Integration of short- and long-term responses to environmental stimuli shape seasonal transcriptome dynamics

Abstract

Plants must respond to various environmental factors that change seasonally. In a previous study, seasonally oscillating genes were identified by a massive time-series transcriptome analysis in a wild population of Arabidopsis halleri ssp. gemmifera, a sister species of Arabidopsis thaliana. To analyze the function of these seasonally oscillating genes, we established an experimental system to mimic seasonal expression trends using A. thaliana. Arabidopsis thaliana plants were cultured under conditions that mimicked average monthly temperatures and daylengths in a "smart growth chamber mini," a hand-made low-cost small chamber. Under different short-term incubations, the seasonal trends of 1627 seasonally oscillating genes were mimicked. These seasonally oscillating genes had varying temporal responsiveness (constant, transient, and incremental). Our findings suggest that plants perceive and integrate information about environmental stimuli in the field by combining seasonally oscillating genes with temporal responsiveness.

Key Pathways and Genes of Arabidopsis thaliana and Arabidopsis halleri Roots under Cadmium Stress Responses: Differences and Similarities

“…This analysis indicated that in A. halleri roots the genes with the strongest significant variation (both positive and negative) among Cd stress and control are, in any case, associated with responses to chemical and generic stimuli. This agrees with the evidence that A. halleri can perceive and respond appropriately to different environmental stimuli, modulating and integrating multiple stimulus information [54] and giving a specific response to a peculiar heavy metal [55]. Specifically, Cd induces oxidative stress due to the impairment between photosynthetic and respiration activities [56], which has also been described in A. halleri [12].…”

“…Indeed, abnormal responses of plants to stress rely on the elimination of crucial players from the stress-related networks [65]. This is because plants respond to specific stresses by modulating complex interconnected pathways in which some genes play crucial roles both in generalized and specific responses to stress [54,55]. In this sense, after hub identification, we detected genes with a significant differential expression under Cd stress by DESeq2 package to confirm hub gene predictions [34,35].…”