Scholarlink

Background <p>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 <i>de novo</i> re-assembled using CLC Genomic Workbench.</p> Methods and results <p>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 <i>Totivirus</i>. 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 <i>Totiviridae</i>. The HTS results were further validated and confirmed through OneStep RT-PCR assay and Sanger sequencing.</p> Conclusion <p>A novel totivirus (STV 1) in the genus <i>Totivirus</i>, family <i>Totiviridae</i> has been identified. This is the first report of dsRNA totivirus STV 1 associated with sugarcane from India.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Discovery of novel ‘sugarcane totivirus 1’ from Saccharum officinarum by high-throughput sequencing

  • 期刊论文

  • 发表日期：

    2025年1月15日

查看全文
  • Nishant Srivastava,
  • Malyaj R. Prajapati,
  • Susheel K. Sharma,
  • Nitika Gupta,
  • Vanita Chandel,
  • Virendra K. Baranwal

摘要

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.