Phylogenetic and population genetic analyses of Stagonosporopsis tanaceti, the cause of ray blight of pyrethrum in Australia

Ray blight is a destructive fungal disease of pyrethrum (Tanacetum cinerariifolium) and a major threat to the Australian pyrethrum industry; the largest producer of pyrethrum worldwide. Multi-gene phylogenies and morphological studies resulted in the recognition of three Stagonosporopsis species as the cause of ray blight on Asteraceae. Stagonosporopsis tanacetiwas described as a new species and the cause of ray blight of pyrethrum in Australia. A de novo genome assembly of paired-end Illumina reads was used to develop a multiplex set of microsatellite markers, which was further employed for temporal and geographical genetic structure analyses of S. tanaceti populations in Australia. Identification of only one mating type gene in the population, high levels of clonality and significant linkage disequilibrium suggested sexual reproduction is absent or infrequent in the Australian pyrethrum fields. Discriminant analysis of principal components (DAPC) and minimum spanning networks detected two distinct clonal lineages in the older populations; each consisting of one dominant multilocus genotype (MLG) and multiple closely-related MLGs at low frequencies. This may be indicative of introduction of two clonal lineages; which have diversified independently in the apparent absence of a sexual stage in the field. Low geographical differentiation among fields in the absence of airborne sexual spores suggests that human-mediated movement of infected seed may be a major source of long distance dispersal. A significant change in the genetic composition of the recent populations of S. tanaceti was detected, which is unlikely to be the result of mutation or recombination, and is subject to further investigation