{"paper_id":"1d1e3253-e2cb-415d-83e8-827dc61d8ec8","body_text":"Unraveling Salt-Responsive Genes in Suaeda salsa through Genomic and Transcriptomic Profiling across Salinity Gradients | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Unraveling Salt-Responsive Genes in Suaeda salsa through Genomic and Transcriptomic Profiling across Salinity Gradients Min Li, Xiangyu Zhou, Jiaxin Wu, Edward M. Golenberg, Dongxiao Zhu, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7624788/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 10 Apr, 2026 Read the published version in BMC Genomics → Version 1 posted 14 You are reading this latest preprint version Abstract Salinity severely limits global crop productivity, prompting a need to uncover plant salinity adaptation strategies. Suaeda salsa (L.) Pall., a halophyte thriving in saline habitats, offers a valuable model to dissect plant growth mechanisms under saline conditions. Although S. salsa genome assembly was recently improved, the corresponding gene annotation remained unpublished. Using the Helixer tool, we generated and released the first publicly available genome annotation for S. salsa, exhibiting high completeness with 92.80% (1,498) complete BUSCOs, thus providing an essential genomic resource. Using the S. salsa genome and annotation as our references, we conducted RNA-seq based transcriptomic profiling of plants subjected to 0, 200, and 400 mM NaCl for 30 days, respectively. We identified 462 significantly differentially expressed annotated genes across all treatments, with 11 key candidates consistently regulated. These genes are involved in key salinity response related activities including ion transport, osmotic adjustment, antioxidant defense, hormone signaling, transcriptional regulation, and genome plasticity. Enrichment analyses further supported their roles in ion homeostasis, redox regulation, and metabolic adjustment. This study provides new insights into S. salsa’s long-term salt tolerance mechanisms during normal development. The findings lay a foundation for future functional studies, comparative evolutionary analyses, and genetic improvement of salt-tolerant crops. Suaeda salsa salinity growth halophyte genome annotation transcriptome Full Text Additional Declarations No competing interests reported. Supplementary Files TableS1.RNASequencingDataStatistics.csv TableS2.PERMANOVAAnalysisResults.csv TableS3.SignificantDEGsSS2vsSS1.csv TableS4.SignificantDEGsSS3vsSS1.csv TableS5.SignificantDEGsSS3vsSS2.csv Cite Share Download PDF Status: Published Journal Publication published 10 Apr, 2026 Read the published version in BMC Genomics → Version 1 posted Editorial decision: Revision requested 30 Dec, 2025 Reviews received at journal 22 Dec, 2025 Reviewers agreed at journal 19 Dec, 2025 Reviewers agreed at journal 14 Dec, 2025 Reviews received at journal 22 Oct, 2025 Reviews received at journal 20 Oct, 2025 Reviewers agreed at journal 17 Oct, 2025 Reviewers agreed at journal 10 Oct, 2025 Reviewers agreed at journal 10 Oct, 2025 Reviewers invited by journal 10 Oct, 2025 Editor invited by journal 19 Sep, 2025 Editor assigned by journal 19 Sep, 2025 Submission checks completed at journal 19 Sep, 2025 First submitted to journal 15 Sep, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. 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