Identification of two putative novel deltapartitiviruses and an enamovirus in coriander transcriptomes

Coriander is a herbaceous spice and condiment crop also known for its medicinal properties. The present study identified two putative novel deltapartitiviruses and an enamovirus tentatively named as Coriandrum sativum deltapartitivirus 1, 2 (CsDPV1, 2) and Coriandrum sativum enamovirus (CsEV) in the publicly available transcriptome-assembled contigs derived from coriander grown in India. CsDPV1 and 2 contained tripartite and bipartite genomes, respectively, with each genome segment encoding a single open reading frame (ORF). CsEV contained five ORFs encoding proteins P0, P1, P2, P3 and P5. Phylogenetic analysis revealed three distinct subgroups of deltapartitiviruses wherein CsDPV1 and 2 grouped in subgroup 3 and 1, respectively, whilst CsEV formed a distinct sub-clade within enamoviruses. Further, the presence of CsDPV2 in fruit samples of one of the cultivars from where the virus was identified was confirmed through RT-PCR assay and Sanger sequencing. The study highlights the need for further studies on understanding the importance and the biological properties of identified novel viruses.

Identification of a putative novel cholivirus in the transcriptome of Gymnema sylvestre R. Br

Gymnema sylvestre is a tropical climber species that is widely used in traditional medicine since ages. In the present study, the transcriptome datasets of G. sylvestre available in public domain were screened for the presence of novel plant viral sequences and a putative novel virus tentatively named as Gymnema sylvestre virus 1 (GysV1) was identified. Coding-complete genome segments of GysV1 that are 6.35 kb (RNA1) and 3.98 kb (RNA2) long possessed a single large open reading frame coding for a polyprotein. BLASTp, sequence identity and phylogenetic analyses revealed the relatedness of GysV1 to the members of the subgenus Cholivirus (genus Sadwavirus; family Secoviridae; order Picornavirales). Based on the species demarcation criteria of the family Secoviridae, GysV1 can be regarded as a new cholivirus member.

Broadening the host range and genetic diversity of waikaviruses

Waikaviruses are monopartite, positive sense, single-stranded RNA viruses that cause economically important plant diseases. Despite their importance, waikaviruses are poorly understood and only ten members are currently recognized. The present study on Sequence Read Archive (SRA)-based data-driven virus discovery (DDVD) identified 22 putative new waikaviruses, nearly doubling the number of known waikaviruses, in SRA libraries of diverse plant species, from ferns to trees. Besides, a highly divergent secoviral sequence with distinct genome features was identified in a wheat transcriptome. Other significant findings of the study include identification of a new waikavirus in a library derived from diseased water chestnut sample wherein a caulimovirus was reported, prediction of coiled-coils in hypothetical protein region of waikaviral polyprotein alignment and phylogenetic clustering of tree-infecting waikaviruses. The study not only reiterates the importance of DDVD in unveiling hitherto hidden viral sequences in plant SRA libraries but also deepens our understanding of waikaviral diversity.

Production of polyclonal antibodies against leek yellow stripe virus (LYSV) coat protein expressed in Escherichia coli and its application in serological diagnostics

Leek yellow stripe virus (LYSV) is one of the most important potyviruses, associated with garlic throughout the world, including India. LYSV causes stunting and yellow streaks in garlic and leek leaves and with other coinfecting viruses leading to severe symptom expression and yield reduction. In this study, we have made the first reported attempt to produce specific polyclonal antibodies to LYSV using expressed recombinant coat protein (CP), which would be useful for screening and routine indexing of the garlic germplasm. The CP gene was cloned, sequenced, and further subcloned in pET-28a(+) expression vector, which yielded ∼35 kDa fusion protein. The fusion protein was obtained in insoluble fraction after purification and its identity was confirmed by SDS-PAGE and western blotting. The purified protein was used as immunogen for production of polyclonal antisera in New Zealand white rabbit. Antisera raised, was able to recognize the corresponding recombinant proteins in western blotting, immunosorbent electron microscopy and dot immunobinding assay (DIBA). Developed antisera to LYSV (titer 1:2000) was used for screening of 21 garlic accessions in antigen coated plate enzyme-linked immunosorbent assay (ACP-ELISA) and 16 accessions were found positive for LYSV, indicating its widespread presence within the collection tested. To the best of our knowledge, this is the first report of a polyclonal antiserum against the in-vitro expressed CP of LYSV and its successful application in diagnosis of LYSV in garlic accessions in India.

Revisiting the amalgaviral landscapes in plant transcriptomes expands the host range of plant amalgaviruses

Plant amalgaviruses are monopartite, double-stranded RNA viruses, capable of vertical transmission through seeds. An attempt to revisit plant transcriptome-assembled contigs for amalgaviral sequences identified 40 putative novel amalgaviruses in 35 plant species, nearly doubling the number of plant amalgaviruses. Of the 35 plant species, 33 are reported to host amalgaviruses for the first time, including a pteridophytic and two gymnospermic species. Coding-complete genomes of all identified viruses were recovered and the putative +1 programmed ribosomal frameshift (PRF) sites were determined. Genomes of 35 identified amalgaviruses contained the conserved +1 PRF motif 'UUU_CGN', while variant versions were predicted in five genomes. Phylogenetic analysis grouped pteridophyte- and gymnosperm-infecting amalgaviruses together in divergent sub-clades while few of the related angiosperm-infecting amalgaviruses infect members of the same plant family, reiterating the co-evolution of plant amalgaviruses and their hosts. The current study paves way for further studies on understanding biological properties of identified viruses.

Exploration of plant transcriptomes reveals five putative novel poleroviruses and an enamovirus

Transcriptome datasets available in public domain serve as valuable resource for identification and characterization of novel viral genomes. Poleroviruses are economically important plant-infecting RNA viruses belonging to the family Solemoviridae. In the present study, we explored the plant transcriptomes available in public domain and identified five putative novel poleroviruses tentatively named as Foeniculum vulgare polerovirus (FvPV), Kalanchoe marnieriana polerovirus (KmPV), Paspalum notatum polerovirus (PnPV), Piper methysticum polerovirus (PmPV), Trachyspermum ammi polerovirus (TaPV) and a novel enamovirus named as Celmisia lyallii enamovirus (ClEV) in Foeniculum vulgare, Kalanchoe marnieriana, Paspalum notatum, Piper methysticum, Trachyspermum ammi and Celmisia lyallii, respectively. Coding-complete genomes (5.56-5.74 kb) of CIEV, KmPV, PnPV, PmPV and TaPV were recovered while only the partial genome of FvPV could be recovered. The genome organization of identified viruses except ClEV is 5'-ORF0-ORF1-ORF2-ORF3a-ORF3-ORF4-ORF5-3' while that of ClEV is 5'-ORF0-ORF1-ORF2-ORF3-ORF5-3'. Phylogenetic analysis revealed that poleroviruses of apiaceous plants formed a monophyletic clade within the genus Polerovirus.

