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.

转录组学（Transcriptomics）即基因表达定量技术，为生态监测提供了一种通用的研究工具。本研究表明，通过对比对至33042个基因模型的转录本开展基因组引导的表达谱分析，可从两个纬度分隔样地采集的美洲山毛榉（American beech）多年份与季节性叶片样本中，分辨出表达差异。尽管哥伦布大交换后大规模森林砍伐造成了种群瓶颈效应，但基于单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的种群遗传背景分析仍获得了足够的遗传变异，可解释种群间与个体间的表达差异。本研究针对连续两年春夏、夏秋转换期的样本开展时序表达谱分析，共鉴定出4197个差异表达的蛋白编码基因。利用差异表达基因的杨属（Populus）直系同源基因，我们重构了蛋白质相互作用组，以表征树木在季节转换期的叶片生理状态。基因集富集分析揭示了一系列基因本体（Gene Ontology, GO）术语，涵盖了可能受非生物因子影响的分子功能与生物学过程，例如干旱恢复及降水过量响应。进一步地，基于324个共调控转录本，我们聚焦于可推定归因于晚春引发物候转变的部分术语。本研究采用保守分析得到的结果表明，扩展基于转录组的森林监测工作，可捕捉到由空气质量、慢性病害以及植食性昆虫暴发等其他因素引发的各类响应——这些因素需要激活或下调基因，以协同调控诸如美洲山毛榉这类长寿树木生存所需的反应规范。