Plant pathogens in the genus Phytophthora are known to cause disease on field crops, nursery plants, and forest trees. The best known example probably is Phytophthora infestans, which triggered the infamous Irish potato famine. Other important Phytophthora species include: P. ramorum (sudden oak death pathogen), P. sojae (soybean root rot pathogen) and P. cinnamomi (broad host range root rot pathogen). Knowledge and understanding of a pathogen’s host range, geographic distribution, genetic diversity, and evolutionary potential is a key to successful disease management. This thesis focused on using phylogeographic principles combined with genomics tools to answer questions regarding the expansion from the center of origin of P. infestans, identifying the putative center of origin for P. cinnamomi and evolution of RxLR (Arginine-any amino acid-Leucine-Arginine) effector genes in three Phytophthora species.
A pathogen’s biology at its center of origin may be different compared to other geographical regions. This has been well demonstrated for the late blight pathogen P. infestans. Toluca Valley of Mexico is considered the center of origin of P. infestans, where it reproduces sexually and both mating types exist in a 1:1 ratio. Very few studies have looked into the population structure outside of Toluca Valley, but still in Mexico. We performed a detailed analyses using microsatellite markers and identified a gradient of genetic diversity in P. infestans populations outside of the Toluca Valley.
We used evidence of equal mating type frequencies, high genetic diversity, sexual reproduction combined with phylogenetics to identify the putative center of origin of broad host range pathogen P. cinnamomi from a global population sample. Our result suggests Asia as the center of origin for the broad host range pathogen P. cinnamomi and subsequent migration out of Asia to Australia and Africa.
Phytophthora species secrete numerous effectors during the process of infection which are thought to modulate the host defense system. One such class of effector is RxLR which help promote the infection and colonization of host cells. Some of these RxLR effectors can be targeted by plant resistance genes to initiate a defense response. The question of which of these genes have been conserved or lost during the evolution of Phytophthora species is largely unknown. Therefore, we used whole genome sequence data and a comparative genomics approach to test the hypothesis of variation in RxLR gene content in three Phytophthora clade 1C species. Our analysis demonstrated both conservation and proliferation of RxLR genes in these species along with high sequence diversity. We also observed emergence of a virulent allele for effector Avr3a in the modern isolates of P. infestans. Balancing selection has acted on the RxLR genes maintaining the high sequence diversity. The ascertainment bias due to mapping of short sequencing reads to the single reference genome was further quantified by assembling the unmapped reads and predicting genes shared by all isolates of P. infestans.
Overall, this thesis broadens our phylogeographic and evolutionary understanding of pathogen Phytophthora species. A key to breeding for disease resistance is highly dependent on the effector repertoire of a pathogen and thus our work can help breeders to screen for resistance gene against the late blight pathogen.