Genome annotation and genotype-phenotype association in two non-model parasites

With the rapid proliferation of high-throughput sequencing methods, both the number and variety of genome assemblies have increased and require rigorous and sophisticated methods for genome annotation. As more species’ genomes are sequenced, the targets of genome annotation projects will more commonly be species with few closely related species that have been analyzed previously. This can be a serious challenge for genome annotation, here defined as the identification and demarcation of gene models in a genome assembly. My PhD research has focused on the application and development of genome annotation methods for non-model organisms. In the first chapter of my thesis, I present a review of the field of genome annotation, which discusses current challenges and bestpractice approaches. In the second chapter of my thesis, I present analyses of the important agronomic pest, Cronartium quercuum sp. fusiforme (CQF), which causes fusiform rust disease in loblolly pine trees. I annotated the genome and used genome-resequencing data to confirm results from a previous linkage mapping study that identified the location of virulence factor 1 (Avr1) and to identify candidate Avr1 genes.