Angelantonio Minafra, Senior Researcher at the National Research Council (CNR), Institute for Sustainable Plant Protection (IPSP), via Amendola, 165/a, 70126-Bari,

Facing the increasing global trade of plant materials – and the parallel risk of plant pathogens spread – there is the need of quick, sensitive, cost effective and generic diagnostic methods to identify and contain causal agents of harmful diseases. To assess the presence of plant virus genomes, sometimes erratic, low concentrated and even latent in symptomless plant tissues, the massive sequencing of total nucleic acids is, to date, an interesting method. Since 2014, the nanopore technology is on the market as a tool of choice, potentially responding to the above needs. Single-stranded nucleic acid ( either DNA or RNA) from a library easily prepared from purified extracts is pushed inside an array of membrane-embedded nanopores by the action of motor proteins (which could unwind the dsDNA or hybrid RNA-cDNA). The passage of each single nucleotide along the polynucleotide chain through the pores is recorded by microelectrodes as a specific change of electric current, which runs across the membrane. A dedicated software (MinKNOW) supervises the data streaming, starting from preliminary base-calling. Remarkably, the WIMP (‘what is in my pot’) program is able to describe in real-time the taxonomic attribution of the produced sequences at the family and genus level, occurring in the first couple of hours of a short run

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