Oxford nanopore sequencing using metabarcoding as detection and identification tool for ‘Candidatus Phytoplasma’ and ‘Ca. Liberibacter’ taxa

Abstract

This study explores the potential of Oxford Nanopore Technology (ONT) using metabarcoding for the detection and identification of the phloematic bacteria ‘Candidatus Phytoplasma’ and ‘Candidatus Liberibacter’. The research involved determining target taxa, selecting candidate barcodes, establishing reference databases and developing and assessing primers. Furthermore, PCR assays, library preparation protocols, and bioinformatics pipelines were tested and optimized. The results demonstrate the capability of ONT metabarcoding for a reliable detection of these pathogens while also highlighting the challenges, particularly the critical need for well-curated reference databases to enhance taxonomic assignments.