Metabarcoding of citrus fruits containing Elsinoe spp.

Citrus fruits, including oranges, lemons, limes, grapefruits, and tangerines, are economically valuable crops globally and within Europe. Imports of citrus fruits pose risks for EU citrus production, notably the introduction of regulated fungal pathogens Elsinoe fawcettii, Elsinoe australis and Elsinoe citricola.For the regulated Elsinoe species, over 50% is imported from countries where the pests have been reported. To prevent the introduction and potential establishment of regulated pathogens in European orchards, diagnostic tests are carried out on symptomatic fruits that may indicate their presence.We aimed to verify the presence of regulated Elsinoe species in symptomatic plant material testing positive for Elsinoe spp. using an rDNA metabarcoding approach. Barcode sequence presence of Elsinoe species other than the regulated ones was observed.The presence of non-regulated Elsinoe species on citrus fruit undercuts the potential for regulated pest diagnosis following a positive genus-level test result. It in addition triggers the need for extended validation of diagnostic tests as exclusivity of tests does not only cover other citrus pathogens, but also related non-regulated Elsinoe species.