Discovery of putative novel viruses in the transcriptomes of endangered plant species native to India and China

Viruses are abundant entities that infect almost every living organism. In recent years, Next Generation Sequencing coupled with bioinformatic analyses is widely adopted for identification of known and unknown viruses in a plant sample. In the present study, nine putative novel viruses were discovered from public domain transcriptome datasets of five endangered plant species by de novo assembly of reads using CLC and SPAdes followed by BLAST analysis. Of the identified viruses, ten coding-complete and five partial genomic segments were recovered. Based on phylogeny and BLAST analysis, the identified viruses were putatively assigned to various plant viral genera except dactylorhiza hatagirea benylike virus that probably represents a new group of plant virus. The methodology followed can be adopted for the discovery of novel viruses in plant species with little genomic information. Viral genome sequences recovered in the study will serve as a valuable resource for further characterization of identified viruses.

Complete genome sequence and genetic organization of a Garlic virus D infecting garlic (Allium sativum) from northern India

The present paper describes first full genome sequence of the Garlic virus D (GarV-D) from northern India with a genome size of 8425 bp long ssRNA. The infected leaves and bulbs of garlic variety Yamuna Safed (G-282) plants suspected for GarV-D infection were collected with the aim to identify contagion virus during March, 2018. The total RNA was extracted from the pooled garlic plants using TRIzol reagent and sequenced using an Illumina HiSeq 2000 platform. BLASTn search in the NCBI database identified contagion as GarV-D (MK518067). It shared 83.63-85.83% nucleotide sequence identities with other (GarV-D) isolates from Argentina (KF550407, KF555653, KR819505) and 83.15% with isolates from China (MF795136, MF363012). Keywords: Allium sativum; Allexivirus; Garlic virus D; India.

Robust Virome Profiling and Whole Genome Reconstruction of Viruses and Viroids Enabled by Use of Available mRNA and sRNA-Seq Datasets in Grapevine (Vitis vinifera L.)

Next-generation sequencing (NGS) based virome analyses of mRNA and sRNA have recently become a routine approach for reliable detection of plant viruses and viroids. In the present study we identified the viral/viroidal spectrum of several Indian grapevine cultivars and reconstructed their whole genomes using the publically available mRNAome and sRNAome datasets. Twenty three viruses and viroids (including two variants of grapevine leafroll associated virus 4) were identified from two tissues (fruit peels and young leaves) of three cultivars among which nine unique grapevine viruses and viroids were identified for the first time in India. Irrespective of the assemblers and tissues used, the mRNA based approach identified more acellular pathogens than the sRNA based approach across cultivars. Further, the mRNAome was on par with the whole transcriptome in viral identification. Through de novo assembly of transcriptomes followed by mapping against reference genome, we reconstructed 19 complete/near complete genomes of identified viruses and viroids. The reconstructed viral genomes included four larger RNA genomes (>13 kb), a DNA genome (RG grapevine geminivirus A), a divergent genome (RG grapevine virus B) and a genome for which no reference is available (RG grapevine virus L). A large number of SNPs detected in this study ascertained the quasispecies nature of viruses. Detection of three recombination events and phylogenetic analyses using reconstructed genomes suggested the possible introduction of viruses and viroids into India from several continents through the planting material. The whole genome sequences generated in this study can serve as a resource for reliable indexing of grapevine viruses and viroids in quarantine stations and certification programs.

Development of RT-PCR degenerate primers for the detection of two mandariviruses infecting citrus cultivars in India

Indian citrus ringspot virus (ICRSV) and Citrus yellow vein clearing virus (CYVCV) are the mandariviruses infecting various citrus cultivars in India and around the world. In the fields, it was observed that citrus plants infected by both the viruses and frequently expressed only ringspot symptoms. The ICRSV-specific polyclonal-antibody used in immuno-sorbent electron microscopy (ISEM) and enzyme linked immuno-sorbent assay (ELISA) could detect only ICRSV in mixed infections. Therefore, the conserved sequences of the RNA dependent RNA polymerase (RdRP) gene of the alphaflexiviruses were exploited for developing a RT-PCR based assay for detection of both the mandariviruses simultaneously, if present. A degenerate primer pair was designed to amplify a ∼435bp fragment by multiple alignments of the RdRP gene sequences of the members of genera Mandarivirus, Potexvirus and Allexivirus. The developed RT-PCR assay was validated for detecting both, CYVCV and ICRSV in mixed infections as well as in single virus-infected citrus plants. The presence of ICRSV or CYVCV or both of them together in such plants were confirmed by using primer pair specific to each of these viruses. Further, the identity of the amplicons was confirmed by sequencing and the virus species were determined with BLASTN analysis. The degenerate primers also amplified the corresponding target sequences of an allexivirus and a potexvirus from the respective infected garlic/ onion and tobacco plants. The use of the degenerate primers for the detection of these virus species of the genus Mandarivirus will be useful in citrus certification programmes.

Updated inventory, evolutionary and expression analyses of G (PDR) type ABC transporter genes of rice

ABC transporters constitute the largest family of transporter proteins in living organisms and divided into eight subfamilies, from A-H. ABCG members, specific to plants and fungi, belong to subfamily G. In this study, we provide updated inventory, detailed account of phylogeny, gene structure characteristics, and expression profiling during reproductive development, abiotic and biotic stresses of members of ABCG gene family in rice along with reannotation and cloning of FL-cDNA of OsABCG50/PDR23. We observed that of the 22 ABCGs/PDRs, four genes evolved as a result of gene duplication events and their expression pattern changed after duplication. Analysis of expression revealed seed and developmental stage preferential expression of five ABCG/PDR members. Transcript levels of eight ABCGs/PDRs were affected by abiotic and biotic stresses. Expression of seven ABCG/PDR genes was also altered by hormonal elicitors. The modulated expression is nicely correlated with the presence of tissue/stress specific cis-acting elements present in putative promoter region.

