Diversity and phylogeography of begomovirus-associated beta satellites of okra in India

<p>Abstract</p> <p>Background</p> <p>Okra (<it>Abelmoschus esculentus</it>; family <it>Malvaceae</it>) is grown in temperate as well as subtropical regions of the world, both for human consumption as a vegetable and for industrial uses. Okra yields are affected by the diseases caused by phyopathogenic viruses. India is the largest producer of okra and in this region a major biotic constraint to production are viruses of the genus <it>Begomovirus</it>. Begomoviruses affecting okra across the Old World are associated with specific, symptom modulating satellites (beta satellites). We describe a comprehensive analysis of the diversity of beta satellites associated with okra in India.</p> <p>Results</p> <p>The full-length sequences of 36 beta satellites, isolated from okra exhibiting typical begomovirus symptoms (leaf curl and yellow vein), were determined. The sequences segregated in to four groups. Two groups correspond to the beta satellites Okra leaf curl beta satellite (OLCuB) and Bhendi yellow vein beta satellite (BYVB) that have previously been identified in okra from the sub-continent. One sequence was distinct from all other, previously isolated beta satellites and represents a new species for which we propose the name Bhendi yellow vein India beta satellite (BYVIB). This new beta satellite was nevertheless closely related to BYVB and OLCuB. Most surprising was the identification of Croton yellow vein mosaic beta satellite (CroYVMB) in okra; a beta satellite not previously identified in a malvaceous plant species. The okra beta satellites were shown to have distinct geographic host ranges with BYVB occurring across India whereas OLCuB was only identified in northwestern India. Okra infections with CroYVMB were only identified across the northern and eastern central regions of India. A more detailed analysis of the sequences showed that OLCuB, BYVB and BYVIB share highest identity with respect βC1 gene. βC1 is the only gene encoded by beta satellites, the product of which is the major pathogenicity determinant of begomovirus-beta satellite complexes and is involved in overcoming host defenses based on RNAi.</p> <p>Conclusion</p> <p>The diversity of beta satellites in okra across the sub-continent is higher than previously realized and is higher than for any other malvaceous plant species so far analyzed. The beta satellites identified in okra show geographic segregation, which has implications for the development and introduction of resistant okra varieties. However, the finding that the βC1 gene of the major okra beta satellites (OLCuB, BYVB and BYVIB) share high sequence identity and provides a possible avenue to achieve a broad spectrum resistance.</p

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Not AvailableOkra samples showing yellow vein mosaic, vein twisting and bushy appearance were collected from different locations of India during the surveys conducted between years 2005–2009. The dot blot and PCR detection revealed that 75.14% of the samples were associated with monopartite begomovirus and remaining samples with bipartite virus. Whitefly transmission was established for three samples representing widely separated geographical locations which are negative to betasatellites and associated with DNA-B. Genome components of these three representative isolates were cloned and sequenced. The analysis of DNA-A-like sequence revealed that three begomovirus isolates shared more than 93% nucleotide sequence identity with bhendi yellow vein mosaic virus from India (BYVMV), a monopartite begomovirus species that was reported previously as causative agent of bhendi yellow mosaic disease in association of bhendi yellow vein mosaic betasatellite. Further, the DNA-B-like sequences associated with the three virus isolates shared no more than 90% sequence identity with tomato leaf curl New Delhi virus (ToLCNDV). Analyses of putative iteron-binding sequence required for trans-replication suggests that begomovirus sequences shared compatible rep-binding iterons with DNA-B of ToLCNDV. Our data suggest that the monopartite begomovirus associated with okra yellow vein disease has captured DNA-B of ToLCNDV to infect okra. Widespread distribution of the complex shows the increasing trend of the capturing of DNA-B of ToLCNDV by monopartite begomoviruses in the Indian subcontinent. The recombination analysis showed that the DNA-A might have been derived from the inter-specific recombination of begomoviruses, while DNA-B was derived from the ToLCNDV infecting different hosts.Not Availabl

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Not AvailableYellow vein mosaic disease of okra is a whitefly transmitted begomovirus causing heavy economic loss in different parts of India. The okra isolate (OY131) of this virus from a bhendi plant [(Abelmoschus esculentus L.) Moench] showing yellow vein mosaic, vein twisting, reduced leaves, and a bushy appearance in the Palem region, New Delhi, India, was characterized in the present study. The complete DNA-A and DNA-B sequences have been determined and are comprised of 2,746 and 2,703 nucleotides, respectively. The betasatellite (DNA-b) component was absent in the sample. The genome organization was typically of biparite begomoviruses, which were characterized earlier. Comparison of DNA-A component with other known begomoviruses suggest that this virus, being only distantly related (85.9% similarity with its nearest relative, BYVMV) to other known begomoviruses, is a new species. We have tentatively assigned the genome to a novel geminivirus species Bhendi yellow vein mosaic Delhi virus [BYVDV - IN (India: Delhi: okra)]. DNA-B showed highest sequence identity (87.8% identical) to that of a ToLCNDV (AY158080). The phylogenetic analysis of the present isolate is distinct from all other viruses; however clusters with ToLCNDV group infect different crops. The recombination analysis revealed that this isolate has sequences originated from ToLCNDV. This is the first known bhendi yellow vein mosaic disease associated bipartite begomovirus from India.Not Availabl

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Not AvailableThe symptoms of chlorotic ring spots and irregular chlorotic patches were recently observed on leaves of landscape-grown jasmine (Jasminum multiflorum Roth) in southern parts of India. The causal agent was mechanically transmitted from symptomatic leaves of jasmine to Nicotiana glutinosa, Capsicum annum, Solanum lycopersicum, Cucurbita pepo and Cucumis sativus. Leaf dip preparations from virus-infected plants in electron microscopy revealed the presence of isometric particles similar to Cucumber mosaic virus (CMV) and bacilliform virus particles of badnavirus. The virus reacted specifically with IgG for CMV and Banana streak virus (BSV) in direct antigen coating, enzyme-linked immunosorbent assay. No reaction was observed with ilar-, poty- and tospo-viruses specific IgG. Reverse transcription polymerase chain reaction with total RNA isolated from symptomatic jasmine leaves and infected N. tabacum 'Xanthi' using CMV coat protein (CMV CP) specific primers amplified the expected product. The association of badna virus with jasmine was confirmed by PCR amplification, cloning and sequencing of 560 bp amplicon corresponding to the reverse transcriptase and ribonuclease H coding region in open reading frame III. The sequence analysis revealed maximum identity to badna virus group Diascorea bacilliform virus (88.5% at nt level) and CMV group IB (96% at nt level). To our knowledge, this is the first report of CMV and badna mixed infection in jasmine in India.Not Availabl

Identification of mixed infection caused by Badnavirus and CMV in Jasmine (<em>Jasminum multiflorum</em> Roth)

437-439The symptoms of chlorotic ring spots and irregular chlorotic patches were recently observed on leaves of landscape-grown jasmine (Jasminum multiflorum Roth) in southern parts of India. The causal agent was mechanically transmitted from symptomatic leaves of jasmine to Nicotiana glutinosa, Capsicum annum, Solanum lycopersicum, Cucurbita pepo and Cucumis sativus. Leaf dip preparations from virus-infected plants in electron microscopy revealed the presence of isometric particles similar to Cucumber mosaic virus (CMV) and bacilliform virus particles of badnavirus. The virus reacted specifically with IgG for CMV and Banana streak virus (BSV) in direct antigen coating, enzyme-linked immunosorbent assay. No reaction was observed with ilar-, poty- and tospo-viruses specific IgG. Reverse transcription polymerase chain reaction with total RNA isolated from symptomatic jasmine leaves and infected N. tabacum 'Xanthi' using CMV coat protein (CMV CP) specific primers amplified the expected product. The association of badna virus with jasmine was confirmed by PCR amplification, cloning and sequencing of 560 bp amplicon corresponding to the reverse transcriptase and ribonuclease H coding region in open reading frame III. The sequence analysis revealed maximum identity to badna virus group Diascorea bacilliform virus (88.5% at nt level) and CMV group IB (96% at nt level). To our knowledge, this is the first report of CMV and badna mixed infection in jasmine in India

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Not AvailableA begomovirus isolate (OY136A) collected from okra plants showing upward leaf curling, vein clearing, vein thickening and yellowing symptoms from Bangalore rural district, Karnataka, India was characterized. The sequence comparisons revealed that, this virus isolate share highest nucleotide identity with isolates of Cotton leaf curl Bangalore virus (CLCuBV) (AY705380) (92.8 %) and Okra enation leaf curl virus (81.1–86.2 %). This is well supported by phylogentic analysis showing, close clustering of the virus isolate with CLCuBV. With this data, based on the current taxonomic criteria for the genus Begomovirus, the present virus isolate is classified as a new strain of CLCuBV, for which CLCuBV-[India: Bangalore: okra: 2006] additional descriptor is proposed. The betasatellite (KC608158) associated with the virus is having more than 95 % sequence similarity with the cotton leaf curl betasatellites (CLCuB) available in the Gen- Bank.The recombination analysis suggested, emergence of this new strain of okra infecting begomovirus might have been from the exchange of genetic material between BYVMV and CLCuMuV. The virus was successfully transmitted by whitefly and grafting. The host range of the virus was shown to be very narrow and limited to two species in the family Malvaceae, okra (Abelmoschus esculentus) and hollyhock (Althaea rosea), and four in the family Solanaceae.Not Availabl

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Not AvailableTwo virus isolates (OY77 and OY81B) from okra plants showing yellow vein mosaic, downward curling and vein twisting symptoms were collected from different farmer’s fields in Karnal, Haryana state, India. The genomes of the two isolates were amplified, cloned, sequenced and analysed. The analysis indicated that the isolates are similar with 89.2% nucleotide sequence identity. Based on the current threshold cut-off value for taxonomy distinguishing the genus begomoviruses species from strains, the two isolates are designated as strains of Cotton leaf curl Alabad virus (CLCuAV) which shared nucleotide sequence identity of 490% with CLCuAV infecting cotton in Pakistan. Phylogenetic and recombination analyses of the major genome component of OY77 and OY81B is derived from different begomviruses (CLCuAV, BYVMV, CLCuMuV) as the foremost parents for evolution of these new recombinant strains.Not Availabl

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Not AvailableAn unusual symptom was noted in okra originating from Haryana state (India) consisting of leaf curl associated with enations. These were distinct from the leaf curl and/or vein yellowing symptoms usually shown by okra. PCR-mediated amplification was used to show the presence of a begomovirus and the complete genome sequences were determined for seven isolates. The sequences showed high levels of nucleotide sequence identity (91.9–99.1 %). In comparison to begomovirus sequences available in the databases the okra sequences showed the highest levels of nucleotide sequence identity (84.5 to 87.1 %) with Mesta yellow vein mosaic virus (MeYVV) and thus were classified as belonging to a novel begomovirus species, tentatively named Okra enation leaf curl virus. In common with the majority of begomoviruses, Okra enation leaf curl virus (OELCuV) was shown to have a recombinant origin. Analysis of the transmission characteristics of a wild-type virus isolate by Bemisia tabaci showed the minimum acquisition access period to be 1 h and the minimum inoculation access period to be 30 min, with female insects transmitting with a greater efficiency than male insects. Under controlled conditions the host range of the virus was shown to be very narrow, limited to two species in the family Malvaceae, okra (Abelmoschus esculentus) and hollyhock (Althaea rosea), and seven in the family Solanaceae.Not Availabl

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Not AvailableBackground: Okra (Abelmoschus esculentus; family Malvaceae) is grown in temperate as well as subtropical regions of the world, both for human consumption as a vegetable and for industrial uses. Okra yields are affected by the diseases caused by phyopathogenic viruses. India is the largest producer of okra and in this region a major biotic constraint to production are viruses of the genus Begomovirus. Begomoviruses affecting okra across the Old World are associated with specific, symptom modulating satellites (beta satellites). We describe a comprehensive analysis of the diversity of beta satellites associated with okra in India. Results: The full-length sequences of 36 beta satellites, isolated from okra exhibiting typical begomovirus symptoms (leaf curl and yellow vein), were determined. The sequences segregated in to four groups. Two groups correspond to the beta satellites Okra leaf curl beta satellite (OLCuB) and Bhendi yellow vein beta satellite (BYVB) that have previously been identified in okra from the sub-continent. One sequence was distinct from all other, previously isolated beta satellites and represents a new species for which we propose the name Bhendi yellow vein India beta satellite (BYVIB). This new beta satellite was nevertheless closely related to BYVB and OLCuB. Most surprising was the identification of Croton yellow vein mosaic beta satellite (CroYVMB) in okra; a beta satellite not previously identified in a malvaceous plant species. The okra beta satellites were shown to have distinct geographic host ranges with BYVB occurring across India whereas OLCuB was only identified in northwestern India. Okra infections with CroYVMB were only identified across the northern and eastern central regions of India. A more detailed analysis of the sequences showed that OLCuB, BYVB and BYVIB share highest identity with respect bC1 gene. bC1 is the only gene encoded by beta satellites, the product of which is the major pathogenicity determinant of begomovirus-beta satellite complexes and is involved in overcoming host defenses based on RNAi. Conclusion: The diversity of beta satellites in okra across the sub-continent is higher than previously realized and is higher than for any other malvaceous plant species so far analyzed. The beta satellites identified in okra show geographic segregation, which has implications for the development and introduction of resistant okra varieties. However, the finding that the bC1 gene of the major okra beta satellites (OLCuB, BYVB and BYVIB) share high sequence identity and provides a possible avenue to achieve a broad spectrum resistance.Not Availabl