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)

Abstract

Summary 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 used de novo transcriptome assembly and RNAseq 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 6413 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 yr of evolution. We also found that the specific treatments driving expression patterns differed between genes with conserved versus diverged patterns of expression. We conclude that natural selection has probably played a role in shaping plastic responses to environment in these species.

Insights into Conifer Giga-Genomes

“…They have been used to conduct various structural and population genome scans for genetic linkage mapping (see below) and for large-scale association studies with phenotypic and environmental variation in spruces, pines, and Douglas fir (Eckert et al, 2012;Prunier et al, 2013;De La Torre et al, 2014b). Present efforts aim at transcriptome-wide association studies and genome-wide association studies (GWAS) utilizing tens of thousands of genetic variants of diverse nature using genotyping chips or resequencing methods (Yeaman et al, 2014).…”

Tree Responses to Environmental Cues

“…Under conditions of climate change, an increase in forest dieback driven by a higher frequency of drought and heat stress events has been predicted (Anderegg et al, 2013). While the majority of studies investigating stress responses and tree mortality has focussed on individual stresses, only a few studies explore tree responses to the combined effect of elevated temperature and drought (Adams et al, 2009;Kolb & Robberecht, 1996;Yeaman et al, 2014;Zhao, Hartmann, Trumbore, Ziegler, & Zhang, 2013). In trees, most work on the combined effects of multiple stresses has focused on physiological responses.…”

“…To date, only a limited number of reports have investigated the regulatory mechanisms underlying plant responses to a combination of stresses (Prasch & Sonnewald, 2013;Rasmussen et al, 2013;Rizhsky et al, 2004;Yeaman et al, 2014). A pioneering study by Rizhsky et al (2004) investigated the effect of drought, heat stress and the combination of the two stresses on the transcriptome of Arabidopsis.…”

Biological Invasions, Climate Change, and Genomics

“…The use of sequence tagging and 'PoolSeq' technologies, together with relatively inexpensive RNA-Seq, genotyping-by-sequencing (GBS) and other reduced-representation library methods, means that data on many thousands of single nucleotide polymorphisms (SNPs) can be collected at moderate cost on multiple samples from a population without a reference genome (Box 1) (e.g. Hohenlohe et al 2010;Elshire et al 2011;Bi et al 2013;Neves et al 2013;Yeaman et al 2014). However, even draft reference genomes or genomes from related species can be useful when implementing these approaches to identify variants.…”