Genome assembly and characterisation of somatic hybridisation between formae specisales of the stem rust fungus Puccinia graminis

Abstract

Puccinia graminis is an obligate biotrophic fungal pathogen causing the cereal stem rust disease and is a significant threat to food security. The most effective method of disease control is through genetic resistance in crops, which relies on an understanding of how these pathogens generate genetic diversity. The genome of P. graminis f. sp. tritici (Pgt) specialised on wheat has been studied extensively, yet nothing is known about any other formae speciales of this species. This research details the first de novo genome assemblies of P. graminis f. sp. secalis (Pgs) specialised on rye, and a putative somatic hybrid between Pgt and Pgs known as ‘scabrum’ rust. It undertakes comparative genomics, transcriptomics and phylogenetic analyses of all three formae speciales. Comparative genomics reveals that Pgs has a comparatively low level of diversity within its genome and that the core P. graminis genome comprises ~ 40 % of genes from each isolate. Biological processes common to all formae speciales were examined at different life stages of the asexual life cycle, and an expression clustering analysis of the transcriptome revealed remarkably similar behaviours in all isolates. Scabrum rusts were shown to be the result of somatic hybridisation between Pgt race 21 and a Pgs isolate, and a phylogenetic analysis of multiple isolates of Pgt, Pgs and scabrum rusts revealed that scabrum rusts throughout Australia have arisen from separate multiple independent somatic hybridisation events. This thesis explores the impacts of somatic hybridisation both within and across formae speciales with respect to generating genetic diversity in Australia and threats it may pose to agriculture.