Nanopore sequencing and analysis of plant pathogenic viruses: more than just rapid diagnostics?
About Monica Kehoe
Dr. Monica Kehoe is a Plant Virologist and Molecular Plant Pathologist working for the Western Australian Department of Primary Industries and Regional Development (WA DPIRD) in the diagnostic and laboratory services section. Her current work focuses mainly on the development, validation and use of molecular methods for plant disease diagnostics across a broad range of broadacre and horticultural crops. Research interests include the cassava brown streak and mosaic viruses, luteoviruses in pulses and oilseeds, grapevine viruses, viruses of vegetable crops, supercomputing for plant disease diagnostics and the use of portable sequencing for rapid diagnostics in plant pathology, in both the field and the laboratory. Monica has a B.Sc from the University of Melbourne, Honours in Plant Virology from Murdoch University, and in 2014 completed her PhD in Plant Virology at the University of Western Australia.
The use of the portable MinION sequencer in plant pathology is rapidly increasing. Many studies have shown that the accuracy, portability and reduced time to result using the MinION are actively changing the way we do diagnostics and new diagnostic development for pests and diseases in agriculture. The first advantage of the MinION is clearly the ability to obtain rapid preliminary IDs of unknown pests and disease in the field. This was demonstrated recently by the Cassava Virus Action Project, taking just 4 hours to identify the virus present in symptomatic cassava plants in the field. The other advantage that can be overlooked is the opportunity to reduce the turn-around time to diagnosis for unknown pests and pathogens in a laboratory setting, as well as avoiding the need for expensive specialised equipment. While much has been made of the advances in in-field diagnostics, we wanted to answer the question of how does the data stack up in a laboratory setting when compared with other technologies? The small start-up costs and easy access to MinION sequencing, compared to other technologies makes it very attractive to plant virologists. Our team took a set of plant RNA samples from field pea with a known viral composition of a Potyvirus (Pea seed-borne mosaic virus - polyadenylated) and a Polerovirus (Turnip yellows virus – non polyadenylated), which we already had an Illumina data set for, and sequenced the samples using a cDNA and direct RNA kit on a MinION. We compared downstream analyses performed with both the Illumina and MinION data. The results of our research suggest that not only is MinION suitable for rapid diagnostics in the laboratory and the field, but it is also useful in a wider research capacity.