Puccinia graminis

Stem (black) rust, caused by Puccinia graminis, has plagued cereal crop production (wheat, barley, rye and oat) since the early days of agriculture. P. graminis is an obligate biotroph with a complex life cycle that includes five spore stages and two hosts. The asexual stage (uredinal) has a broad host range that includes cereals and grasses. P. graminis f. sp. tritici (Pgt), the form that infects wheat and barley, has a large (~90 Mb) and complex genome in which repetitive elements occupy approximately 44 % of the assembly. A set of 17,773 predicted genes was compared to other fungal genomes, which identified a core set of approximately 8,000 proteins that are shared between Pgt and the popular rust pathogen, Melampsora larici-populina. This shared set included expanded gene families involved in cell wall modification, transport and antioxidant defence. Many genes in these expanded families as well as species-specific small secreted genes are highly transcriptionally upregulated during the infection of wheat by Pgt, consistent with the hypothesis that they play an important role during the infection process. Mining genome and transcriptome data, over 1,000 candidate effector proteins were identified. Genome-wide SNP data derived from re-sequencing of the genomes of several Pgt isolates has enabled the development of a Pgt SNP chip, as well as a rapid molecular diagnostic assay for the Ug99 lineage.