Genome characterization of citrus yellow vein-clearing virus: limited heterogeneity of viral genomes in Mandarivirus-infecting different citrus species

Citrus yellow vein-clearing virus (CYVCV) is a mandarivirus infecting citrus producing yellow vein-clearing symptoms. The leaf samples collected during surveys of different citrus-growing areas in India exhibited diverse symptoms and 40% of the plants were positive for CYVCV in RT-PCR, indicating the wide distribution of the virus in India. It was reported for first time that CYVCV infects kinnow mandarin and sweet oranges and produces chlorotic ringspots symptoms identical to Indian citrus ringspot virus (ICRSV). The complete genome sequences of CYVCV infecting four citrus cultivars have been deciphered through overlapping primers. All the four genomes comprise of 7531 nucleotides excluding the 3' poly (A) tail. The sequence identity of genomes of four CYVCV isolates in the present study ranged from 95.2 to 99.8% with genome sequences of 31 CYVCV isolates available in public domain and the mean genomic diversity was 0.017, indicating low level of heterogeneity. The phylogenetic analysis revealed that CYVCV isolates from India, Pakistan, and Turkey were clustered in the same clad apart from China isolates. The least normalized dN/dS mean value (0.092) indicated that RdRP region evolved under relatively stronger selection constraints than the other five coding regions of CYVCV. The four intragenic putative recombination events detected in RDP4 program occurred naturally in CYVCV genome, indicating the evolutionary progress of the virus. Tajima's and Fu and Li's D parameters were performed using genomic sequences in DnaSP v5 program and the retrieved negative values indicated the presence of limited genetic variability in CYVCV genomes. To the best of our knowledge, this is the first comprehensive report on molecular characterization of CYVCV from India. It will be helpful in understanding the evolutionary relationship of CYVCV and ICRSV.

Changes in salivary output after induction at high-altitude areas and its effects on dental caries among Indian Army troops

BACKGROUND

This study was aimed to evaluate the changes in salivary output and its effect on dental caries among Indian troops after 6 months of stay at high-altitude area (HAA).

METHODS

All troops undergo mandatory dental checkup during acclimatization phase before deployment at HAA. Two thousand troops who fulfilled inclusion and exclusion criteria were selected, and consent for the study was obtained. Stimulated and unstimulated salivary samples were collected, the decayed, missing, and filled teeth (DMFT) index was evaluated, and required dental treatment was completed. The same salivary samples were collected after 6 months (on deinduction) to evaluate the salivary output. The DMFT index was re-evaluated to check the initiation of caries.

RESULTS

The mean values of unstimulated and stimulated saliva at the initial visit were 4.105 and 17.03 gm, respectively, whereas the mean values of unstimulated and stimulated saliva after 180 days were 3.034 and 15.831 gm, respectively. Salivary flow was found to be significantly decreased after 6 months both in unstimulated and stimulated saliva. The mean DMFT at the time of induction of the study was 6.18 ± 3.03, and on deinduction, it was 7.22 ± 3.45 with p < 0.001, which was highly statistically significant.

CONCLUSION

A decrease in body fluids and changed sympathetic and parasympathetic at HAA lead to decreased salivary secretions. Low water intake, high carbohydrate solid diet, negligible supply of fresh food, difficulty in maintenance of oral hygiene, and overall stress due to loneliness are all contributory factors for an increase in dental caries. It clearly demonstrates that prolonged stay at HAA affects salivary volume outflow, both stimulated and unstimulated, which has a corresponding effect on new caries.

Change in subfoveal choroidal thickness in diabetes and in various grades of diabetic retinopathy

Background

To evaluate subfoveal choroidal thickness (SFCT) change in diabetes and in various grades of diabetic retinopathy (DR) in comparison to age-matched healthy subjects.

Methods

This prospective observational study included 100 eyes of diabetic patients without DR (group D), 100 eyes with DR (group R), and 100 eyes of healthy subjects (group N). The assessment included demographics, duration of diabetes, comprehensive ocular examination, fundus photography with/without fundus fluorescein angiography, spectral domain optical coherence tomography with enhanced depth imaging to assess SFCT.

Results

The SFCT was comparable between groups N (310.65 ± 37.34 µm) and D (308.48 ± 30.06 µm; P = 0.60), but was significantly lower in R (296.52 ± 21.41 µm; P < 0.01). The SFCT was significantly lower in proliferative DR (n = 36; SFCT = 284.56 ± 21.09 µm) as compared to non-proliferative DR (n = 64; SFCT = 303.25 ± 18.59 µm; P < 0.001). The SFCT had moderately negative correlation with severity of DR (R = − 0.50; P < 0.01). The difference in SFCT when compared with normal subjects was significant only in severe/very severe non-proliferative DR (294.47 ± 15.65 µm; P < 0.01) and in proliferative DR (284.56 ± 21.09 µm; P < 0.01). There was a negative correlation of SFCT with the duration of diabetes (R = − 0.41; P < 0.01).

Conclusion

SFCT decreases with increasing duration of diabetes. The decrease is significant after the onset of severe DR, and is proportionate to the severity of DR.

PNEUMATIC RETINOPEXY IN RHEGMATOGENOUS RETINAL DETACHMENT

Existing surgical modes for retinal detachment are elaborate and extremely complex. We have treated 20 cases of rhegmatogenous retinal detachment with pneumatic retinopexy which is Iess time consuming and does not require hospitalization. After pneumatic retinopexy reattachment of retina was achieved in 15 (75%) eyes. In 2 eyes retinal reattachment was achieved after repeating intravitreal injection of sulphur hexafluoride gas. Remaining 3 eyes were secondarily treated with scleral buckle surgery. One case needed vitreoretinal surgery. In pneumatic retinopexy there is minimum tissue handling and functional results are good.

First record of Pepper cryptic virus 2 in chilli (Capsicum annuum) in India

The occurrence of Pepper cryptic virus 2 was confirmed by RT-PCR and partial sequencing of coat protein gene in chilli cultivars Jwalamukhi and Jwalasakhi grown in the experimental farm at IARI, New Delhi. To the best of our knowledge this is the first report of occurrence of cryptovirus in chilli in India.

