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..., American beech leaves have been felled from the canopy through Spring, Summer and Fall between 2017 and 2018. For subcanopy trees we used a 12m pruner pole. Sample collections were done in the morning to avoid expression changes throughout the day. For each sample, 10 leaf discs were punched into 2ml extraction vials containing 3 steel balls of 3mm in diameter, and flash frozen in liquid nitrogen in the field (SI Fig. S2). Frozen samples were then transferred to a -80 freezer at the end of the day. RNA extractions were carried out using E.Z.N.A Plant RNA Kit by Omega Bio-Tek (Norcross, GA, USA). Quality metrics for extracted RNA were determined using the Agilent Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA) and samples containing genomic DNA contaminants were treated with DNAse I (ThermoFisher Scientific, Waltham, MA). Illumina TruSeq libraries were prepared for each sample RNA (Illumina Inc., San Diego, CA, USA). Libraries were indexed and pooled to be sequenced o..., , # Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech

## Description of the Data and file structure

Public access to the two beech genomes assembled by the University of Connecticut and the Cornell University: \
There are six items in this submission.

\[1] An Excel formatted multi-tab spreadsheet containing sample list (gray shading denotes missing or low quality samples not included in the study), genome alignment rates, transcript raw counts, ordination results, list of top 20 differentially expressed genes, g:Profiler output permalinks, kinship matrix, Kendalls correlation values and an annotated list of 324 leaf phenology-related gene orthologs.
\[2] A compressed Variant Call Format (VCF) file containing SNP variations of 40 trees (20 from Harvard Forest and 20 from the SERC ForestGEO forest dynamics plots) aligned to the draft American beech genome assembled by the University of Connecticut.
\[3] Fasta formatted am...