title: Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans.
abstract: As the oomycete pathogen causing potato late blight disease, Phytophthora infestans triggered the famous 19th-century Irish potato famine and remains the leading cause of global commercial potato crop destruction. But the geographic origin of the genotype that caused this devastating initial outbreak remains disputed, as does the New World center of origin of the species itself. Both Mexico and South America have been proposed, generating considerable controversy. Here, we readdress the pathogen's origins using a genomic data set encompassing 71 globally sourced modern and historical samples of P. infestans and the hybrid species P. andina, a close relative known only from the Andean highlands. Previous studies have suggested that the nuclear DNA lineage behind the initial outbreaks in Europe in 1845 is now extinct. Analysis of P. andina's phased haplotypes recovered eight haploid genome sequences, four of which represent a previously unknown basal lineage of P. infestans closely related to the famine-era lineage. Our analyses further reveal that clonal lineages of both P. andina and historical P. infestans diverged earlier than modern Mexican lineages, casting doubt on recent claims of a Mexican center of origin. Finally, we use haplotype phasing to demonstrate that basal branches of the clade comprising Mexican samples are occupied by clonal isolates collected from wild Solanum hosts, suggesting that modern Mexican P. infestans diversified on Solanum tuberosum after a host jump from a wild species and that the origins of P. infestans are more complex than was previously thought.
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Department of Integrative Biology, Center for Theoretical Evolutionary Genomics, University of California, Berkeley sameoldmike@gmail.com.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Martin
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Filipe G
authors.initials: FG
authors.lastname: Vieira
authors.affiliation: School of Biological Sciences, University of Sydney, Sydney, NSW, Australia.
authors.forename: Simon Y W
authors.initials: SY
authors.lastname: Ho
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Nathan
authors.initials: N
authors.lastname: Wales
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Mikkel
authors.initials: M
authors.lastname: Schubert
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Andaine
authors.initials: A
authors.lastname: Seguin-Orlando
authors.affiliation: Department of Plant Pathology, North Carolina State University.
authors.forename: Jean B
authors.initials: JB
authors.lastname: Ristaino
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, WA, Australia.
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert
mesh_terms: D019143:Evolution, Molecular; D051456:Gene Flow; D016678:Genome; D054629:Genome, Mitochondrial; D023281:Genomics / Q000379:methods; D005838:Genotype; D006239:Haplotypes; D006824:Hybridization, Genetic; D015810:Linkage Disequilibrium; D010802:Phylogeny; D055750:Phytophthora infestans / Q000145:classification* / Q000235:genetics*; D010935:Plant Diseases; D012098:Reproduction / Q000235:genetics; D013020:South America
keywords: Phytophthora andina; Phytophthora infestans; pathogen; phylogenomics; plant disease; population genomics