Simultaneous Detection of Brown Rot- and Soft Rot-Causing Bacterial Pathogens from Potato Tubers Through Multiplex PCR

Ralstonia solanacearum (Smith) Yabuuchi et al. and Erwinia carotovora subsp. carotovora (Jones) Bergey et al. (Pectobacterium carotovorum subsp. carotovorum) are the two major bacterial pathogens of potato causing brown rot (wilt) and soft rot diseases, respectively, in the field and during storage. Reliable and early detection of these pathogens are keys to avoid occurrence of these diseases in potato crops and reduce yield loss. In the present study, multiplex polymerase chain reaction (PCR) protocol was developed for simultaneous detection of R. solanacearum and E. carotovora subsp. carotovora from potato tubers. A set of oligos targeting the pectatelyase (pel) gene of E. carotovora subsp. carotovora and the universal primers based on 16S r RNA gene of R. solanacearum were used. The standardized multiplex PCR protocol could detect R. solanacearum and E. carotovora subsp. carotovora up to 0.01 and 1.0 ng of genomic DNA, respectively. The protocol was further validated on 96 stored potato tuber samples, collected from different potato-growing states of India, viz. Uttarakhand, Odisha, Meghalaya and Delhi. 53.1 % tuber samples were positive for R. solanacearum, and 15.1 % of samples were positive for E. carotovora subsp. carotovora, and both the pathogens were positive in 26.0 % samples when BIO-PCR was used. This method offers sensitive, specific, reliable and fast detection of two major bacterial pathogens from potato tubers simultaneously, particularly pathogen-free seed certification in large scale.

Identification and Expression Profiling of the Lectin Gene Superfamily in Mulberry

Lectins are a diverse group of ubiquitously present, highly specific sugar-binding proteins. Members of this large gene family have been assigned broad biological functions from defense to acting as storage proteins. Despite possessing several interesting characteristics, their functions remain essentially undefined. Mulberry ( spp.) known for its medicinal benefits is also a rich source of lectins. Using an exhaustive hidden Markov model (HMM)-based search, we identified the lectin gene complement in C.K. Schneid with around 197 members. These putative lectin genes were classified into 12 distinct gene families based on the presence of characteristic sugar-binding domains. Members of this superfamily were assigned varied gene ontologies (GOs) to identify putative functions and determine cellular localizations. Interestingly, characteristic expression patterns were observed across the lectin superfamily in response to a variety of environmental cues. This is suggestive of specialized functions under diverse conditions possibly by linking the specificity of sugar recognition with mediating precise stress responses in plants. The identification of putative gene family members from the genus developed in this study can find wide applicability in lectin gene identification and characterization. It can also contribute immensely in the understanding of lectins from mulberry with potential medicinal uses.

Development of multiplex polymerase chain reaction assay for simultaneous detection of clostero-, badna- and mandari-viruses along with huanglongbing bacterium in citrus trees

Citrus trees harbor a large number of viral and bacterial pathogens. Citrus yellow vein clearing virus (CYVCV), Indian citrus ringspot virus (ICRSV), Citrus yellow mosaic virus (CYMV), Citrus tristeza virus (CTV) and a bacterium, Candidatus Liberibacter asiaticus (CLa) associated with huanglongbing (HLB) disease, the most prevalent pathogens in citrus orchards of different regions in India and are responsible for debilitating citriculture. For detection of these viral and bacterial pathogens a quick, sensitive and cost effective detection method is required. With this objective a multiplex polymerase chain reaction (mPCR) assay was developed for simultaneous detection of four viruses and a bacterium in citrus. Several sets of primers were designed for each virus based on the retrieved reference sequences from the GenBank. A primer pair published previously was used for greening bacterium. Each pair of primers was evaluated for their sensitivity and differentiation by simplex and mPCR. The constant amplified products were identified on the basis of molecular size in mPCR and were compared with standard PCR. The amplicons were cloned and results were confirmed with sequencing analysis. The mPCR assay was validated using naturally infected field samples for one or more citrus viruses and the huanglongbing bacterium. The mPCR assay developed here will aid in the production of virus free planting materials and rapid indexing for certification of citrus budwood programme.

Incidence of Lettuce mosaic virus in lettuce and its detection by polyclonal antibodies produced against recombinant coat protein expressed in Escherichia coli

Lettuce mosaic virus (LMV), a member of the genus Potyvirus of family Potyviridae, causes mosaic disease in lettuce has recently been identified in India. The virus is seed borne and secondary infection occurs through aphids. To ensure virus freedom in seeds it is important to develop diagnostic tools, for serological methods the production of polyclonal antibodies is a prerequisite. The coat protein (CP) gene of LMV was amplified, cloned and expressed using pET-28a vector in Escherichia coli BL21DE3 competent cells. The LMV CP was expressed as a fusion protein containing a fragment of the E. coli His tag. The LMV CP/His protein reacted positively with a commercial antiserum against LMV in an immunoblot assay. Polyclonal antibodies purified from serum of rabbits immunized with the fusion protein gave positive results when LMV infected lettuce (Lactuca sativa) was tested at 1:1000 dilution in PTA-ELISA. These were used for specific detection of LMV in screening lettuce accessions. The efficacy of the raised polyclonal antiserum was high and it can be utilized in quarantine and clean seed production.

Comparative transcriptomics and comprehensive marker resource development in mulberry

BACKGROUND

High potential of Morus laevigata and Morus serrata has been proposed in the breeding programs for Morus sp. However, due to the lack of dense molecular markers this goal is still in its nascent stage and not yet realized. We thus, sequenced the transcriptomes of these two wild Morus species and utilized the data for marker development.

RESULTS

We generated 87.0 and 80.3 Mb of transcriptome data from M. laevigata and M. serrata, respectively. The transcriptomes from M. laevigata and M. serrata, were assembled into 95,181 and 85,269 transcripts, respectively, and annotated. We identified around 24,049 Simple Sequence Repeats (SSRs), 1,201,326 Single Nucleotide Polymorphisms (SNPs) and 67,875 Insertion-Deletions (InDels). The variants having a higher impact were also identified and their effect was further investigated.

