23
DOI: https://doi.org/10.1186/s43141-023-00561-2
English
eng
Elwan, Esraa A.
Contributor
<div id="abs0005" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0010" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Background</h3><div class="u-margin-s-bottom" id="sp0030" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;"><span style="margin: 0px; padding: 0px;">The quick and accurate identification of viruses is essential for <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/plant-disease-management" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">plant disease management</a>. Next-generation sequencing (NGS) technology may allow the discovery, detection, and identification of </span><a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/plant-pathogens" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">plant pathogens</a>. This study adopted RNA-sequencing (RNA-Seq) technology to explore the viruses in three potato plants (S3, S4, and S6) growing under field conditions.</div></div><div id="abs0010" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0015" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Results</h3><div class="u-margin-s-bottom" id="sp0035" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;"><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;">Potato-known infecting viruses, such as <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/alfalfa-mosaic-virus" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">alfalfa mosaic virus</a><span style="margin: 0px; padding: 0px;"> (AMV), <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/potato-leafroll-virus" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">potato leafroll virus</a> (PLRV), and </span></span><a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/potato-virus-y" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">potato virus Y</a><span style="margin: 0px; padding: 0px;"> (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 <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/tomato-chlorosis-virus" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">tomato chlorosis virus</a> (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 </span></span><a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/mycovirus" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">mycovirus</a> sequences derived from ourmia-like viruses and </span><span style="margin: 0px; padding: 0px;"><em style="margin: 0px; padding: 0px;"><a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/alternaria-alternata" title="Learn more about Alternaria alternata from ScienceDirect's AI-generated Topic Pages" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Alternaria alternata</a></em></span><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"> <a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/chrysovirus" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">chrysovirus</a> were also identified in sample S4, confirming the complexity of the potato </span><a href="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/microbiome" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">microbiome</a> under field conditions.</span></div></div><div id="abs0015" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0020" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Conclusion</h3><div class="u-margin-s-bottom" id="sp0040" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;">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.</div></div>
Elsevier
December 2023
pdf
Journal of Genetic Engineering and Biotechnology
Exploring virus presence in field-collected potato leaf samples using RNA sequencing
mixed material
Elsevier