Exploring virus presence in field-collected potato leaf samples using RNA sequencing.

IF 3.6 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Esraa A Elwan, Mona Rabie, Engy E Abdel Aleem, Faiza A Fattouh, Meenakshi S Kagda, Heba A H Zaghloul
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Abstract

Background: The quick and accurate identification of viruses is essential for plant disease management. Next-generation sequencing (NGS) technology may allow the discovery, detection, and identification of plant pathogens. This study adopted RNA-sequencing (RNA-Seq) technology to explore the viruses in three potato plants (S3, S4, and S6) growing under field conditions.

Results: Potato-known infecting viruses, such as alfalfa mosaic virus (AMV), potato leafroll virus (PLRV), and potato virus Y (PVY), were identified using bioinformatics programs and validated using RT-PCR. The presence of these potato viruses was also confirmed by visual inspection of host symptoms. In addition, the nearly complete genome of PLRV and the complete or partial genome sequence of multipartite virus segments have been identified. Besides the three major potato viruses that BLASTn analysis revealed were present in our samples, BLASTx analysis revealed some reads are derived from other potato viruses, such as potato virus V (PVV), Andean potato latent virus (APLV), and tomato chlorosis virus (ToCV), which are not frequently reported in potato field screenings in Egypt. Other microbial agents, such as bacteria and fungi, were also identified in the examined sample sequences. Some mycovirus sequences derived from ourmia-like viruses and Alternaria alternata chrysovirus were also identified in sample S4, confirming the complexity of the potato microbiome under field conditions.

Conclusion: NGS quickly and accurately identifies potato plant viruses under field conditions. Implementing this technology on a larger scale is recommended to explore potato fields and imported plants, where symptoms may be absent, unspecific, or only triggered under certain conditions.

Abstract Image

Abstract Image

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利用RNA测序技术探索病毒在田间采集的马铃薯叶片样本中的存在。
背景:快速准确地识别病毒对植物病害管理至关重要。下一代测序(NGS)技术可能允许发现、检测和鉴定植物病原体。本研究采用RNA测序(RNA-Seq)技术,对3株马铃薯(S3、S4和S6)在田间条件下生长的病毒进行了研究。结果:利用生物信息学程序鉴定了已知的马铃薯感染病毒,如苜蓿花叶病毒(AMV)、马铃薯卷叶病毒(PLRV)和马铃薯Y病毒(PVY),并用RT-PCR进行了验证。通过肉眼观察宿主症状也证实了这些马铃薯病毒的存在。此外,已经鉴定出PLRV的几乎完整的基因组和多部分病毒片段的完整或部分基因组序列。除了BLASTn分析显示我们的样本中存在三种主要的马铃薯病毒外,BLASTx分析显示一些读数来源于其他马铃薯病毒,如马铃薯病毒V(PVV)、安第斯马铃薯潜伏病毒(APLV)和番茄黄化病毒(ToCV),这些病毒在埃及的马铃薯田间筛选中并不常见。其他微生物制剂,如细菌和真菌,也在检查的样本序列中被鉴定。在样品S4中还鉴定了一些来源于类脲原病病毒和金黄色链格孢病毒的分枝病毒序列,证实了马铃薯微生物组在田间条件下的复杂性。结论:NGS能在田间条件下快速准确地鉴定马铃薯植物病毒。建议在更大范围内实施这项技术,以探索马铃薯田和进口植物,因为这些地方的症状可能不存在、不特定或仅在特定条件下触发。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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