Molecular Evolution and Gene Expression in Lodgepole Pine and Interior Spruce

Plasticity helps species cope with variable environments, and will be an import component of how species respond to climate change, particularly for long-lived organisms such as forest trees. Studying gene expression allows us to characterize plasticity in response to abiotic factors across thousands of genes. However, the relationship between phenotypic plasticity and molecular evolution remains poorly understood. Here, we explore how gene expression varies among 48 lodgepole pine and 41 interior spruce individuals exposed to one of seven treatments representing a range of moisture, temperature, and light regimes. We performed RNAseq from root, stem, and leaf tissue, yielding approximately 3.8 Gb of data per library. Following this we assembled a reference transcriptome for each species with Trinity and used RSEM and EdgeR to estimate expression levels for each gene in our transcriptome and identify differences in expression among treatments.  We found 8894 and 11618 differentially expressed genes in spruce and pine, respectively. Following this we identified orthologs between pine and spruce, determined the rate of sequence evolution in both the UTRs and coding regions of these othologs, as well as the divergence in gene expression among species across treatments. We also calculated the proportion of adaptive substitutions fixed by selection (alpha). Several genomic factors are predicted to be associated with sequence evolution including gene expression level, divergence and specificity across environments. These results are important for understanding the determinants of protein evolution and the impact of plasticity on the genome.