Elwan Esraa A, Rabie Mona, Aleem Engy E Abdel, Fattouh Faiza A, Kagda Meenakshi S, Zaghloul Heba A H
Department of Botany and Microbiology, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt.
Genetics Department, School of Medicine, Stanford University, Stanford, CA, USA.
J Genet Eng Biotechnol. 2023 Oct 20;21(1):106. doi: 10.1186/s43141-023-00561-2.
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.
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.
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.
快速准确地鉴定病毒对于植物病害管理至关重要。下一代测序（NGS）技术可能有助于发现、检测和鉴定植物病原体。本研究采用RNA测序（RNA-Seq）技术探索在田间条件下生长的三株马铃薯植株（S3、S4和S6）中的病毒。
使用生物信息学程序鉴定了已知感染马铃薯的病毒，如苜蓿花叶病毒（AMV）、马铃薯卷叶病毒（PLRV）和马铃薯Y病毒（PVY），并通过RT-PCR进行了验证。通过对寄主症状的目视检查也证实了这些马铃薯病毒的存在。此外，还鉴定出了PLRV的近乎完整基因组以及多分体病毒片段的完整或部分基因组序列。除了BLASTn分析显示存在于我们样本中的三种主要马铃薯病毒外，BLASTx分析还显示一些读数来自其他马铃薯病毒，如马铃薯V病毒（PVV）、安第斯马铃薯潜隐病毒（APLV）和番茄褪绿病毒（ToCV），这些病毒在埃及马铃薯田间筛查中并不经常报道。在检测的样本序列中还鉴定出了其他微生物因子，如细菌和真菌。在样本S4中还鉴定出了一些源自类欧米亚病毒和链格孢金色病毒的真菌病毒序列，证实了田间条件下马铃薯微生物组的复杂性。
NGS能在田间条件下快速准确地鉴定马铃薯植株病毒。建议大规模应用该技术来探索马铃薯田和进口植物，因为这些地方可能没有症状、症状不特异或仅在特定条件下才会出现症状。
