A chromosome-scale reference genome and single-nucleus root atlas reveal the cellular and molecular basis of coastal adaptation in sand bean ( Strophostyles helvola )

Plants adapted to saline coastal habitats provide valuable systems for understanding how natural selection reshapes stress-response programs, yet the cellular and molecular basis of this adaptation remains poorly resolved. Here, we generated a chromosome-scale reference genome and a single- nucleus transcriptomic atlas of roots from sand bean ( Strophostyles helvola ), a wild legume represented by salt-tolerant Beach and salt-sensitive Inland ecotypes. The atlas comprised 87,901 nuclei assigned to 25 transcriptional clusters representing 16 major root cell types. Salt exposure elicited cell-type-specific transcriptional responses that differed between Beach and Inland roots. Beach roots preferentially maintained respiration-, energy metabolism-, and protein-homeostasis- associated functions, whereas Inland roots showed stronger induction of canonical abiotic-stress, ABA, water-deficit, hypoxia, and oxidative-stress programs. Integrating baseline ecotype differences with salt-responsive expression revealed that many genes induced by salt in Inland roots were already expressed at higher levels in untreated Beach roots. This baseline-enriched configuration comprised a broadly distributed regulatory backbone, including ERF-family transcription factors and RING-type E3 ubiquitin ligases, together with cell-type-associated modules involving ion and water transport at the root-soil interface, redox and dehydration protection in outer-root tissues, endodermal barrier-associated genes, and vascular regulatory candidates. These findings support a model in which Beach salt tolerance is associated not with entirely distinct stress-response pathways, but with the pre-existing and spatially organized deployment of conserved protective programs that remain responsive to salt exposure. Our study establishes genomic and cellular resources for sand beans and provides a framework for investigating how natural variation in the regulation and cellular organization of conserved pathways contributes to environmental stress tolerance.