Genome evolution and regulatory dynamics underlying salt stress tolerance in the halophyte Halogeton arachnoideus

Plants inhabiting extreme environments provide valuable genetic resources for studying stress-resistance mechanisms. Halogeton arachnoideus (Amaranthaceae sensu lato) is a typical halophyte native to saline habitats, yet the molecular mechanisms underpinning its adaptation remain unclear. Here, we present a high-quality, chromosome-scale genome assembly using PacBio HiFi long-read sequencing and high-throughput chromosome conformation capture (Hi-C) technologies. The genome is highly repetitive and dominated by long terminal repeat retrotransposons, which shape genome architecture and potentially modulate gene regulatory landscapes. Although no lineage-specific whole-genome duplication (WGD) event is detected, genes derived from ancient WGD and tandem duplications likely provide evolutionary substrates for salt-associated responses. Transcriptomic analyses under moderate and high salinity treatments reveal extensive transcriptional remodeling. Gene regulatory networks analyses uncover stress-induced rewiring and decentralization. Transcription factor families (MYB, AP2/ERF, WRKY, and bHLH) constitute major components of the salt-responsive regulatory landscape, while NAC and C₂H₂ factors display concentration-specific regulatory activity. We also detect a shift in regulatory hubs from early to initial acclimation stress phases, pointing to a coordinated but temporally coarse regulatory transition. Together, this integrative genomic and transcriptomic framework provides insights into the evolutionary processes and regulatory organization associated with salt responsiveness in H. arachnoideus and provides a foundation for improving salt-tolerant crops.