P-184 - Elucidating the emergence of Alternaria alternata as major pathogen of solanaceous crops

Alternaria alternata is a ubiquitous fungus that can have endophytic and pathogenic lifestyles. Until recently, the species was considered relatively unimportant as a pathogen and was managed well with common fungicides. In recent years A. alternata has emerged as major pathogen on a broad range of hosts. On solanaceous crops, it is now one of the dominant pathogens associated with the early blight disease complex, also in regions where it previously was not found. Knowing that A. alternata is considered a broad host range pathogen, we asked the questions: to which extent does A. alternata show host and geographic specificity? What is the role of wild host plants plants for its emergence and survival? And, what are the genomic elements that allow this asexual pathogen to adapt. We collected over 1000 suspected Alternaria-infected leaves from potatoes, tomatoes, and wild hosts in three climate zones and from different farm types in Serbia and Germany, and outgroup samples from different hosts and regions.

We show the result of short read whole-genome sequencing of 400 selected isolates from our sample set, elucidating their population substructure, admixture, the influence of the host and potential for gene transfer or recombination. Further, using ONT sequencing we find that A. alternata are highly syntenic, but isolates show variation in mobile genomic elements (starships). These might drive the emergence of this pathogen on new host and in new areas.