Nanopore sequencing for the identification of Zymoseptoria tritici populations

Zymoseptoria tritici is the causal agent of Septoria tritici blotch, the most important disease affecting wheat crops, responsible for up to 50% loss in yield. Azoles and SDHIs are the main groups of fungicides used to control the disease. The efficacy of these fungicides has decreased in recent years due to resistance development. Resistance can be a result of mutations in the target genes, mutations in upstream regulatory elements that result in over-expression of target proteins and the overexpression of transporters that remove toxic compounds from cells. In the current study we used nanopore sequencing to analyse isolates and mock communities that comprised mixtures of two or three isolates. We demonstrated that we were able to determine the most abundant isolates of more complex populations, however, less abundant members of populations were difficult to resolve due to random and recurrent sequencing errors. Nevertheless, we estimated that we were able to identify haplotypes that were present at a frequency of at least 5% of the population. The method is fast and inexpensive and could be useful prior to sprays to better understand the most abundant members of the populations to facilitate selection of the most appropriate active to control them.