A Barcoded ITS Primer-Based Nanopore Sequencing Protocol for Detection of <i>Alternaria</i> Species and Other Fungal Pathogens in Diverse Plant Hosts.

ABSTRACT: Alternaria is a genus that contains several important plant pathogens affecting nearly 400 plant species worldwide, including economically important crops such as grapes, citrus, and ornamental plants. Rapid, scalable, and efficient methods of pathogen detection are crucial for managing plant diseases and ensuring agricultural productivity. Current amplicon sequencing protocols for Alternaria detection often require the enzymatic barcoding of amplicons, increasing hands-on time, cost, and contamination risk. We present a proof-of-concept study using custom barcoded primers, combining universal primers targeting ITS1 and ITS2 regions (600 bp) coupled with Oxford Nanopore Technologies (ONT) barcode sequences. Sequencing was performed on infected grapevine, mandarin orange, thuj

SUBMITTER: Baramidze V 

PROVIDER: S-EPMC12027965 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature