UC Riverside

The oomycetes are a group of filamentous diploid organisms that superficially resemble true fungi, but instead belong to the kingdom Stramenopiles. Many oomycetes are responsible for devastating diseases of plants, including Phytophthora infestans, the cause of late blight on potato and tomato, and the notorious agent behind the Irish potato famine in the mid 1840s. P. infestans remains as destructive today as it was in the past due to its ability to spread through explosively through susceptible fields given ideal conditions and rapid adaptability to environmental stresses, host defenses, and chemical control. To understand this remarkable adaptability, we examined laboratory- generated sexual population and observed a major genetic locus conferring resistance to the popular fungicide metalaxyl segregating through the progeny. We found that this locus was genetically separate from a previously described locus shown to confer resistance to metalaxyl. Identification of the genes underlying our new major locus was unsuccessful due to the unassembled nature of the currently available reference genome for P. infestans. We sought to construct a new reference genome using a combination of third generation sequencing and scaffolding technology, as well as utilizing two sexual populations of P. infestans to construct genetic maps to assembly of chromosome-sized scaffolds. A large interval of markers strongly associated with metalaxyl resistance was identified at the end of chromosome three. 130 genes were identified in this interval, several of which may play a role in the resistance phenotype. This new reference genome also allowed us to examine the extent of structural variation and genome plasticity within our sexual populations, and we observed considerable plasticity in the forms of whole genome triploidy, tetraploidy, and individual aneuploid chromosomes. Transcriptomic analysis similarly revealed extensive variation among progeny, and our results conclude that sexual reproduction has the potential to induce massive levels of variation in a short period of time in P. infestans.