一种新发现的葡萄叶相关病毒S的高通量测序研究

IF 3.5 Q3 Biochemistry, Genetics and Molecular Biology
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
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引用次数: 0

摘要

从植物样本中获得的转录组数据通常包含大量来自病毒基因组的reads,这些reads通常是在RNA提取过程中共同分离的。这是通过病毒RNA与寄主植物RNA同时存在而发生的,导致转录组数据中包含病毒序列。方法与结果本研究利用植物病毒生物信息学检测管道,对葡萄叶卷烟症状叶片的RNA进行高通量测序(HTS),鉴定出Ampelovirus属的一个新成员——葡萄叶卷烟相关病毒S (GLRaV-S)。glravs的基因组RNA测量了13102个核苷酸(nts),包含5个开放阅读框(ORF)。同源性分析表明,glav - s基因组序列与已知蛇病毒序列的同源性为23.0% ~ 53.3%。基于基因组序列的系统发育分析表明,glav - s聚在同一支耳病毒中。然而,glravs的RdRp和HSP70h序列与II亚群聚集,而CP序列与I亚群聚集。结论基于种划分标准,glravs是closteroviriae科Ampelovirus属的一个新发现种。这项新病毒鉴定的研究将有助于制定一个强有力的认证程序,为葡萄健康植株的生产提供依据。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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.
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来源期刊
Journal of Genetic Engineering and Biotechnology
Journal of Genetic Engineering and Biotechnology Biochemistry, Genetics and Molecular Biology-Biotechnology
CiteScore
5.70
自引率
5.70%
发文量
159
审稿时长
16 weeks
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
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