Revisiting the Colletotrichum species causing anthracnose of almond in Australia

Almond production is a significant horticulture crop for Australia. Serious yield losses can be caused by the fungal disease anthracnose, caused by Colletotrichum species that infect the fruit and leaves. Genomic sequence data for gene extraction, along with multigene phylogenetic analyses and whole genome average nucleotide identity (ANI) analysis were used to determine the phylogeny of Colletotrichum isolates collected from almonds across Australia. Multigene phylogenetic analyses of six gene regions (ITS, tub2, gapdh, chs-1, act and his3) identified C. acutatum sensu stricto, C. fioriniae and C. simmondsii as pathogens of almond. Similar topology was observed using ANI, which provided increased resolution within C. acutatum, with isolates separating largely according to geographic origin. The ANI analysis also supported three separate species with isolates within each species sharing >98.7% ANI (species cut off = 95%), while between species there was