Halophytes have evolved specialized strategies to cope with high salinity. The extreme halophyte sea lavender (Limonium bicolor) lacks trichomes but possesses salt glands on its epidermis that can excrete harmful ions, such as sodium, to avoid salt damage. Here, we report a high-quality, 2.92-Gb, chromosome-scale L. bicolor genome assembly based on a combination of Illumina short reads, single-molecule, real-time long reads, chromosome conformation capture (Hi-C) data, and Bionano genome maps, greatly enriching the genomic information on recretohalophytes with multicellular salt glands. Although the L. bicolor genome contains genes that show similarity to trichome fate genes from Arabidopsis thaliana, it lacks homologs of the decision fate genes GLABRA3, ENHANCER OF GLABRA3, GLABRA2, TRANSPARENT TESTA GLABRA2, and SIAMESE, providing a molecular explanation for the absence of trichomes in this species. We identified key genes (LbHLH and LbTTG1) controlling salt gland development among classical trichome homologous genes and confirmed their roles by showing that their mutations markedly disrupted salt gland initiation, salt secretion, and salt tolerance, thus offering genetic support for the long-standing hypothesis that salt glands and trichomes may share a common origin. In addition, a whole-genome duplication event occurred in the L. bicolor genome after its divergence from Tartary buckwheat and may have contributed to its adaptation to high salinity. The L. bicolor genome resource and genetic evidence reported in this study provide profound insights into plant salt tolerance mechanisms that may facilitate the engineering of salt-tolerant crops.

盐生植物已经进化出专门的策略来应对高盐度。极端盐生植物海薰衣草（Limonium bicolor）缺乏毛状体，但其表皮上有盐腺，可以排出钠等有害离子，以避免盐害。在这里，我们报告了基于 Illumina 短读长、单分子、实时长读长、染色体构象捕获 (Hi-C) 数据的组合的高质量、2.92-Gb、染色体级双色乳杆菌基因组组装，和 Bionano 基因组图谱，极大地丰富了具有多细胞盐腺的盐生植物的基因组信息。尽管L. bicolor基因组包含与拟南芥的毛状体命运基因相似的基因，它缺乏决定命运基因GLABRA3、ENHANCER OF GLABRA3、GLABRA2、TRANSPARENT TESTA GLABRA2和SIAMESE的同源物，为该物种没有毛状体提供了分子解释。我们确定了控制经典毛状体同源基因中盐腺发育的关键基因（LbHLH 和 LbTTG1），并通过显示它们的突变显着破坏盐腺起始、盐分泌和耐盐性来证实它们的作用，从而为长期存在的假设提供遗传支持盐腺和毛状体可能有共同的起源。此外，在L. bicolor中发生了全基因组复制事件与苦荞分离后的基因组，可能有助于其适应高盐度。本研究报告的L. bicolor基因组资源和遗传证据为植物耐盐机制提供了深刻的见解，可能有助于耐盐作物的工程化。