Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech

Transcriptomics, the quantification of gene expression, provides a versatile tool for ecological monitoring. Here, we show that through genome-guided profiling of transcripts mapping to 33,042 gene models, expression differences can be discerned among multi-year and seasonal leaf samples collected from American beech trees at two latitudinally separated sites. Despite a bottleneck imposed due to large-scale post-Columbian deforestation, the SNP-based population genetic background analysis has yielded sufficient variation to account for differences between populations and among individuals. Our time series of expression analyses during spring-summer and summer-fall transitions for two consecutive years involved 4,197 differentially expressed protein-coding genes. Using Populus orthologs of the differentially expressed genes, we reconstructed a protein-protein interactome as a representation of the leaf physiological states of trees during the seasonal transitions. Gene set enrichment ana...