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The wheat stem rust fungus  Puccinia graminis  f. sp.  tritici  ( Pgt ) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian  Pgt  isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American  Pgt  isolate CDL 75-36-700-3 (p7a) and  de novo  assembly were performed resulting in a 92 Mbp reference genome for  Pgt  isolate 21-0. Approximately 13 Mbp of  de novo  assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other  Pgt  rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian  Pgt  isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes ( Sr5 ,  Sr11 ,  Sr27 ,  SrSatu ) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.

frontiers in plant science

Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes