Selaginella sellowii gene regulatory networks reveal distinct transcriptional strategies for dehydration stress and recovery

Abstract

Vegetative desiccation tolerance (VDT) enables resurrection plants to withstand extreme water loss, yet its system-level regulation remains incompletely understood. Here, we interrogated the VDT landscape in Selaginella sellowii using time-series RNA-seq and a computational pipeline that integrates ensemble network inference, graph attention networks (GATs), and protein language models (PLMs). Specifically, we captured the transcriptional response to water potentials characteristic of resurrection plants but lethal to most species, including –4, –10, and –150 MPa. Our analysis revealed two distinct strategies for dehydration tolerance based on stress severity. Intermediate dehydration elicits a complex transcriptional response associated with active damage control, while extreme dehydration shifts to a minimalist, stable transcriptome. Network analysis identified 12 persistent regulators bridging quiescence and recovery. GAT embedding further demonstrated that these regulators undergo context-specific functional reprogramming to drive rapid cellular reconstruction. This study establishes a regulatory blueprint for VDT, identifies key mechanisms linking quiescence to coordinated recovery, and provides a robust methodological framework for decoding complex gene regulatory networks (GRNs).