纳米病毒学:长时间读取 dsRNA 的测序,用于植物病毒和病毒的快速检测
Vahid J Javaran1,2, Abdonaser Poursalavati1,2, Pierre Lemoyne1
1Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada.
Frontiers in microbiology
|July 7, 2023
概括
一种新的基于dsRNA的纳米孔序列测序方法 (dsRNAcD) 可靠地检测葡萄葡萄病毒和病毒. 这种具有成本效益的方法超越了传统方法,可以识别即使是稀少的病原体,从而改善植物健康.
科学领域:
- 植物病理学 植物病理学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 全球需要在植物中快速,可靠的病毒病原体检测.
- 经过认证的清洁植物材料对于控制疾病传播的重要性.
- 现有的病毒病诊断工具的局限性.
研究的目的:
- 开发和验证基于dsRNA的纳米孔测序协议,用于葡萄葡萄病毒和病毒检测.
- 将基于dsRNA的新方法 (dsRNAcD) 与直接RNA测序 (rdTotalRNA) 和Illumina测序 (dsRNA-MiSeq) 进行比较.
- 评估分类学分类工作流程,以获得准确的读取分配.
主要方法:
- 从dsRNA (dsRNAcD) 协议开发并验证了一种直接cDNA测序.
- 将dSRNAcD与从rRNA缺少总RNA (rdTotalRNA) 的直接RNA测序进行比较.
- 使用Illumina MiSeq测序 (dsRNA-MiSeq) 作为一个基准.
- 评估了 DIAMOND & MEGAN (DIA & MEG) 和离心机和近期离心机 (Cent & Rec) 的数据分析.
主要成果:
- dsRNAcD的病毒读数明显高于rdTotalRNA.
- dsRNAcD检测到dSRNA-MiSeq.识别的所有病毒和病毒.
- dsRNAcD确定了rdTotalRNA遗漏的低丰度病毒.
- 由于宿主读取错误注释,rdTotalRNA产生了一个错误的阳性病毒体识别.
- 无论是DIA & MEG还是Cent & Rec的工作流程,都显示出类似的结果,具有明显的优势.
结论:
- dsRNAcD测序是一种可靠和敏感的方法,用于检测葡萄树中的病毒和病毒.
- 拟议的数据分析工作流程确保一致的病原体检测.
- 这种方法对葡萄树特别有价值,葡萄树经常遭受混合病毒感染.
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