Comprehensive virome profiling of sugarcane and simplified duplex OneStep RT-PCR assay reveals the prevalence of sugarcane streak mosaic virus along with sugarcane yellow leaf virus in India
Background: 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...
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Elsevier
2024-12-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1687157X24001458 |
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| author | Nishant Srivastava Malyaj R. Prajapati Rakesh Kumar Pooja Bhardwaj Nitika Gupta Vanita Chandel Susheel K. Sharma Virendra K. Baranwal |
| author_facet | Nishant Srivastava Malyaj R. Prajapati Rakesh Kumar Pooja Bhardwaj Nitika Gupta Vanita Chandel Susheel K. Sharma Virendra K. Baranwal |
| author_sort | Nishant Srivastava |
| collection | DOAJ |
| description | Background: 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. 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. Conclusion: 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. |
| format | Article |
| id | doaj-art-36e475b47f604bea9dadc8899e39266d |
| institution | OA Journals |
| issn | 1687-157X |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
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| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj-art-36e475b47f604bea9dadc8899e39266d2025-08-20T01:59:35ZengElsevierJournal of Genetic Engineering and Biotechnology1687-157X2024-12-0122410044210.1016/j.jgeb.2024.100442Comprehensive virome profiling of sugarcane and simplified duplex OneStep RT-PCR assay reveals the prevalence of sugarcane streak mosaic virus along with sugarcane yellow leaf virus in IndiaNishant Srivastava0Malyaj R. Prajapati1Rakesh Kumar2Pooja Bhardwaj3Nitika Gupta4Vanita Chandel5Susheel K. Sharma6Virendra K. Baranwal7Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; Amity Institute of Virology & Immunology, Amity University Uttar Pradesh, Noida 201313, IndiaAdvanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaAdvanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaAdvanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaAdvanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaAmity Institute of Virology & Immunology, Amity University Uttar Pradesh, Noida 201313, IndiaAdvanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaAdvanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; Corresponding author.Background: 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. 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. Conclusion: 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.http://www.sciencedirect.com/science/article/pii/S1687157X24001458ViromeSugarcaneSCSMVSCYLVSCMVDuplex OneStep RT-PCR |
| spellingShingle | Nishant Srivastava Malyaj R. Prajapati Rakesh Kumar Pooja Bhardwaj Nitika Gupta Vanita Chandel Susheel K. Sharma Virendra K. Baranwal Comprehensive virome profiling of sugarcane and simplified duplex OneStep RT-PCR assay reveals the prevalence of sugarcane streak mosaic virus along with sugarcane yellow leaf virus in India Journal of Genetic Engineering and Biotechnology Virome Sugarcane SCSMV SCYLV SCMV Duplex OneStep RT-PCR |
| title | Comprehensive virome profiling of sugarcane and simplified duplex OneStep RT-PCR assay reveals the prevalence of sugarcane streak mosaic virus along with sugarcane yellow leaf virus in India |
| title_full | Comprehensive virome profiling of sugarcane and simplified duplex OneStep RT-PCR assay reveals the prevalence of sugarcane streak mosaic virus along with sugarcane yellow leaf virus in India |
| title_fullStr | Comprehensive virome profiling of sugarcane and simplified duplex OneStep RT-PCR assay reveals the prevalence of sugarcane streak mosaic virus along with sugarcane yellow leaf virus in India |
| title_full_unstemmed | Comprehensive virome profiling of sugarcane and simplified duplex OneStep RT-PCR assay reveals the prevalence of sugarcane streak mosaic virus along with sugarcane yellow leaf virus in India |
| title_short | Comprehensive virome profiling of sugarcane and simplified duplex OneStep RT-PCR assay reveals the prevalence of sugarcane streak mosaic virus along with sugarcane yellow leaf virus in India |
| title_sort | comprehensive virome profiling of sugarcane and simplified duplex onestep rt pcr assay reveals the prevalence of sugarcane streak mosaic virus along with sugarcane yellow leaf virus in india |
| topic | Virome Sugarcane SCSMV SCYLV SCMV Duplex OneStep RT-PCR |
| url | http://www.sciencedirect.com/science/article/pii/S1687157X24001458 |
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