SummarySpartina alterniflora is an exo‐recretohalophyte Poaceae species that is able to grow well in seashore, but the genomic basis underlying its adaptation to salt tolerance remains unknown. Here, we report a high‐quality, chromosome‐level genome assembly of S. alterniflora constructed through PacBio HiFi sequencing, combined with high‐throughput chromosome conformation capture (Hi‐C) technology and Illumina‐based transcriptomic analyses. The final 1.58 Gb genome assembly has a contig N50 size of 46.74 Mb. Phylogenetic analysis suggests that S. alterniflora diverged from Zoysia japonica approximately 21.72 million years ago (MYA). Moreover, whole‐genome duplication (WGD) events in S. alterniflora appear to have expanded gene families and transcription factors relevant to salt tolerance and adaptation to saline environments. Comparative genomics analyses identified numerous species‐specific genes, significantly expanded genes and positively selected genes that are enriched for ‘ion transport’ and ‘response to salt stress’. RNA‐seq analysis identified several ion transporter genes including the high‐affinity K+ transporters (HKTs), SaHKT1;2, SaHKT1;3 and SaHKT1;8, and high copy number of Salt Overly Sensitive (SOS) up‐regulated under high salt conditions, and the overexpression of SaHKT2;4 in Arabidopsis thaliana conferred salt tolerance to the plant, suggesting specialized roles for S. alterniflora to adapt to saline environments. Integrated metabolomics and transcriptomics analyses revealed that salt stress activate glutathione metabolism, with differential expressions of several genes such as γ‐ECS, GSH‐S, GPX, GST and PCS in the glutathione metabolism. This study suggests several adaptive mechanisms that could contribute our understanding of evolutional basis of the halophyte.

中文翻译：

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互花米草基因组序列提供了对外泌盐植物耐盐机制的见解

概括互花米草是一种外泌盐植物禾本科能够在海边生长良好的物种，但其适应耐盐性的基因组基础仍然未知。在这里，我们报告了高质量的染色体水平基因组组装互花米草通过 PacBio HiFi 测序结合高通量染色体构象捕获 (Hi-C) 技术和基于 Illumina 的转录组分析构建。最终的 1.58 Gb 基因组组装的重叠群 N50 大小为 46.74 Mb。系统发育分析表明互花米草偏离了结缕草大约2172万年前（MYA）。此外，全基因组复制（WGD）事件互花米草似乎具有扩大的与耐盐性和适应盐环境相关的基因家族和转录因子。比较基因组学分析发现了许多物种特异性基因、显着扩展的基因和积极选择的基因，这些基因富集了“离子运输”和“对盐胁迫的反应”。 RNA-seq 分析鉴定了几个离子转运蛋白基因，包括高亲和力 K+运输者（HKT),萨HKT1;2,萨HKT1;3和萨HKT1;8，和高拷贝数盐过度敏感（求救）在高盐条件下上调，并且过度表达萨HKT2;4在拟南芥赋予植物耐盐性，表明互花米草以适应盐分环境。综合代谢组学和转录组学分析表明，盐胁迫激活谷胱甘肽代谢，并导致多个基因的差异表达，例如γ-ECS,谷胱甘肽S,GPX,消费税和件在谷胱甘肽代谢中。这项研究提出了几种适应性机制，可以帮助我们理解盐生植物的进化基础。