The adaptive evolution of the plant pathogen Albugo candida

Albugo candida is a plant pathogen that has been reported on many host species. While multiple host-specific races have long been recognized in A. candida, the genetic variation of these races has never been explored in nature and little is known about how the pathogen has adapted to its many hosts. Recently, evidence of genetic exchanges between races suggested that hybridization played an important role in the evolution of A. candida races. The authors also demonstrated that host-specific races of A. candida can co-occur, provided the immune system of the host is compromised by a compatible race. This immunosuppression by A. candida had previously been shown to allow growth of other pathogens. To study both these phenomena (the evolution of and the host immunosuppression imposed by A. candida), a capture array was designed to sequence 187 loci (~660,000 bp) from A. candida and loci from 47 other plant pathogens. In Chapter 3, I explain the rationale and methodology behind this approach. I show that it is cost-effective and that it may be used to identify microorganisms directly from a leaf and make inference about pathogen abundance within samples. In Chapter 4, genetic diversity of A. candida is analysed at a 400 kb contig and 32 diversity-tracking genes. Races are identified based on genetic divergence and recombination is investigated within and between races. In Chapter 5, I investigate genetic diversity at heterozygous sites to study the ploidy level and the reproductive mode of A. candida races as well as to detect mixed A. candida infections and loss-of-heterozygosity events. In this thesis, I demonstrate that A. candida races adapt to their hosts using complex mechanisms and that some may, in the long term, speciate. I also provide a novel method which may be used to interrogate microbial diversity directly from the field