Stone fruits and pome fruits are cultivated commercially worldwide. In India, they are grown in temperate regions, which mainly includes Jammu and Kashmir, Uttarakhand, Himachal Pradesh and some North-Eastern states. In this study, an attempt has been made to identify the Prunus necrotic ringspot virus (PNRSV) infecting stone and pome fruits in India and to characterise them on the molecular level. Surveys were conducted in the temperate fruit-growing areas and incidence of PNRSV was detected by serological and molecular means in almond, apple, cherry, nectarine, peach, plum and wild cherry. Further diversity analysis of PNRSV was performed using bioinformatics tools such as clustalW, DNA Data Bank of Japan, MultAlin and Recombination Detection Programme. PNRSV was detected in plum, peach, cherry, almond, nectarine, wild cherry and apple. In the diversity analysis study on the basis of coat protein gene, it was found that the isolates showed identity levels from 82 to 100%. In a plum isolate, a stretch of amino acids from 207 to 221 was found variable from Indian and other isolates. In one of the Indian apple isolates, “NR” repeats at 41–44 position (characteristic of PV-32 group, Group I) were identified. Phylogenetic analysis revealed that Indian isolates are falling in Group-I. Movement protein was also amplified from peach and multiple alignment studies showed that N-terminus was mostly conserved, whereas the C-terminal was highly variable.

Sugarcane is host of many viral pathogens that affects its growth and productivity. High-throughput sequencing (HTS) is comprehensive diagnostic platform that permit the precise detection of viral pathogens to resolve the disease epidemiology of the crop, thus providing the phytosanitary status of plants. The current work was designed to comprehend the virome profiling of sugarcane belonging to five varieties collected from the major crop producing states in India. Additionally, a duplex OneStep RT-PCR assay was optimized for simplified detection of prevalent viruses in single reaction run along with validation and confirmation of HTS results. The complete genome sequences of sugarcane streak mosaic virus (SCSMV), sugarcane yellow leaf virus (SCYLV) and sugarcane mosaic virus (SCMV) consisted of 9790, 5849 and 9600 nucleotides (nt) respectively were obtained excluding 5′ UTR and 3′ poly (A) tail from sugarcane samples belonging to different varieties. SCSMV and SCMV had single ORF encoding 3130 and 3063 amino acids (aa) respectively, whereas SCYLV genome comprised of six ORFs. The proteolytic cleavage sites in polyprotein region of SCSMV and SCMV revealed the unique amino acid motifs. SCSMV generated the highest number of single nucleotide variants (SNVs) 876 suggesting that it is more susceptible to mutations than other elucidated viruses in HTS. Recombination events revealed the origin of SCSMV_UP isolate from Indian and Iranian isolates as major and minor parents respectively. Further, validation assay by simplified duplex OneStep RT-PCR revealed the prevalence of SCSMV and SCYLV as mixed infection in sugarcane samples with 28 % incidence. The assay could detect the viruses up to 100 pg/µL of RNA concentration. The first comprehensive report of sugarcane virome and use of an optimized duplex OneStep RT-PCR assay revealed the prevalence of SCSMV and SCYLV in sugarcane from India. The study also provides an insight into genetic variations in the coding region of SCSMV and SCMV and emergence of diverse variants present in a viral population. A simplified duplex OneStep RT-PCR assay for simultaneous and expeditious detection of prevalent viruses in sugarcane would be useful in certification programme for production of virus-free planting materials.

Current research work exploited astonishing properties of nanoparticles in polymerase chain reaction (PCR). Present research employs the magnesium oxide nanoparticles in polymerase chain reaction (PCR) in place of magnesium chloride which results in significant reduction in time of the conventional PCR procedure, reduction in concentration of the magnesium used and smearless DNA. The rationale behind the use of magnesium oxide nanoparticles is its unique properties such as highly stable, good dispensability and less toxic effects. The preliminary results explicated that magnesium oxide nano-particles ultimately show enhancement in reaction efficiency.