AUTHOR=Dia Nay C. , Cottyn Bart , Blom Jochen , Smits Theo H. M. , Pothier Joël F. 

TITLE=Differentiation of the Xanthomonas hortorum – Xanthomonas hydrangeae Species Complex Using Sensitive and Selective LAMP Assays

JOURNAL=Frontiers in Agronomy

VOLUME=4

YEAR=2022

URL=https://www.frontiersin.org/journals/agronomy/articles/10.3389/fagro.2022.898778

DOI=10.3389/fagro.2022.898778

ISSN=2673-3218

ABSTRACT=<p>The seven pathovars of <italic>Xanthomonas hortorum</italic> and <italic>Xanthomonas hydrangeae</italic>, referred to as the <italic>X. hortorum</italic> – <italic>X. hydrangeae</italic> species complex, cause disease on a multitude of plants, including crops, ornamental and wild plants. Cross-pathogenicity was proven for some of the strains within this species complex. It is thus important to have highly specific and fast diagnostics methods for members of the <italic>X. hortorum</italic> – <italic>X. hydrangeae</italic> species complex. A comparative genomic analysis was conducted for representative members within the complex to identify singletons for use as genomic targets for the assays. Seven loop-mediated isothermal amplification (LAMP) diagnostics assays were developed for the detection of six clades within the <italic>X. hortorum</italic> – <italic>X. hydrangeae</italic> species complex, in addition to one assay specific for the entire species complex. Primer sets were tested on a set of 62 reference strains. The primer sets amplified their respective targets within 15 minutes. Based on the reference set, all assays had a sensitivity, specificity, and efficiency of 100%. The assays were used on a validation set of 60 strains. According to the LAMP results, out of the 60 strains, 39 strains were assigned to one of the clades within the complex, 9 were assigned to the complex but to yet undefined clades within the complex, and 12 strains were previously misclassified as <italic>X. hortorum</italic> since their genomic DNA did not yield amplification with any of the assays. The seven genome-based assays are promising for use as diagnostic tools for various members within the <italic>X. hortorum</italic> – <italic>X. hydrangeae</italic> species complex, and for assigning new and historical isolates to this complex.</p>