CONCLUSIONS

The transcriptome resource from the wildly growing mulberry species developed in this study can find wide applicability in gene identification and/or characterization. It can also contribute immensely in the existing mulberry improvement programs.

Simultaneous detection of four garlic viruses by multiplex reverse transcription PCR and their distribution in Indian garlic accessions

Indian garlic is infected with Onion yellow dwarf virus (OYDV), Shallot latent virus (SLV), Garlic common latent virus (GarCLV) and allexiviruses. Identity and distribution of garlic viruses in various garlic accessions from different geographical regions of India were investigated. OYDV and allexiviruses were observed in all the garlic accessions, while SLV and GarCLV were observed only in a few accessions. A multiplex reverse transcription (RT)-PCR method was developed for the simultaneous detection and identification of OYDV, SLV, GarCLV and Allexivirus infecting garlic accessions in India. This multiplex protocol standardized in this study will be useful in indexing of garlic viruses and production of virus free seed material.

First Report of Grapevine leafroll-associated virus 1 Infecting Grapevines in India

Viticulture, one of the most remunerative farming enterprises of India, is seriously affected by leafroll disease, which accounts for 62% of the losses in grape production worldwide due to viral diseases (4). Grapevine leafroll-associated virus 3 and 1 (GLRaV-3 and GLRaV-1) of the family Closteroviridae are the two most common viruses associated with the leafroll disease of grapevine (1). GLRaV-3 was previously confirmed in India through RT-PCR, cloning, and sequencing (2). A survey was conducted during 2010 and 2011 in the Nashik and Pune regions of western India and reddening of interveinal areas and downward rolling, typical symptoms of leafroll disease in dark fruited cultivars, were observed, first in 2010 and subsequently in 2011. Fourteen leafroll symptomatic samples from seven cultivars of seven vineyards were collected during 2011. Samples were subjected to double antibody sandwich (DAS)-ELISA using commercially available antibodies against GLRaV-3 and GLRaV-1 (Bioreba, Reinach, Switzerland) (2). An asymptomatic sample from another cultivar of a different vineyard and samples from two plantlets of two different cultivars produced in tissue culture were used as negative controls. GLRaV-1 was detected in two cultivars, Shiraj (Nashik region) and Pinot Noir (Pune region) using DAS-ELISA. GLRaV-1 was detected either alone in cultivar Pinot Noir or as mixed infection with GLRaV-3 in cultivar Shiraj. To further confirm the presence of GLRaV-1 in these two cultivars, crude extract from petioles of these two cultivars were subjected to one step reverse transcription (RT)-PCR using GLRaV-1 specific primers pORF9F and pORF9R (GGCTCGAGATGGCGTCACTTATACCTA and CCTCTAGACACCAAATTGCTAGCGA, respectively) (3). The ˜650 bp amplicons were cloned in pGEM-T easy vector and three independent clones of each amplicon were sequenced in both directions. The cloned amplified product was 646 bp, including 630 bp of p24 protein (ORF9) of GLRaV-1. Comparative sequence analysis, using the BioEdit 7.0.3 program ( http://www.mbio.ncsu.edu/BioEdit/BioEdit.html ), of ORF9 of the virus under study from the cultivars Pinot Noir and Shiraj shared maximum sequence identity of 95.8 and 96.1%, respectively, at the nucleotide level with the Clatervine isolate from the United States (GenBank Accession No. HQ833477). The corresponding values of maximum identities at the amino acid level were 96.6 and 96.1%, respectively, with the same Clatervine isolate. The maximum identity between these two isolates of GLRaV-1 was 96.1% at nucleotide level and 95.7% at amino acid level. To the best of our knowledge, this study represents the first report of GLRaV-1 from India. Grape production in India could be impacted by this virus; thus, identification of the virus is important. References: (1) B. Akbas et al. Hort. Sc. (Prague). 36: 97, 2009. (2) S. Kumar et al. Virus Genes. 45:195, 2012. (3) A. Little and M. A. Rezaian. Arch. Virol. 151:753, 2006. (4) A. Little et al. Virus Res. 80:109, 2001.

First Report of Garlic virus X Infecting Garlic in India

Garlic (Allium sativum) is an important crop in several states of India. Filamentous viruses such as Onion yellow dwarf virus (OYDV), Shallot latent virus (SLV), and Garlic common latent virus (GarCLV) have been reported previously in different garlic cultivars from India (4). These viruses are transmitted from generation to generation through cloves and cause severe reduction in yield and quality. During December 2010, garlic plants were observed with mosaic leaf symptoms and stunting in an experimental field at the Indian Agricultural Research Institute, Delhi. Cloves and leaves from 3-month-old symptomatic plants of five different cultivars (G-282, IC-375416, Ruag, Yamuna Safed, and ACC-40), originally from different regions of India, were collected from the field in Delhi and total RNA was extracted using an RNeasy Plant Mini Kit (Qiagen, Valencia, CA). The presence of OYDV and GarCLV was confirmed by reverse transcription (RT)-PCR in all cultivars, while the presence of SLV was only confirmed in cv. G-282 by RT-PCR. Since Allexiviruses are common in garlic, their detection in cloves was confirmed by RT-PCR using primers ALLEX 1 and ALLEX 2 (2). An ~200-bp amplification product was observed in all five cultivars. To further characterize the Allexivirus in these cultivars, an amplicon of ~900 bp was amplified with Allex-CP (1) and ALLEX 2 (2) primers and cloned and sequenced. BLAST analysis of the nucleotide sequences from five garlic cultivars showed identity with different allexiviruses, Garlic virus A (GarV-A) (74 to 83%), Garlic virus E (GarV-E) (74 to 80%), Garlic virus D (GarV-D) (76 to 79%), and Garlic virus X (GarV-X) (75 to 78%). Since species demarcation in the genus Allexivirus is based on the coat protein (CP) gene (3), another set of primers, 5'-MYT KGA GTG GCT VAC ACA YAT-3' and 5'-ATT RAA GTC GTG RGG ATG CAT-3' was designed. These primers were derived from conserved regions of ORF4 and ORF5 (CP) sequences of allexiviruses available in the NCBI database and used in RT-PCR to obtain the complete CP. An ~1.5-kb amplicon was obtained only in cv. G-282 that originated from the southern part of India. A similar amplicon was obtained from Chenopodium amaranticolor mechanically inoculated with leaf sap from cv. G-282. Sequences (1,422 bp) obtained from three clones each from garlic cv. G-282 and C. amaranticolor were identical and BLAST analysis of the consensus nucleotide sequence showed maximum identity of 75 to 81% with isolates of GarV-X. The 1,422 nucleotide sequence was comprised of 690 bp of ORF4 (partial) and 732 bp of the CP. The coat protein sequence (GenBank Accession No. HQ822272) shared a 79.6 to 81.1% identity in nucleotide and 89.3 to 90.9% in amino acid sequence with different isolates of GarV-X (GenBank Accession Nos. AJ292229, U89243, and GQ475426). To our knowledge, this is the first report of GarV-X in a garlic cultivar from India. The characterization and identification of allexiviruses is important for production of virus-free garlic plants through tissue culture in India. References: (1) J. Chen et al. Arch. Virol. 149:435, 2004. (2) C. I. Dovas et al. J. Phytopathol.149:731, 2001. (3) C. M. Fauquet et al. Virus Taxonomy-VIIIth Report of the ICTV, Academic Press, London, 2005. (4) S. Majumder and V. K. Baranwal. Plant Dis. 93:106, 2009.

