Chromatin accessibility and transcriptome analyses reveal stress-responsive regulatory elements in Zygophyllum xanthoxylum

Abstract The adaptive evolution of xerophytes to abiotic stresses is intimately linked with evolutionarily conserved cis-regulatory elements (CREs). However, the key CREs and conserved noncoding sequences (CNSs) involved in stress responses remain largely unexplored. In this study, we investigated the epigenetic regulatory mechanisms of the xerophyte Zygophyllum xanthoxylum under abiotic stress using an integrated multi-omics approach. Using ATAC-seq, we mapped genome-wide chromatin accessibility profiles in shoots and roots under heat, salt, and drought treatments, identifying 2,423 to 77,497 high-quality accessible chromatin regions (ACRs). Z. xanthoxylum employs distinct chromatin remodeling strategies for different stresses: chromatin tends to open under salt and drought conditions but close under heat stress. By integrating RNA-seq data, we correlated ACR dynamics with gene expression changes and identified significant alterations in transcription factor binding profiles within these accessible regions. We validated a stress-responsive regulatory pathway where the ZxNF-YC10-ZxAPK1 module induces promoter-associated ACR opening, leading to gene expression upregulation. Comparative genomic analysis across 5 xerophyte species identified 165,896 phylogenetically CNSs containing critical transcription factor binding sites. These species-specific CNSs were significantly enriched within central regions of ACRs and exhibited higher overlap with root ACRs, suggesting they may represent crucial CREs that evolved during adaptation to adverse environments. Our study provides a comprehensive chromatin accessibility atlas for Z. xanthoxylum under diverse abiotic stresses and establishes cross-species CNS resources that may facilitate genetic improvement of stress-tolerant crops.