Molecular mechanisms underlie the stabilization of gene regulatory networks for adaptive evolution of mangrove plants

Maintaining the stability of gene regulatory networks (GRNs) is a major challenge for plants facing environmental stresses, yet how long-term genetic changes stabilize GRNs during stress adaptation remains largely unexplored. Here, we investigate GRN evolution in mangroves, which originated from inland ancestors and adapted to intertidal zones characterized by fluctuating stressors. Gene expression under changing salinity is much more stable in the representative mangrove plant Rhizophoraapiculata than in its inland relative Carallia pectinifolia. Many genes that are salt-induced in C. pectinifolia are constitutively and highly expressed in R. apiculata, whereas genes repressed by salt-which are mainly involved in growth and development-are constitutively downregulated. This shift from stress-responsive to preactivated expression has likely enhanced GRN stability at the cost of growth, consistent with the "growth-defense trade-off" hypothesis. These expression changes are predominantly associated with duplicated genes originated from whole-genome duplications. Consistent with its stable gene expression, R. apiculata also exhibits stable chromatin accessibility, having lost many salt-responsive accessible chromatin regions (ACRs) that are associated with genome-wide elimination of transposable elements. The removal of salt-responsive regulatory elements on ACRs-which are typically closed under high salinity-promotes the preactivated expression of upstream hub transcription factors and stabilizes the expression of numerous downstream targets. It has also reduced the regulatory complexity of mangrove GRNs, yielding smaller, simpler networks that are predicted to be more stable under classical network theory. In summary, our findings reveal genomic mechanisms that stabilize GRNs in mangroves adapted to fluctuating environments and have broader implications for plant GRN evolution under future climate change.