Sequence Comparison and Phylogeny of Nucleotide Sequence of Coat Protein and Nucleic Acid Binding Protein of a Distinct Isolate of Shallot virus X from India

Shallot virus X (ShVX), a type species in the genus Allexivirus of the family Alfaflexiviridae has been associated with shallot plants in India and other shallot growing countries like Russia, Germany, Netherland, and New Zealand. Coat protein (CP) and nucleic acid binding protein (NB) region of the virus was obtained by reverse transcriptase polymerase chain reaction from scales leaves of shallot bulbs. The partial cDNA contained two open reading frames encoding proteins of molecular weights of 28.66 and 14.18 kDa belonging to Flexi_CP super-family and viral NB super-family, respectively. The percent identity and phylogenetic analysis of amino acid sequences of CP and NB region of the virus associated with shallot indicated that it was a distinct isolate of ShVX.

Molecular Detection of 16SrXI Group Phytoplasma Associated with Root (Wilt) Disease of Coconut (Cocos nucifera) in India

Coconut palm (Cocos nucifera L.), a versatile tree crop with multifarious uses, is important for the livelihood security of millions of people in India. Root (wilt) disease (RWD) is a major production constraint causing an estimated yield loss of 968 million nuts in southern India. Affected palms show bending of leaflets (flaccidity), foliar yellowing, and marginal necrosis. Phytoplasmas have been observed to be associated with this disease by electron microscopy (EM) and transmission (3) but not characterized. Attempts made in the past decade to detect a phytoplasma associated with RWD through PCR using universal primers had inconsistent results so we designed two primer sets (1F7 [AGTGCTTAACACTGTCCTGCTA]/7R3 [TTGTAGCCCAGATCATAAGGGGCA], 3Fwd [ACCTGCCTTTAAGACGAGGA]/3Rev [AAAGGAGGTGATCCATCCCCACCT]) and seminested primer pair 1F7/7R2 (GACAAGGGTTGCGCTCGTTTT), 3Fwd/5Rev (ACCCCGAGAACGTATTCACCGCGA) from sequencing of a 1.8-kb fragment (GenBank No. FJ794816) amplified by primers P1/P7 from a diseased sample. These new primer pairs were used for the detection of phytoplasma from five symptomatic and five asymptomatic palms from Kasaragod (where disease is not endemic), 14 symptomatic palms from Kayamkulam (endemic area), and 10 palms from disease-free areas (Kidu, Karnataka) using PCR. DNA was extracted from 3 g of spindle leaf (two to three leaflets) midrib tissues using a modified phytoplasma enrichment protocol in which an addition of 5% polyvinylpolypyrrolidone (MW of 40,000) during tissue grinding was essential. PCR was performed for 35 cycles with an annealing temperature of 63°C to avoid nonspecific amplification. A 1.3-kb amplicon was seen in two of the five samples and the positive control sample (sugarcane grassy shoot DNA) using the seminested primer pair 3Fwd/3Rev-3Fwd/5Rev. The amplicons were cloned and sequenced and a representative sequence was deposited in GenBank (GQ850122). With the 1F7/7R3-1F7/7R2 seminested primers, a 493-bp product was obtained from 13 of 14 palms from Kayamkulam and all five diseased palms from Kasaragod. No amplification was seen from healthy palms. A BLAST search showed that the RWD phytoplasma 16S rRNA gene sequence has >96% nt identity with 16SrXI and 16SrXIV group phytoplasmas and 99% identity with sugarcane white leaf phytoplasma (AB052874), On the basis of the identity of the 16Sr RNA gene 3Fwd/5Rev region, RWD phytoplasma belongs to the 16SrXI group. A phylogenetic tree (neighbor-joining method) also revealed clustering of the coconut phytoplasma with the 16SrXI group phytoplasmas and virtual restriction fragment length polymorphism analysis (4) also placed it into group 16SrXI. Other phytoplasmas infecting coconut are found in groups 16SrIV (1) and 16SrXIV (2). Our RWD phytoplasma sequence does not match an earlier reported Kerala (wilt) coconut phytoplasma sequence (AY158660) and the latter sequence does not have similarity with any known phytoplasma sequences in the database. To our knowledge, this is first report of the association of 16SrXI group phytoplasma with the root wilt disease of coconut in India. These findings could be used for the early detection of root wilt disease phytoplasma in breeding materials and to develop a DNA-based diagnostic kit. References: (1) N. A. Harrison et al. Ann. Appl. Biol. 153:85, 2008. (2) N. Nejat et al. Am. J. Appl. Sci. 6:1331, 2009. (3) M. Sasikala et al. Eur. J. Plant Pathol. 94:191, 2005. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2007.

