Regulation of gene expression in incompatible/compatible reactions between stripe rust isolates from western Canada and wheat

We evaluated the interaction at the transcriptome level between two Puccinia striiformis f.sp. tritici (Pst) western Canadian isolates, LSW3_2012_SP2 and SWS484_SPF, with resistant and susceptible hosts. The number of clean Illumina paired-ends reads obtained from inoculated tissues in compatible and incompatible reactions with isolates SWS484 and LSW3 ranged from 78 M to 184 M. To validate Pst transcripts involved in the infection process, over 2.9 M reads were obtained from intact RNA isolated from LSW3 infected haustoria. Mapping of reads against the PST-78 transcripts reference reveals that 54% of the reads are mapped in the compatible reaction while only 0.5% did map in the incompatible reaction. The proportion of the reads mapping to cereal transcriptomes was 28% and 86% for compatible and incompatible reactions. These results show an important differential regulation of genes in both the fungal pathogen and the wheat host. Genes differentially regulated between the incompatible and compatible reactions were characterized by annotation and GO term classification. A list of potential effectors present in both LSW3 haustoria-enriched tissues and infected leaf tissues will be presented. As we used Illumina Mate Pair (MP) and PacBio technologies to obtain larger contigs and scaffolds for these two Pst isolates, the distribution of putative effectors has been mapped to the scaffolds and results will be presented in elucidating sequences involved in these specific reactions.