Comparative analysis highlights variable genome content of wheat rusts and divergence of the mating loci

Abstract

AbstractThree members of thePuccinigenus,P. triticina(Pt),P. striiformis f.sp. tritici(Pst), andP. graminis f.sp. tritici(Pgt), 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 ofPtandPstwere sequenced and compared to that ofPgtto 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.Pthad the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; by comparison repeats occupy 31.5% forPstand 36.5% forPgt. We find all three genomes are highly heterozygous, withPst(5.97 SNPs/kb) nearly twice the level detected inPt(2.57 SNPs/kb) and that previously reported forPgt. Of 1,358 predicted effectors inPt, 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 enzyme degradation. Two allelic homeodomain, HD1 and HD2, pairs and three pheromone receptor (STE3) mating-type genes were identified in each dikaryoticPucciniaspecies. The HD proteins were active in a heterologousUstilago maydismating assay and host induced gene silencing of the HD andSTE3alleles reduced wheat host infection.