First Report of Garlic common latent virus in Garlic from India

Garlic (Allium sativum L.) is one of the most important culinary herbs in the Indian subcontinent. Several viruses belonging to genera Potyvirus, Carlavirus, and Allexivirus are known to infect garlic (2,3). Garlic accessions grown on the research farm of the Indian Agricultural Research Institute, New Delhi, were tested for the presence of Onion yellow dwarf virus (OYDV), Shallot latent virus (SLV), and Garlic common latent virus (GarCLV). Leaves showing mild to severe mosaic symptoms were collected in January of 2008 from five accessions of garlic (Pusa Selection-34, G-1, Selection-17, G-282, and PGS-14) from the experimental plots. Direct antigen coated (DAC)-ELISA was performed with antisera to OYDV, GarCLV (Bioreba, Reinach, Switzerland), and Garlic latent virus (GarLV) (synonym for SLV) obtained from D. E. Lesemann, (Braunschweig, Germany). Total RNA was extracted from 100 mg of leaves with the RNeasy Plant Mini kit (Qiagen, Maryland) according to the manufacturer's protocol. Reverse transcription (RT)-PCR and DAC-ELISA confirmed the presence of OYDV and SLV in all selection lines, both of which were reported previously from garlic in India (1). The occurrence of GarCLV was confirmed by DAC-ELISA and RT- PCR using a primer pair 5'-AAATGTTAATCGCTAAACGACC-3' and 5'-CTTTGTGGATTTTCGGTAAG-3' designed from the conserved region of open reading frame (ORF) 5 (coat protein) and ORF 6 (nucleic acid binding protein) of GarCLV (GenBank Accession Nos. AB004566, X81138, and X81139). Expected amplicons of ∼500 bp for GarCLV were obtained from all garlic lines tested, confirming that all five garlic lines had mixed infections of OYDV, SLV, and GarCLV. The amplicons obtained from Pusa Selection-34 were directly sequenced and the 536-bp nucleotide sequence (GenBank Accession No. FJ154841) showed a sequence identity of 87% compared with GarCLV (GenBank Accession No. AB004566). To our knowledge, this is the first report of GarCLV in garlic cultivars in India. Our study demonstrates that GarCLV occurs frequently in mixed infections with OYDV and SLV and the potential impact of these mixed infections on garlic production needs to be evaluated. References: (1) S. Majumder et al. J. Plant Pathol. 90:369, 2008. (2) P. Van Dijk. Acta Hortic. 358:299, 1994. (3) D. G. A. Walkey and D. N. Antill. J. Hortic. Sci, 64:53, 1989.

Detection of Citrus exocortis viroid, Iresine viroid, and Tomato chlorotic dwarf viroid in New Ornamental Host Plants in India

Columnea latent viroid, originating from ornamental plants, is known to be harmful to crop plants (2). Despite the potential threat to crop plants, the importance of ornamental plants in viroid evolution is not fully appreciated. Availability of a Pospiviroid genus-specific primer pair (1) to detect the most prevalent viroids in ornamental plants and a simplified nucleic acid preparation protocol (3) for use in reverse-transcription polymerase chain reaction (RT-PCR) have facilitated surveys of ornamental plants for pospiviroids. Using the above protocol in India, leaf and shoot samples were collected randomly from roadside beds consisting of ground covers or creepers/trailing plants at the IARI campus, New Delhi. These were extracted in 50 mM NaOH + 2.5 mM EDTA solution, centrifuged to sediment the coarse debris from sap, and 10 μl of the supernatant was spotted on a nitrocellulose membrane. Individual spots were eluted with distilled sterile water (30 μl) and the eluates were used for RT-PCR detection of viroids (3). Amplified fragments or subsequently cloned plasmids were also purified using NaOH-EDTA membrane protocol. Cloning and sequencing of amplicons (195 to 224 bp) revealed a very high sequence identity with specific viroids from the viroid sequence database (NCBI). Among the 19 plant samples assayed, only three plant species were infected by viroids, although none of them exhibited any symptoms. The three plant species included: (i) moss verbena, Glandularia puchella (Verbenaceae, native to Argentina and Chile, now established in several regions of the world), infected with a viroid (Accession No. DQ846884) having 99% sequence identity to Citrus exocortis viroid (CEVd) (Accession No. S67446); (ii) trailing verbena, Verbena × hybrida (Verbenaceae, ornamental plant), doubly infected with a viroid (Accession No. DQ846885) having 95% sequence identity to CEVd (Accession No. DQ094297) and infected with another viroid (Accession No. DQ846883) having 98% sequence identity to Tomato chlorotic dwarf viroid (TCDVd) (Accession No. AF162131); and (iii) red joyweed, Alternanthera sessilis (Amaranthaceae, a perennial weed herb) infected with a viroid (Accession No. DQ846886) having 96% sequence identity to Iresine viroid (IrVd) (Accession No. DQ094293). CEVd and TCDVd were mechanically transferred to tomato seedlings causing reduced growth of plants, smaller leaves, and bunchy-top appearance of plants, symptoms similar to those typically observed with other isolates of these viroids. As expected from previous studies, IrVd was not transmitted to tomato plants. Natural infection of verbena with CEVd has been detected in North America (2) but this was a novel observation in India. Additional novel observations include: A. sessilis as a new host for IrVd; and TCDVd is the first crop viroid to be isolated from a naturally infected ornamental plant. The significance of these viroid findings in ground cover and widely grown ornamental plants may lie in their potential role in spreading the viroids to citrus plants in citrus-growing countries such as India. References: (1) H. Bostan et al. J. Virol. Methods 116:189, 2004, (2) R. P. Singh and J. A. Teixeira da Silva. Floriculture, Ornamental Plant Biotechnol. 3:531, 2006. (3) R. P. Singh et al. J. Virol. Methods 132:204, 2006.

