Genome characterization of a newly discovered grapevine leafroll-associated virus S, in the genus ampelovirus by high-throughput sequencing
Background: Transcriptome data obtained from plant samples often contain significant numbers of reads originating from viral genomes, which are typically co-isolated during the RNA extraction process. This occurs through the simultaneous presence of viral RNA alongside host plant RNA, leading to the...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-06-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1687157X25000381 |
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| author | Malyaj R. Prajapati Nitika Gupta Mailem Yazing Shimray Jayesh Gehlot Abhinav Tiwari Pooja Thapa Damini Diksha Somnath Kadappa Holkar Pallavi Jagannath Mahajan Sujoy Saha Virendra Kumar Baranwal Susheel Kumar Sharma |
| author_facet | Malyaj R. Prajapati Nitika Gupta Mailem Yazing Shimray Jayesh Gehlot Abhinav Tiwari Pooja Thapa Damini Diksha Somnath Kadappa Holkar Pallavi Jagannath Mahajan Sujoy Saha Virendra Kumar Baranwal Susheel Kumar Sharma |
| author_sort | Malyaj R. Prajapati |
| collection | DOAJ |
| description | Background: Transcriptome data obtained from plant samples often contain significant numbers of reads originating from viral genomes, which are typically co-isolated during the RNA extraction process. This occurs through the simultaneous presence of viral RNA alongside host plant RNA, leading to the inclusion of viral sequences in the transcriptomic data. Methods and results: Here, we identify a novel member of the genus Ampelovirus, grapevine leafroll-associated virus S (GLRaV-S) by employing the high-throughput sequencing (HTS) of RNA of grape leaves showing leafroll symptoms using a bioinformatic pipeline for plant virus detection. The genomic RNA of GLRaV-S, measured 13,102 nucleotides (nts) and encompasses five open reading frames (ORF). Homology analysis of GLRaV-S genome showed sequence identity of 23.0 – 53.3 % with the sequences of known ampeloviruses. Phylogenetic analysis based on genome sequences showed that GLRaV-S clustered in a same clade of ampeloviruses. However, the RdRp and HSP70h of GLRaV-S clustered with subgroup II while the CP sequences clustered with subgroup I of ampeloviruses. Conclusions: Based on the species demarcation criteria, GLRaV-S represents a newly discovered species within the genus Ampelovirus of the Closteroviridae family. This study on identification of novel virus will be useful in developing a robust certification program for the production of healthy plants of grapevine. |
| format | Article |
| id | doaj-art-b6fdddcca0dd4f68a1fb3fc4e34d09e0 |
| institution | DOAJ |
| issn | 1687-157X |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj-art-b6fdddcca0dd4f68a1fb3fc4e34d09e02025-08-20T03:14:09ZengElsevierJournal of Genetic Engineering and Biotechnology1687-157X2025-06-0123210049410.1016/j.jgeb.2025.100494Genome characterization of a newly discovered grapevine leafroll-associated virus S, in the genus ampelovirus by high-throughput sequencingMalyaj R. Prajapati0Nitika Gupta1Mailem Yazing Shimray2Jayesh Gehlot3Abhinav Tiwari4Pooja Thapa5Damini Diksha6Somnath Kadappa Holkar7Pallavi Jagannath Mahajan8Sujoy Saha9Virendra Kumar Baranwal10Susheel Kumar Sharma11Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaAdvanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaAdvanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaAdvanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaAdvanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaAdvanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaAdvanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, IndiaICAR-National Research Centre for Grapes, Manjari Farm, Pune 412307 Maharashtra, IndiaZonal Agricultural Research Station, Ganeshkhind, Pune 411007 Maharashtra, IndiaICAR-National Research Centre for Grapes, Manjari Farm, Pune 412307 Maharashtra, IndiaAdvanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; Corresponding authors.Advanced Centre for Plant Virology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India; Corresponding authors.Background: Transcriptome data obtained from plant samples often contain significant numbers of reads originating from viral genomes, which are typically co-isolated during the RNA extraction process. This occurs through the simultaneous presence of viral RNA alongside host plant RNA, leading to the inclusion of viral sequences in the transcriptomic data. Methods and results: Here, we identify a novel member of the genus Ampelovirus, grapevine leafroll-associated virus S (GLRaV-S) by employing the high-throughput sequencing (HTS) of RNA of grape leaves showing leafroll symptoms using a bioinformatic pipeline for plant virus detection. The genomic RNA of GLRaV-S, measured 13,102 nucleotides (nts) and encompasses five open reading frames (ORF). Homology analysis of GLRaV-S genome showed sequence identity of 23.0 – 53.3 % with the sequences of known ampeloviruses. Phylogenetic analysis based on genome sequences showed that GLRaV-S clustered in a same clade of ampeloviruses. However, the RdRp and HSP70h of GLRaV-S clustered with subgroup II while the CP sequences clustered with subgroup I of ampeloviruses. Conclusions: Based on the species demarcation criteria, GLRaV-S represents a newly discovered species within the genus Ampelovirus of the Closteroviridae family. This study on identification of novel virus will be useful in developing a robust certification program for the production of healthy plants of grapevine.http://www.sciencedirect.com/science/article/pii/S1687157X25000381GrapevineNovel virusHTSGLRaV-SAmpelovirus |
| spellingShingle | Malyaj R. Prajapati Nitika Gupta Mailem Yazing Shimray Jayesh Gehlot Abhinav Tiwari Pooja Thapa Damini Diksha Somnath Kadappa Holkar Pallavi Jagannath Mahajan Sujoy Saha Virendra Kumar Baranwal Susheel Kumar Sharma Genome characterization of a newly discovered grapevine leafroll-associated virus S, in the genus ampelovirus by high-throughput sequencing Journal of Genetic Engineering and Biotechnology Grapevine Novel virus HTS GLRaV-S Ampelovirus |
| title | Genome characterization of a newly discovered grapevine leafroll-associated virus S, in the genus ampelovirus by high-throughput sequencing |
| title_full | Genome characterization of a newly discovered grapevine leafroll-associated virus S, in the genus ampelovirus by high-throughput sequencing |
| title_fullStr | Genome characterization of a newly discovered grapevine leafroll-associated virus S, in the genus ampelovirus by high-throughput sequencing |
| title_full_unstemmed | Genome characterization of a newly discovered grapevine leafroll-associated virus S, in the genus ampelovirus by high-throughput sequencing |
| title_short | Genome characterization of a newly discovered grapevine leafroll-associated virus S, in the genus ampelovirus by high-throughput sequencing |
| title_sort | genome characterization of a newly discovered grapevine leafroll associated virus s in the genus ampelovirus by high throughput sequencing |
| topic | Grapevine Novel virus HTS GLRaV-S Ampelovirus |
| url | http://www.sciencedirect.com/science/article/pii/S1687157X25000381 |
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