miRNA–mRNA integrated analysis reveals candidate genes associated with salt stress response in Halophytic <i>Sonneratia apetala</i>

<i>Sonneratia apetala</i> is a pioneering species of mangrove plants, which has evolved various mechanisms to tolerate salt-stress due to their long-term exposure to a salinized environment as compared to the of terrestrial freshwater plants. However, limited attempt has been made to uncover the underlying molecular mechanism of their saline adaptation. Here, we integrated mRNA and microRNA (miRNA) sequencing to identify the genes and pathways that may be involved in salt stress-response in the roots of <i>S. apetala</i>. A comprehensive full‑length transcriptome containing 295,501 high‑quality unigenes was obtained by PacBio sequencing technology. Of these, 6,686 genes exhibited significantly differential accumulation after salt stress treatment (<i>p</i> &lt; 0.001, <i>Q</i> &lt; 0.01). They were mainly implicated in plant signal transduction and diverse metabolic pathways, such as those involving phenylpropanoid biosynthesis, plant-pathogen interaction and protein processing. Also, our results identified the regulatory interaction between miRNA-target counterparts during salt stress. Taken together, we present the first global overview of the transcriptome of <i>S. apetala</i> roots, and identify potentially important genes and pathways associated with salt tolerance for further investigation. This study is expected to deliver novel insights in understanding the regulatory mechanism in <i>S. apetala</i> response to salt stress.

无瓣海桑（Sonneratia apetala）是红树林植物中的先锋物种。相较于陆生淡水植物，其长期暴露于盐渍化环境中，因此演化出多种耐盐胁迫机制。然而，目前针对其盐适应的潜在分子机制的研究仍较为有限。本研究整合了信使RNA（messenger RNA，mRNA）与微小RNA（microRNA，miRNA）测序技术，以鉴定无瓣海桑根系中可能参与盐胁迫应答的基因与通路。通过PacBio测序技术，我们获得了包含295501条高质量单基因簇（unigene）的完整全长转录组。其中，6686个基因在盐胁迫处理后呈现显著差异表达（p < 0.001, Q < 0.01）。这些基因主要参与植物信号转导及多种代谢通路，包括苯丙烷类生物合成、植物-病原体互作以及蛋白质加工等途径。此外，本研究还鉴定出盐胁迫过程中miRNA与其靶标基因之间的调控互作关系。综上，本研究首次全面解析了无瓣海桑根系的转录组特征，鉴定出一批与耐盐相关的潜在关键基因及通路，为后续研究奠定了基础。本研究有望为解析无瓣海桑响应盐胁迫的调控机制提供全新视角。

搜集汇总

背景与挑战

背景概述

该数据集通过整合mRNA和microRNA测序，研究了红树植物海桑（Sonneratia apetala）根部在盐胁迫下的分子响应机制。研究利用PacBio测序技术获得了包含295,501个高质量unigenes的全长转录组，并鉴定出6,686个在盐胁迫后表达显著差异的基因，这些基因主要参与植物信号转导和多种代谢通路，如苯丙素生物合成和植物-病原互作。此外，数据集还揭示了miRNA与靶基因之间的调控相互作用，为理解海桑的耐盐性提供了首次全局转录组概览和潜在候选基因。