Martin, Michael David8; Cappellini, Enrico8; Samaniego Castruita, Jose Alfredo9; Zepeda Mendoza, Marie Lisandra9; Campos, Paula9; Seguin-Orlando, Andaine9; Wales, Nathan9; Orlando, Ludovic Antoine Alexandre9; Ho, Simon Y.W.4; Dietrich, Fred S.5; Mieczkowski, Piotr A.6; Heitman, Joseph5; Willerslev, Eske9; Krogh, Anders10; Ristaino, Jean B.11; Gilbert, M Thomas P9
1 Natural History Museum of Denmark, Natural History Museum of Denmark, Faculty of Science, Københavns Universitet2 Computational and RNA Biology, Department of Biology, Faculty of Science, Københavns Universitet3 Natural History Museum of Denmark, Faculty of Science, Københavns Universitet4 University of Sydney5 Duke University Medical Center6 University of North Carolina, Charlotte7 North Carolina State University8 Natural History Museum of Denmark, Faculty of Science, Københavns Universitet9 Natural History Museum of Denmark, Natural History Museum of Denmark, Faculty of Science, Københavns Universitet10 Computational and RNA Biology, Department of Biology, Faculty of Science, Københavns Universitet11 North Carolina State University
Responsible for the Irish potato famine of 1845-49, the oomycete pathogen Phytophthora infestans caused persistent, devastating outbreaks of potato late blight across Europe in the 19th century. Despite continued interest in the history and spread of the pathogen, the genome of the famine-era strain remains entirely unknown. Here we characterize temporal genomic changes in introduced P. infestans. We shotgun sequence five 19th-century European strains from archival herbarium samples-including the oldest known European specimen, collected in 1845 from the first reported source of introduction. We then compare their genomes to those of extant isolates. We report multiple distinct genotypes in historical Europe and a suite of infection-related genes different from modern strains. At virulence-related loci, several now-ubiquitous genotypes were absent from the historical gene pool. At least one of these genotypes encodes a virulent phenotype in modern strains, which helps explain the 20th century's episodic replacements of European P. infestans lineages.