First Report of Papaya ringspot virus W in Sponge Gourd from India

During August 2004, symptoms resembling a virus disease were observed in commercial cultivation of sponge gourd (Luffa cylindrica (L.) M. Roem. [cv. Chikni]) in Pune, India. Affected plants exhibited mosaic mottling, vein banding, and downward marginal curling on leaves. The incidence of disease was 10 to 30% based on the symptoms and confirmed using enzyme-linked immunosorbent assay (ELISA). Six fields of sponge gourd were visited, and 30 samples were collected randomly. Samples from affected fields were analyzed for the presence of virus by mechanical inoculation. Symptoms typical of those observed in the original field plants appeared 10 days after inoculation on sponge gourd. The virus isolate produced local lesions on Chenopodium amaranticolor and systemic symptoms on Cucumis melo, Cucumis sativus, Cucurbita maxima, Cucurbita pepo, L. acutangula, and L. cylindrica, but did not produce symptoms on Carica papaya (cvs. CO2 and Red Lady), Nicotiana glutinosa, N. tabacum (cv. White Burley), or Vigna unguiculata. Field-infected sponge gourd and all indicator plants were tested using double-antibody sandwich (DAS)-ELISA. The virus was identified as Papaya ringspot virus-W (PRSV-W) using DAS-ELISA (Agdia, Elkhart, IN). A strong, positive reaction was obtained with antiserum to PRSV-W but not with antisera to PRSV-P, Cucumber mosaic virus, Squash mosaic virus, Zucchini yellow mosaic virus, and Groundnut bud necrosis virus. To ensure virus purity, the isolate was passed through three successive single-lesion transfers on C. amaranticolor. Flexuous filamentous particles 775 nm long were observed with electron microscopy of leaf-dip preparation from symptomatic sponge gourd leaves. The virus particles were then decorated with a second PRSV-W antiserum obtained from the Plant Virology Unit, IARI, New Delhi. PRSV-W on sponge gourd has previously been reported from Taiwan (1). To our knowledge, this is the first report of natural occurrence of PRSV-W on sponge gourd in India. Reference: (1.) C. H. Huang et al. J. Agri. Res. China 36:413, 1987.

Sodium sulphite yields improved DNA of higher stability for PCR detection of Citrus yellow mosaic virus from citrus leaves

Citrus yellow mosaic virus (CYMV), a non-enveloped bacilliform DNA virus causes a severe mosaic disease in sweet oranges in India. CYMV is weakly immunogenic, thus serodiagnosis is not a preferred method for its detection. As an alternative a rapid and reliable detection protocol by polymerase chain reaction (PCR) was developed. However, high levels of polyphenolics and tannins in citrus leaves generally interfered with obtaining good quality DNA, and thus affected the reliable detection of virus by PCR. Consequently, we evaluated the addition of sodium sulphite to a DNA extraction protocol used previously and compared the two methods with a commercially available plant DNeasy Kit (Qiagen). The addition of sodium sulphite improved the yield, quality and stability of DNA. The CYMV DNA was not only amplified at lower template DNA concentration, but also provided better DNA yields. In addition, the sodium sulphite extracted DNA survived at various temperatures much longer than those extracted without addition of sodium sulphite or with the commercial kit. The amplified product of CYMV DNA was cloned, sequenced and found to have 89% sequence identity with the only other sequenced Indian isolate of CYMV.

First Report of Citrus Greening Disease and Associated Bacterium "Candidatus Liberibacter asiaticus" from Bhutan

During July 2002, surveys of mandarin orchards were conducted in Punakha Valley and Wangdue districts of Bhutan. Symptoms of the greening disease were observed in most of the orchard. The incidence of disease was recorded up to 30% in 24 private orchards with more than 5,000 trees total. Affected trees were generally stunted with leaves showing symptoms of mottling. Sometimes, symptoms were seen only on one part of the canopy. The greening disease is caused by a fastidious phloem restricted bacterium, "Candidatus Liberibacter asiaticus" in Asian countries and "Candidatus Liberibacter africanus" in African countries. To confirm the presence of this bacterium causing greening disease in Bhutan, 33 leaf samples were collected from seven locations in Bhutan and stored at -80°C. Petioles and midribs were used for extraction of DNA using DNeasy Plant Mini Kit (Qiagen Gmbh, Hilden, Germany). Polymerase chain reaction (PCR) was initially performed with a sample from Rimchu, Bhutan using primer pair 5'TATAAAGGTTGACCTTTCGAGTTT/5'ACAAAAGCAGAAATAGCACGAACAA previously designed for amplification of ribosomal protein genes of β-operon of two liberibacter species (1). An amplicon of approximately 700 bp was obtained. The size of the PCR product is similar to that amplified from "Candidatus Liberibacter asiaticus". The amplicon was cloned in pGEM-T easy vector and sequenced. The clone was 703 nt long and showed 100% sequence homology with the corresponding sequence of "Candidatus Liberibacter asiaticus" confirming that "Candidatus Liberibacter asiaticus" is the cause of greening disease in Bhutan. Later, one sample from each location was analyzed and found to be positive to greening. To our knowledge, this is the first report of this bacterium and greening disease in Bhutan, and citrus greening appears to be the main cause of declining citrus in the Punakha Region of Bhutan. Reference: (1) A. Jocquellet et al. Page 363 in: Proc. Conf. Int. Organ. Citrus Virol. 14th. IOCV, Riverside, CA, 2000.

Depurination of ribosomal RNA and inhibition of viral RNA translation by an antiviral protein of Celosia cristata

An antiviral protein (25 kD) isolated from leaves of Celosia cristata (CCP 25) was tested for depurination study on ribosomal RNA from yeast. Ribosomal RNA yielded 360 nucleotide base fragment after treatment with CCP 25 indicating that CCP 25 was a ribosome inactivating protein. CCP 25 also inhibited translation of brome mosaic virus (BMV) and pokeweed mosaic virus (PMV) RNAs in rabbit reticulocyte translation system. The radioactive assay showed that incorporation of [35S]-methionine was less in translation proteins of BMV nucleic acid when CCP 25 was added to translation system. This indicated that antiviral protein from Celosia cristata not only depurinated ribosomal RNA but also inhibited translation of viral RNA in vitro.

Purification and properties of growth stage-dependent antiviral proteins from the leaves of Celosia cristata

Two antiviral glycoproteins, active against mechanical transmission of two tobamoviruses, tobacco mosaic virus and sunnhemp rosette virus, and citrus ring spot virus (ungrouped), were purified from the dried leaves of Celosia cristata. These proteins, called CCP-25 and CCP-27, have M(r) 25 and 27 kDa, respectively. Their concentration was found to vary between the pre-flowering and post-flowering stages of C. cristata90% lesion formation at a concentration of 20-30 µg ml(-1). They were resistant to proteases in the native state, but were readily digested when denatured. Both of them imparted actinomycin D sensitive resistance by inhibiting local lesions on Nicotiana tabacum cv. Samsun NN by tobacco mosaic virus. Their application, individually, also resulted in high resistance in systemic hosts to sunnhemp rosette virus, and citrus ring spot virus, respectively.