The Genomics of Adaptation to Climate: de novo Assembly and Gene Expression Analysis of Interior Spruce and Lodgepole Pine

Here, we present the results of transcriptome sequencing projects that we undertook in lodgepole pine (Pinus contorta) and Interior spruce (Picea engelmanii x Picea glauca). To assemble reference transcriptomes from each species, we sequenced RNA libraries created using tissues from growing tips, roots, and stems from 48 pine individuals and 41 spruce individuals. These individuals had been grown under seven different treatments wich varied in their temperature, moisture, and light regimes, in order to represent a range of biologically realistic environments. We used Trinity to create de novo assemblies for each species by combining together sequence files from seven different individuals prior to running the assembly program. To estimate gene expression, we used RSEM to align the individual transcript reads for each library back to the reference transcriptomes from Trinity. We found 10428 genes that were differentially expressed in pine (between the seven experimental treatments), compared to  7650 genes in spruce. Following the removal of short contigs, contaminating sequence, and contigs with no detectable expression, our draft reference transcriptomes contain 33746 genes for pine and 40862 genes in spruce. We present results of GO analysis and discuss how these draft transcriptomes can be used to design probes for targeted sequence capture.