Nanopore sequencing in surveillance of fungicide resistance

Abstract

By detecting plant pathogens as early as possible, swift action can be taken to mitigate the spread of disease. Monitoring fungicide is another key part of effective disease control as pathogens can develop resistance to fungicides, rendering them ineffective. The area of plant disease management is advancing apace thanks to innovative research incorporating technical advances in detection and monitoring. For example, Dr Semcheddine Cherrad, Research and Development Manager at Conidia Coniphy, is conducting innovative studies on microbiological assessment and contamination control. The research team at Conidia Coniphy has been working on the detection of plant pathogens and monitoring of fungicide resistance for over 15 years and the teamâ–™s collective efforts in bioassay and molecular analysis, combined with the adoption of new technologies and processes is overcoming challenges in the field. For example, the researchers are utilising new generation sequencing (NGS) with long-read sequencing to generate huge datasets on DNA molecules of genes coding for proteins targeted by fungicides. The team has developed a tool for mould identification called ID-Fungi Plates (IDFP). It is a user-friendly medium that accelerates the identification of fungal pathogens by Maldi-tof. They have also developed a software called FUNGI MESURE, which can quantify fungal spores in samples, providing an accurate overview of fungal measures and facilitating lab routine tasks of methods with fungi. In addition, a database established by the team called FUNGI DNA supports the identification and study of fungal strains through DNA analysis.