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Many crop disease outbreaks are characterized by clonal expansions of single pathogenic lineages that in some instances reach pandemic proportions. Understanding the timescales of clonal lineage expan- sions is important for evolutionary studies and the implementation of informed disease response programs. We have previously determined that the population structure of the rice blast fungus Magnaporthe (Syn. Pyricularia) oryzae is characterized by three pandemic clonal lin- eages that are globally distributed and expanded in the last 300 years. However, the time frames of a particular clonal lineage in a given geo- graphical region remain to be investigated. To answer this question we have sequenced historical genomes of European M. oryzae strains derived from herbarium specimens. By analyzing these century-old ge- nomes in conjunction with a set of hundreds of modern genomes, we determined the genetic continuity of the same clonal lineage in Europe for more than 100 years. To identify genetic changes that have permitted the persistence of the same clonal lineage in spite of radical changes in agricultural practices across several decades, we ascer- tained absolute difference in single nucleotide polymorphisms (SNPs) and presence/absence of genes variants (PAVs) between historical and present-day genomes. Moreover, we used a set of mini-Chromo- somes (mChr) ascertained in present-day European isolates as a ref- erence dataset to determine the mChr content of historical genomes. Our analysis quantified and timed the emergence of major drivers of phenotypic diversity (SNPs, PAVs and mChr) and generate a set of can- didate genomic regions that might have played a role in the adaptation and evolutionary success of a clonal lineage of M. oryzae in Europe.
