DOI: 10.5061/dryad.fxpnvx0vp
title: Leaf gene expression trajectories during the growing season are consistent between sites and years in American beech

description: 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.
description: 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 on the Illumina NovaSeq 6000 platform as 150 nucleotide long
 paired end reads targeting ~14 million total reads per sample (Illumina
 Inc., San Diego, CA, USA). Sequences are uploaded to the NCBI Sequence
 Read Archive (SRA) with the bioproject number PRJNA630305.
description: # 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 amino acid sequences
 of protein models predicted from the draft genome assembly. \[4] A Fasta
 formatted subset of 4197 protein sequences corresponding to the
 differentially expressed transcripts. This set was used to construct the
 interactome network using the STRING database. \[5] A Fasta file formatted
 draft American beech genome assembly used in this study. Assembly was
 computed by Shasta assembler. \[6] A text file compiling representative
 snippets from the command line and code used in the manuscript. ##
 Sharing/access Information Links to other publicly accessible locations of
 the data: \ RNA-seq derived raw
 FASTQ read sequences are uploaded to the NCBI Sequence Read Archive (SRA)
 with the bioproject number PRJNA630305. Was data derived from another
 source? If yes, list source(s):