TY - JOUR T1 - Comparative analysis highlights variable genome content of wheat rusts and divergence of the mating loci JF - bioRxiv DO - 10.1101/060665 SP - 060665 AU - Christina A. Cuomo AU - Guus Bakkeren AU - Hala Badr Khalil AU - Vinay Panwar AU - David Joly AU - Rob Linning AU - Sharadha Sakthikumar AU - Xiao Song AU - Xian Adiconis AU - Lin Fan AU - Jonathan M. Goldberg AU - Joshua Z. Levin AU - Sarah Young AU - Qiandong Zeng AU - Yehoshua Anikster AU - Myron Bruce AU - Meinan Wang AU - Chuntao Yin AU - Brent McCallum AU - Les J. Szabo AU - Scot Hulbert AU - Xianming Chen AU - John P. Fellers Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/06/24/060665.abstract N2 - Three members of the Puccini genus, P. triticina (Pt), P. striiformis f.sp. tritici(Pst), and P. 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 of Pt and Pst were sequenced and compared to that of Pgt 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. Pt 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; by comparison repeats occupy 31.5% for Pst and 36.5% for Pgt. We find all three genomes are highly heterozygous, with Pst (5.97 SNPs/kb) nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt. Of 1,358 predicted effectors in Pt, 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 dikaryotic Puccinia species. The HD proteins were active in a heterologous Ustilago maydis mating assay and host induced gene silencing of the HD and STE3 alleles reduced wheat host infection. ER -