Discovery of novel 'sugarcane totivirus 1' from Saccharum officinarum by high-throughput sequencing.

IF 2.8 4区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY Molecular Biology Reports Pub Date : 2025-01-15 DOI:10.1007/s11033-025-10221-y

Nishant Srivastava, Malyaj R Prajapati, Susheel K Sharma, Nitika Gupta, Vanita Chandel, Virendra K Baranwal

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Abstract

Background: Sugarcane is cultivated globally and affected by more than 125 pathogens, which lead to various plant diseases. In recent years, high-throughput sequencing (HTS)-based genome analyses have been broadly adopted for the discovery of both characterized and un-characterized viruses from plant samples. In this study, the HTS data of sugarcane pooled sample retrieved from sequence read archive (SRA) were de novo re-assembled using CLC Genomic Workbench.

Methods and results: The genomic sequence of a novel dsRNA totivirus, 5,384 nucleotides (nt) long, excluding the 5' untranslated region (UTR) and 3' UTR, was discovered and named sugarcane totivirus 1 (STV 1). The genome contains two open reading frames (ORFs): a putative coat protein (CP) encoding 866 amino acids (aa) and RNA-dependent RNA polymerase (RdRp) encoding 824 aa. Phylogenetic studies based on the genomic sequences (nt), and the aa sequences of CP as well as RdRp regions revealed that STV 1 is closely related to other members of the genus Totivirus. Pairwise sequence identity of CP and RdRp aa sequences showed 30.0-51.5% and 26.3-47.2% similarity, respectively with other members of the family Totiviridae. The HTS results were further validated and confirmed through OneStep RT-PCR assay and Sanger sequencing.

Conclusion: A novel totivirus (STV 1) in the genus Totivirus, family Totiviridae has been identified. This is the first report of dsRNA totivirus STV 1 associated with sugarcane from India.

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利用高通量测序技术从甘蔗糖精中发现新型甘蔗全身性病毒1。

背景：甘蔗在全球范围内种植，受到超过125种病原菌的影响，导致各种植物病害。近年来，基于高通量测序（HTS）的基因组分析已被广泛用于从植物样本中发现特征和非特征病毒。本研究利用CLC Genomic Workbench对从序列读取档案（SRA）中检索到的甘蔗池样的HTS数据进行重新组装。方法与结果：发现了一种新的dsRNA全病毒的基因组序列，全长5384个核苷酸（nt），不包括5‘非翻译区（UTR）和3’非翻译区（UTR），并将其命名为甘蔗全病毒1 （STV 1）。该基因组包含两个开放阅读框（orf）：编码866个氨基酸（aa）的推定外壳蛋白（CP）和编码824个氨基酸的RNA依赖性RNA聚合酶（RdRp）。基于基因组序列（nt）、CP区和RdRp区aa序列的系统发育研究表明，STV - 1与Totivirus属其他成员亲缘关系密切。CP和rdrpaa序列与Totiviridae其他成员的同源性分别为30.0 ~ 51.5%和26.3 ~ 47.2%。通过OneStep RT-PCR和Sanger测序进一步验证HTS结果。结论：已鉴定出一种托提病毒科托提病毒属的新型托提病毒（STV 1）。这是首次报道与印度甘蔗相关的全病毒STV - 1。

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来源期刊

Molecular Biology Reports 生物-生化与分子生物学

CiteScore

5.00

自引率

0.00%

发文量

1048

审稿时长

5.6 months

期刊介绍： Molecular Biology Reports publishes original research papers and review articles that demonstrate novel molecular and cellular findings in both eukaryotes (animals, plants, algae, funghi) and prokaryotes (bacteria and archaea).The journal publishes results of both fundamental and translational research as well as new techniques that advance experimental progress in the field and presents original research papers, short communications and (mini-) reviews.