Elucidating population structure, genetic diversity and host specificity of Alternaria alternata from diverse regions and wild and domestic host plants

Alternaria spp. are cosmopolitan, ubiquitous necrotrophic fungal pathogens that infect a broad range of hosts. They cause early blight and leaf spot disease, which induce significant harvest losses. We collected suspected Alternaria-infected leaves from potatoes, tomatoes, and wild hosts in three different climate zones and from different farm types at sites equal in distance in Serbia and Germany. Using molecular markers, we identified the pathogens. The infections were caused predominantly by small-spored species of Alternaria of the section Alternaria, like Alternaria alternata. Morphological observations confirmed the molecular identification. The sequencing of the three molecular markers Alt A1, RPB2 and GAPDH reveals an equal distribution of five haplotypes of section Alternaria for all host plants, farm types, and climate zones. Comparative genetic diversity analyses such as Pi and Tajima´s D also show a similar genetic diversity for isolates from different host plants. Using only these three markers, Alternaria populations seem to be genetically heterogeneous at a continental scale and across hosts and climates, indicating the pathogen's ability to thrive in diverse environments. Nevertheless, phenotyping by detached leaf assays revealed a higher virulence in isolates originating from wild host plants. Whole-genome sequencing of 220 A. Alternata isolates from our sample set further elucidates their populations admixture, the influence of the host and potential for gene transfer or recombination. The widespread occurrence of distinct genotypes, combined with evidence for admixture and recombination, suggests a higher adaptive capacity in this pathogen, which poses challenges for disease management