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Title: Transcriptome amplification coupled with nanopore sequencing as a surveillance tool for plant pathogens in plant and insect tissues

Author
item RIBIERO-BRONZATO, ALINE - Mississippi State University
item Sherman, Diana
item Stone, Andrew
item WILSON, VICTORIA - Mississippi State University
item Schneider, William
item KING, JONAS - Mississippi State University

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/5/2018
Publication Date: 6/20/2018
Citation: Ribiero-Bronzato, A., Sherman, D.J., Stone, A.L., Wilson, V., Schneider, W.L., King, J. 2018. Transcriptome amplification coupled with nanopore sequencing as a surveillance tool for plant pathogens in plant and insect tissues. Plant Disease. 102:1648-1652. https://doi.org/10.1094/PDIS-04-17-0488-RE.
DOI: https://doi.org/10.1094/PDIS-04-17-0488-RE

Interpretive Summary: One of the most critical weapons in the fight against plant diseases is early detection, the ability to correctly identify the microbe that is causing a given disease outbreak. Many plant disease detection assays exist, but the vast majority of these assays are limited to identifying a single microbe at a time. A new technology, called next-generation sequencing (NGS), was developed for determining the genetic sequence of organisms. This technology has been used as a tool to detect microbes, but the huge amount of data generated by the technology makes next-generation sequencing microbe detection difficult, imprecise and slow. Previous work with NGS diagnostics has demonstrated the ability to detect plant pathogens in multiple species of plants. This work takes the technology a step farther, using a novel sequencing platform (the Oxford MinION) to detect both microbes in plants and insects. The MinION is the smallest and most portable NGS sequencer on the market today, not much larger than a thumb drive. This lays the groundwork for a field usable NGS system that could detect both microbes and insect pests from a variety of environmental samples.

Technical Abstract: There are many plant pathogen-specific diagnostic assays, based on PCR and immune-detection. However, the ability to test for large numbers of pathogens simultaneously is lacking. Next generation sequencing (NGS) allows one to detect all organisms within a given sample, but has computational limitations during assembly and similarity searching of sequence data which extend the time needed to make a diagnostic decision. Previous work with NGS diagnostics has demonstrated the ability to detect plant pathogens in multiple species of plants. This work takes the technology a step farther, using a novel sequencing platform (the Oxford MinION) to detect both RNA viruses and bacteria in plants and insect vectors. The MinION is the smallest and most portable NGS sequencer on the market today, not much larger than a thumb drive. The MinION sequencer was able to detect Plum pox virus from both peaches and aphid vectors. In addition, the MinION was able to detect Candidatus Liberibacter asiaticus from psyllids. This lays the groundwork for a field usable NGS system that could detect both pathogens and vectors from a variety of environmental samples.