We evaluated Pst-wheat interaction at the transcriptome level between Pst isolate LSW3_2012_SP2 and Avocet/Yr5 (R), and Avocet S (S). For the compatible interaction we used a dataset of 9.3 M Illumina paired-end clean reads in which ?300,000 reads mapped against nearly 9,000 contigs of the PST-78 reference transcriptome, whereas 3.5 M reads mapped against a partial wheat transcriptome of 13,300 contigs. Pst transcripts in the infected wheat tissues amounted to about 10% of the mapped transcripts. In the incompatible reaction, we used a dataset of 13.2 M clean reads and ?27,000 reads mapped against nearly 2,900 Pst transcriptome contigs while 7.7 M reads mapped against 18,800 wheat transcripts. These results show an important differential regulation of genes in both the fungal pathogen and the wheat host. More than 3 times the number of distinct Pst transcripts was identified in the compatible reaction than the incompatible reaction. Genes differentially regulated between the incompatible and compatible reactions will be compared in terms of functionality and GO term classification. To validate Pst transcripts involved in the infection process, we adapted a leaf rust haustorial isolation protocol for characterization of proteins and modified it to protect the integrity of RNA in enriched Pst haustoria. A list of potential effectors present in LSW3_2012_SP2 and verified in haustoria-enriched tissues will be presented.