Data from: Conservation and divergence of gene expression plasticity following c. 140 million years of evolution in lodgepole pine (Pinus contorta) and interior spruce (Picea glauca × Picea engelmannii)

Species respond to environmental stress through a combination of genetic
adaptation and phenotypic plasticity, both of which may be important for
survival in the face of climatic change. By characterizing the molecular
basis of plastic responses and comparing patterns among species, it is
possible to identify how such traits evolve. Here, we use de novo
transcriptome assembly and RNA-seq to explore how patterns of gene
expression differ in response to temperature, moisture, and light regime
treatments in lodgepole pine (Pinus contorta) and interior spruce (a
natural hybrid population of Picea glauca and Picea engelmannii). We found
wide evidence for an effect of treatment on expression within each
species, with 6,413 and 11,658 differentially expressed genes identified
in spruce and pine, respectively. Comparing patterns of expression among
these species, we found that 74% of all orthologs with differential
expression had a pattern that was conserved in both species, despite 140
million years of evolution. We also found that the specific treatments
driving expression patterns differed between genes with conserved vs.
diverged patterns of expression. We conclude that natural selection has
likely played a role in shaping plastic responses to environment in these
species.