De novo transcriptome assembly of whitebark pine (Pinus albicaulis) for white pine blister rust resistance study. Whitebark pine (Pinus albicaulis) reference transcriptome and white pine blister rust resistance

Whitebark pine (Pinus albicaulis) is an ecologically important species that is susceptible to white pine blister rust (WPBR), a lethal disease caused by the non-native fungal pathogen Cronartium ribicola. At Dorena Genetic Resource Center in Oregon, needle tissue was collected from the half-sibling progeny of a putatively resistant tree (Mt. Rainier 'Shadow Lake 39'). Needles were sampled and flash-frozen for individuals before (control) and 3 days post-inoculation with basidiospores. RNA was extracted from needles of four individuals representing 4 conditions: CR= control resistant, CS= control susceptible, IR= inoculated resistant, IS= inoculated susceptible. Libraries were prepared to be strand-specific, size-selected, and multiplexed over four lanes of Illumina MiSeq to generate paired-end reads (2x300bp). Quality-controlled reads were assembled de novo using Trinity into a reference transcriptome. Transcripts were functionally annotated with BLAST-derived descriptions, gene ontology terms, and predicted protein products. To study differential gene expression associated with WPBR resistance, pooled libraries from 24 individuals were multiplexed over 6 lanes of Illumina HiSeq 2000 to generate single-end 100bp reads. Reads were mapped to the reference transcripts to generate read counts as inputs for differential gene expression analysis.