title: Reconstructing genome evolution in historic samples of the Irish potato famine pathogen.
abstract: 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.
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark. sameoldmike@gmail.com
authors.forename: Michael D
authors.initials: MD
authors.lastname: Martin
authors.forename: Enrico
authors.initials: E
authors.lastname: Cappellini
authors.forename: Jose A
authors.initials: JA
authors.lastname: Samaniego
authors.forename: M Lisandra
authors.initials: ML
authors.lastname: Zepeda
authors.forename: Paula F
authors.initials: PF
authors.lastname: Campos
authors.forename: Andaine
authors.initials: A
authors.lastname: Seguin-Orlando
authors.forename: Nathan
authors.initials: N
authors.lastname: Wales
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
authors.forename: Simon Y W
authors.initials: SY
authors.lastname: Ho
authors.forename: Fred S
authors.initials: FS
authors.lastname: Dietrich
authors.forename: Piotr A
authors.initials: PA
authors.lastname: Mieczkowski
authors.forename: Joseph
authors.initials: J
authors.lastname: Heitman
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.forename: Anders
authors.initials: A
authors.lastname: Krogh
authors.forename: Jean B
authors.initials: JB
authors.lastname: Ristaino
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert
mesh_terms: D019143:Evolution, Molecular; D016681:Genome, Fungal; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D049672:History, 19th Century; D006801:Humans; D007494:Ireland; D010641:Phenotype; D010802:Phylogeny; D055750:Phytophthora infestans / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity*; D010935:Plant Diseases / Q000266:history / Q000382:microbiology*; D011198:Solanum tuberosum / Q000382:microbiology*; D013217:Starvation / Q000266:history / Q000382:microbiology*; D014774:Virulence