Individual sequencing libraries for each cDNA preparation were constructed and sequenced using a 454 sequencer as previously described . The cDNA preparations were sheared to approximately 500 bp fragment lengths. Adaptor sequences containing unique barcodes for each library were ligated to the fragmented cDNAs and immobilized on beads. The libraries for the five disease-resistant trees were pooled and the libraries for the five disease-susceptible trees were combined for separate multiplex sequencing, each on a different half of the same plate. Multiplex sequencing of the library pools was performed on an FLX model 454 DNA sequencer (Roche Diagnostics) at Penn State University. The DNA sequence files for each of the ten cDNA libraries were selected and compiled from the batch sequencing raw data files using a Newbler 454 software utility, based on the unique barcodes assigned to each of the libraries. Sequences generated in this study were submitted to the Short Read Archive at the National Center for Biotechnology Information, accessions numbers SRX1781388 to SRX1781397, for NCBI BioProject Accession PRJNA321730 (NCBI: http://www.ncbi.nlm.nih.gov).