Tandem gene duplication facilitates intertidal adaptation in atypical mangrove plants

SUMMARY Mangrove plants, originating from inland ancestors, have independently adapted to extreme intertidal zones characterized by salt and hypoxia stress. While typical mangroves exhibit specialized phenotypes, like viviparous seeds and salt secretion, atypical clades that have thrived without such traits are particularly suitable for exploring the molecular and physiological basis underlying plant adaptation to intertidal zones. We assembled a chromosome‐level genome of an atypical mangrove, Scyphiphora hydrophylacea , the only mangrove species in Gentianales. Similar to other mangroves, S. hydrophylacea colonized intertidal zones during climatic optimum periods of sea‐level rise. Despite lacking recent whole‐genome duplications (WGDs), its genome acquired extensive tandem gene duplications (TDs), leading to the rapid expansion of key salt‐ and hypoxia‐related genes. Transcriptome data further corroborated that TD‐driven gene expansions contribute to stress tolerance. Specifically, the expansion of genes involved in cation transmembrane transport, osmotic regulation, and oxidative stress response may enhance salinity tolerance, and the expansion of signal transduction and energy metabolism genes in hypoxia‐response pathways may confer waterlogging tolerance. Therefore, in the absence of large‐scale gene duplication, the rapid expansion of core genes involved in salt and hypoxia tolerance through tandem duplication may represent a key force driving the adaptation of atypical mangroves. These findings also provide valuable insights for crop improvement strategies aimed at enhancing environmental resilience while maintaining phenotypic stability.