Historic herbarium specimens used to understand the source and origins of the Irish famine pathogen, Phytophthora infestans

Background/Question/Methods .

Phytophthora infestans, an oomycete pathogen, caused the Irish potato famine and is a threat to food security globally. Phytophthora infestans was the first species in the genus described and left a path of devastation on potato in its wake in the US, Ireland and Europe in the nineteenth century. Several important research questions of interest include the identity and source of famine-era outbreaks, understanding the evolutionary history of the Ic clade of Phytophthora, and the center of origin of the disease. Two theories exist that either Mexico or the Andean region is the center of origin of the pathogen and source of disease outbreaks. We are also interested in the evolution of the pathogen over the past 150 years and understanding differences in historic and modern day genomes. We have tracked recent and historic genotypes of P. infestans using mtDNA haplotyping, multilocus genotyping, and next generation sequencing. We are also using geospatial analytics and archival data-mining to map historic outbreaks.

Results/Conclusions

A single lineage named US-1 (Ib mtDNA haplotype) was globally distributed in the 20^th century and was proposed as the ‘famine-era’ lineage of P. infestans with a Mexican origin. We conducted the first direct PCR amplification of mtDNA genes from 19^th-century herbarium samples of blight-afflicted potato leaves and our data indicated that instead, a Ia mtDNA haplotype was the culprit. The same unique multilocus SSR genotype, named FAM-1, caused historic outbreaks in both the US and Europe. The FAM-1 lineage was widespread for over 100 years, and shared allelic diversity with the oldest specimens collected in Colombia and Costa Rica but not Mexico. FAM-1 formed a genetic group distinct from more recent modern aggressive lineages. Data from whole genome sequences from herbarium samples with P. infestans also links ancestral lineages to the Andes. The FAM-1 and US-1 clonal lineages were basal in the tree, from historic samples collected outside Mexico, and diverged much earlier than present-day lineages in Mexico, the US and Europe. The FAM-1 lineage was also a parent to the hybrid species P. andina which only exists in the Andean region. Thus, herbarium specimens are providing new information on the population biology of old outbreaks