respond to invasion by pathogens with multi component defense responses particularly in incompatible interaction. With the aim of understanding, a biochemical approach was attempted to study the cellular redox status in early stages of yellow vein mosaic virus infection associated with different age's plant of Hibiscus cannabinus. Comparative analysis of GSH and GSSG content in infected and control plant of different ages indicated that infected plants are under oxidative or nitrosative stress condition. A significant change was observed in Glutathione Reductase, Catalase and Ascorbate Peroxidase level in early stage of infection. We also showed microscopic evidence of nitrosylated thiols in infected leaves, stems and roots of H. cannabinus. Furthermore, we identified few defense related proteins in infected plant using MALDI TOF mass spectrometric analysis.

Both malvaceous and non-malvaceous betasatellites are associated with two wild cotton species grown under field conditions in Pakistan

Betasatellites are symptom-modulating DNA satellites that are associated with the majority of monopartite begomoviruses in the Old World. Betasatellites show both geographical and host-specific relatedness; those isolated from malvaceous hosts form one group and those isolated from non-malvaceous hosts form the second group. Real-time PCR based estimation of begomovirus DNA in cotton species grown in a living herbarium under field conditions at the Central Cotton Research Institute (CCRI), Multan was carried out to understand their role in the ongoing cotton leaf curl disease (CLCuD) epidemic in Pakistan. The levels of begomovirus DNA in cotton species from the herbarium was found to be several folds lower than symptomatic plants of commercially grown cotton. Among herbarium species Gossypium anomalum, G. robinsoni and G. somalense contained higher levels of begomovirus DNA in comparison to other wild species. Characterization of betasatellites from two cotton species (G. anomalum and G. somalense) was carried out to understand their role in accumulation of begomovirus DNA. Here, we show that the two wild species of cotton are associated with Cotton leaf Multan betasatellite (CLCuMB), a malvaceous betasatellite associated with CLCuD, as well as Chili leaf curl betasatellite, a non-malvaceous betasatellite not previously identified in a malvaceous host. This is the first evidence of the presence of a non-malvaceous betasatellite in malvaceous hosts.

Production of nitric oxide in host-virus interaction: a case study with a compatible Begomovirus-Kenaf host-pathosystem

Nitric oxide (NO) plays a key role in plant diseases resistance. Here we have first time demonstrated that begomovirus infection in susceptible H. cannabinus plants, results in elevated NO and reactive nitrogen species production during early infection stage not only in infected leaf but also in root and shoot. Production of NO was further confirmed by oxyhemoglobin assay. Furthermore, we used Phenyl alanine ammonia lyase as marker of pathogenesis related enzyme. In addition evidence for protein tyrosine nitration during the early stage of viral infection clearly showed the involvement of nitrosative stress.

Distribution, epidemiology and molecular variability of the begomovirus complexes associated with yellow vein mosaic disease of mesta in India

Yellow vein mosaic disease of mesta (Hibiscus spp.) poses a serious threat to the cultivation of this crop in India. The disease was found to be associated with two different whitefly-transmitted monopartite begomoviruses, Mesta yellow vein mosaic virus and Mesta yellow vein mosaic Bahraich virus, together with two betasatellite species, Cotton leaf curl Multan betasatellite and Ludwigia leaf distortion betasatellite. These begomovirus complexes were detected in different combinations throughout the mesta growing regions of India. All the eight cultivars tested were highly susceptible to the disease. The effect of the disease in terms of loss in fibre yield was greatest (around 70%) in plants that were inoculated at an early stage of growth. A regression approach was adopted to consider the relationship of whitefly vector populations with weather conditions and disease spread which explained that different conducive weather factors facilitated the build up of whitefly populations and contributed to the spread of the disease.