Calm in the midst of the storm: inferring gene expression stability in flowering plants

Abstract

Introduction Gene expression in plants is inherently dynamic, shifting rapidly during development and in response to environmental stimuli. However, many essential cellular processes require remarkable transcriptomic stability. The identity, genomic features, and evolutionary conservation of stably expressed genes (SEGs) in plants across broad evolutionary scales remain poorly understood. Results We analyzed comprehensive transcriptome atlases from five species representing major clades of angiosperms (Arabidopsis thaliana, Fagopyrum esculentum, Solanum lycopersicum, Phalaenopsis equestris, and Zea mays) to identify genes with consistently low expression variation across organs, developmental stages, and environmental conditions. We identified 672 orthogroups that are universally stable across angiosperms; these are predominantly single-copy genes enriched for fundamental cellular functions including DNA repair, mRNA splicing, and translation. Validation using independent datasets and additional species confirmed that stability is maintained across diverse genotypes, conditions, and species. SEGs tend to be longer, have more exons, and exhibit lower GC content than other expressed genes. Using multiomics information available for Arabidopsis, we also explored epigenetic and functional characteristics associated with stability. Loss-of-function mutations in SEGs result in lethality far more frequently than in ubiquitously expressed genes, and protein abundance is similarly stable. SEGs have a significantly higher level of gene body methylation and H3K4me1 marks. Conclusions Our results reveal several genomic and epigenetic features that distinguish SEGs from ubiquitously expressed genes. They also suggest that SEG stability is not governed by specific regulatory motifs, but is rather “by default” state driven by a distinctive chromatin architecture.