Long read metagenomic sequencing allows sensitive detection of the high impact plant pathogen Xylella fastidiosa and phylogenetic reconstruction with outbreak resolution

Using the ONT MinION long sequencer, we can detect and precisely identify Xylella fastidiosa subspecies. Using a metagenome-assembled genome (MAG) with enough quality, phylogenetic reconstruction with SNP resolution was achieved. The MAG was placed in a clade with isolated form Georgia, USA.