automating-citrus-budwood-processing-for-downstream-pathogen

Automating Citrus Budwood Processing for Downstream Pathogen Detection Through Instrument Engineering

Graft-transmissible, phloem-limited pathogens of citrus such as viruses, viroids, and bacteria are responsible for devastating epidemics and serious ...

Technology Evolving Solutions (TES)

University of California Riverside

Biological indexing is based upon the ability of certain plants, referred to as indicator plants or indicators, to produce specific symptoms when inoculated with a pathogen using mechanical means or grafting. In the case of citrus viroids, clonal indicators are grafted on to vigorous rootstocks such as rough lemon (Citrus × granulata Raf.). The 'Arizona-861-S-1' citron clonal indicator (C. medica L.) can detect and bioamplify all citrus viroids; however, for specific citrus variants of the hop stunt viroid (i.e., CVd-IIb and CVd-IIc), the clonal indicator 'Parson's special # 9' mandarin (C. reticulata Blanco) is preferred. Inoculation techniques and symptom expression are described in detail. Other supporting elements, such as greenhouse conditions and propagation techniques, are also presented.

Study and Detection of Citrus Viroids in Woody Hosts.

High-throughput nucleic acid extraction is critical for the implementation of modern viroid detection assays. Successful large-scale nursery, field surveys, and other regulatory, quarantine, or research diagnostic programs are increasingly dependent on high-throughput tissue pulverization and nucleic acid extraction protocols. Magnetic bead-based approaches using semi-automated robotic equipment allow high-throughput extraction and purification of high-quality uniform total nucleic acids for each individual sample. Here, we describe a streamlined and optimized protocol for citrus tissue processing and RNA extraction that can be used for downstream applications such as viroid detection by reverse transcription-quantitative polymerase chain reaction.

High-Throughput RNA Extraction from Citrus Tissues for the Detection of Viroids.

Multiplex quantitative polymerase chain reaction (multiplex qPCR) enables the amplification of more than one target in a single reaction using different reporter dyes with distinct fluorescent spectra. The number of reporter fluorophores is typically restricted to three or four, depending upon the capability of the real-time PCR platform and software used. Each target is amplified by a different set of primers and a uniquely labeled probe that distinguishes each PCR amplicon. Thus, the levels of several targets of interest can be quantified in real time. By combining several reactions in a single tube, multiplex qPCR reduces the quantity, and cost of reagents needed to screen a sample for multiple targets. Specificity and efficiency are not affected by the inclusion of the three assays in a multiplex reaction.

Real-Time Detection of Viroids Using Singleplex and Multiplex Quantitative Polymerase Chain Reaction.

Quantitative polymerase chain reaction (qPCR) and reverse transcription (RT)-qPCR have now become the gold standard for molecular diagnostics because of its sensitivity, specificity, and reproducibility. In addition, qPCR diagnostics are flexible because they can be scaled for high- or low-throughput applications. Here we describe an optimized assay and workflow for the universal detection of eight citrus viroid species and their variants by RT-qPCR. The assay allows for quick and efficient molecular detection of viroids without the need to run RT-qPCR for each individual viroid species.

SYBR Green RT-qPCR for the Universal Detection of Citrus Viroids.

The QuantiGene Plex assay is a molecular non-polymerase chain reaction (PCR)-based multiplex method adapted for citrus viroid detection and identification. Here, we describe the procedures to utilize the QuantiGene Plex assay as a high-throughput screening tool for viroids in purified or crude RNA extracts from citrus tissues.

QuantiGene Plex Assay: A Method for High-Throughput Multiplex Citrus Viroid Detection and Identification.

E-probe Diagnostic for Nucleic Acid Analysis (EDNA) is a user-friendly bioinformatic tool that has been adapted for the detection and identification of citrus exocortis viroid (CEVd). Here, we describe the procedures for RNA extraction from citrus tissues, library and sequencing preparation, and the utilization of EDNA Mi-Finder online platform on raw high-throughput sequencing (HTS) data.

Article	Year
Study and Detection of Citrus Viroids in Woody Hosts. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34845680	2022
High-Throughput RNA Extraction from Citrus Tissues for the Detection of Viroids. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34845684	2022
Real-Time Detection of Viroids Using Singleplex and Multiplex Quantitative Polymerase Chain Reaction. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34845695	2022
SYBR Green RT-qPCR for the Universal Detection of Citrus Viroids. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34845697	2022
QuantiGene Plex Assay: A Method for High-Throughput Multiplex Citrus Viroid Detection and Identification. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34845700	2022
An In Silico Detection of a Citrus Viroid from Raw High-Throughput Sequencing Data. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34845702	2022

Georgios Vidalakis

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