Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci

Three members of the <i>Puccinia</i> genus, <i>Puccinia</i><i>triticina</i> (<i>Pt</i>), <i>P</i><i>striiformis</i> f.sp. <i>tritici</i> (<i>Pst</i>), and <i>P</i><i>graminis</i> f.sp. <i>tritici</i> (<i>Pgt</i>), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of <i>Pt</i> and <i>Pst</i> were sequenced and compared to that of <i>Pgt</i> to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection. <i>Pt</i> had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% for <i>Pst</i> and 36.5% for <i>Pgt</i> We find all three genomes are highly heterozygous, with <i>Pst</i> [5.97 single nucleotide polymorphisms (SNPs)/kb] nearly twice the level detected in <i>Pt</i> (2.57 SNPs/kb) and that previously reported for <i>Pgt</i> Of 1358 predicted effectors in <i>Pt</i>, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic <i>Puccinia</i> species along with three pheromone receptor (<i>STE3</i>) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous <i>Ustilago maydis</i> mating assay and host-induced gene silencing (HIGS) of the HD and <i>STE3</i> alleles reduced wheat host infection.