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Pest and pathogen losses jeopardise global food security and ever since the 19 th  century Irish famine, potato late blight has exemplified this threat. The causal oomycete pathogen,  Phytophthora infestans , undergoes major population shifts in agricultural systems via the successive emergence and migration of asexual lineages. The phenotypic and genotypic bases of these selective sweeps are largely unknown but management strategies need to adapt to reflect the changing pathogen population. Here, we used molecular markers to document the emergence of a lineage, termed  13_A2 , in the European  P. infestans  population, and its rapid displacement of other lineages to exceed 75% of the pathogen population across Great Britain in less than three years. We show that isolates of the  13_A2  lineage are among the most aggressive on cultivated potatoes, outcompete other aggressive lineages in the field, and overcome previously effective forms of plant host resistance. Genome analyses of a  13_A2  isolate revealed extensive genetic and expression polymorphisms particularly in effector genes. Copy number variations, gene gains and losses, amino-acid replacements and changes in expression patterns of disease effector genes within the  13_A2  isolate likely contribute to enhanced virulence and aggressiveness to drive this population displacement. Importantly,  13_A2  isolates carry intact and  in planta  induced  Avrblb1 ,  Avrblb2  and  Avrvnt1  effector genes that trigger resistance in potato lines carrying the corresponding  R  immune receptor genes  Rpi-blb1 ,  Rpi-blb2 , and  Rpi-vnt1.1 . These findings point towards a strategy for deploying genetic resistance to mitigate the impact of the  13_A2  lineage and illustrate how pathogen population monitoring, combined with genome analysis, informs the management of devastating disease epidemics.

Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen