{"title":"一种新发现的葡萄叶相关病毒S的高通量测序研究","authors":"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","doi":"10.1016/j.jgeb.2025.100494","DOIUrl":null,"url":null,"abstract":"<div><h3>Background</h3><div>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.</div></div><div><h3>Methods and results</h3><div>Here, we identify a novel member of the genus <em>Ampelovirus</em>, 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.</div></div><div><h3>Conclusions</h3><div>Based on the species demarcation criteria, GLRaV-S represents a newly discovered species within the genus <em>Ampelovirus</em> of the <em>Closteroviridae</em> 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.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100494"},"PeriodicalIF":3.5000,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genome characterization of a newly discovered grapevine leafroll-associated virus S, in the genus ampelovirus by high-throughput sequencing\",\"authors\":\"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\",\"doi\":\"10.1016/j.jgeb.2025.100494\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background</h3><div>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.</div></div><div><h3>Methods and results</h3><div>Here, we identify a novel member of the genus <em>Ampelovirus</em>, 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.</div></div><div><h3>Conclusions</h3><div>Based on the species demarcation criteria, GLRaV-S represents a newly discovered species within the genus <em>Ampelovirus</em> of the <em>Closteroviridae</em> 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.</div></div>\",\"PeriodicalId\":53463,\"journal\":{\"name\":\"Journal of Genetic Engineering and Biotechnology\",\"volume\":\"23 2\",\"pages\":\"Article 100494\"},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2025-04-25\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Genetic Engineering and Biotechnology\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1687157X25000381\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"Biochemistry, Genetics and Molecular Biology\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Genetic Engineering and Biotechnology","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1687157X25000381","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
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 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.
期刊介绍:
Journal of genetic engineering and biotechnology is devoted to rapid publication of full-length research papers that leads to significant contribution in advancing knowledge in genetic engineering and biotechnology and provide novel perspectives in this research area. JGEB includes all major themes related to genetic engineering and recombinant DNA. The area of interest of JGEB includes but not restricted to: •Plant genetics •Animal genetics •Bacterial enzymes •Agricultural Biotechnology, •Biochemistry, •Biophysics, •Bioinformatics, •Environmental Biotechnology, •Industrial Biotechnology, •Microbial biotechnology, •Medical Biotechnology, •Bioenergy, Biosafety, •Biosecurity, •Bioethics, •GMOS, •Genomic, •Proteomic JGEB accepts