Detection of Phytophthora, Pythium, Globisporangium, Hyaloperonospora and Plasmopara species in High-Throughput Sequencing data by using Microbe Finder (MiFi)

The EDNA pipeline, implemented through the Microbe Finder (MiFi) web application, was used to design short species-specific sequences (e-probes). E-probes were further tested with metagenomes generated using Nanopore sequencing (MinION; Oxford Nanopore Technologies). The Nanopore sequencing sample was prepared using genomic DNA of tomato (Solanum lycopersicum L.) spiked with different percentages of Phytophthora nicotianae genomic DNA.