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 analysis revealed GO terms that highlight molecular functions and biological processes possibly influenced by abiotic forcings such as recovery from drought and response to excess precipitation. Further, based on 324 co-regulated transcripts, we focused on a subset of terms that could be putatively attributed to phenological shifts due to late spring. Our conservative results indicate that extended transcriptome-based monitoring of forests can capture ranges of responses arising from other factors including air quality, chronic disease as well as herbivore outbreaks that require activation and/or downregulation of genes collectively tuning reaction norms needed for the survival of long-living trees such as the American beech.