Genomic resources to study virulence and evolution of cereal rust fungi

Abstract

Stem rust caused by Puccinia graminis f. sp. tritici (Pgt) and crown rust caused by Pucciniacoronata f. sp. avenae (Pca) are global threats the production of wheat and oat, respectively. Fast evolving populations of both Pgt and Pca limit the efficacy of plant genetic resistance and constrain disease management strategies. Chapter 1 provides background information about both rust fungi and their biology, shares a comprehensive review of the available genome resources in the rusts, and highlights some advancements in rust research and how they can be utilized. Chapter 2 describes a study where my colleagues and I developed a pipeline for identifying candidate susceptibility genes for future study of stem rust virulence using comparative transcriptome-based and orthology-guided approaches. The analysis was targeted to genes with differential expression in T. aestivum and genes suppressed or not affected in B. distachyon and reports several processes potentially linked to susceptibility to Pgt, such as cell death suppression and impairment of photosynthesis. The approach was complemented with a gene co-expression network analysis to identify wheat targets to deliver resistance to Pgt through removal or modification of putative susceptibility genes. This work could help further the understanding of the molecular mechanisms that lead to rust infection and disease susceptibility; this in turn could deliver novel strategies to deploy crop resistance through genetic loss of disease susceptibility. A significant contribution of this work is a pipeline that can be adapted to study virulence of other rust fungi. Finally, Chapter 3 describes a high-quality genome assembly of Pca isolate 203. The ultimate goal of the assembly is to provide the first fully haplotype-phased, chromosome level reference for Pca. To this end, PacBio long reads and Illumina short reads were obtained to create the initial draft assembly, while Hi-C reads were collected to order contigs and phase the genome. Contigs were assigned to haplotype bins using gene synteny initially, and these bins were aligned to the Pgt 21-0 A haplotype genome to evaluate the probable number of chromosomes and possible chromosome sizes. Future steps for completing the high-quality assembly include an iterative process to fix haplotype phase swaps through manual curation and scaffolding, final chromosome assignment, and annotation with RNAseq data. A collection of publications with my contributions is provided in the appendix section.