State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, People's Republic of China.
BMC Plant Biol. 2019 Jan 11;19(1):23. doi: 10.1186/s12870-018-1626-5.
Water stress seriously constrains plant growth and yield. Long non-coding RNAs (lncRNAs) serve as versatile regulators in various biological regulatory processes. To date, the systematic screening and potential functions of lncRNA have not yet been characterized in Cleistogenes songorica, especially under water stress conditions.
In this study, we obtained the root and shoot transcriptomes of young C. songorica plants subjected to different degrees of water stress and recovery treatments by Illumina-based RNA-seq. A total of 3397 lncRNAs were identified through bioinformatics analysis. LncRNA differential expression analysis indicated that the higher response of roots compared to shoots during water stress and recovery. We further identified the 1644 transcription factors, 189 of which were corresponded to 163 lncRNAs in C. songorica. Though comparative analyses with major Poaceae species based on blast, 81 water stress-related orthologues regulated to lncRNAs were identified as a core of evolutionary conserved genes important to regulate water stress responses in the family. Among these target genes, two genes were found to be involved in the abscisic acid (ABA) signalling pathway, and four genes were enriched for starch and sucrose metabolism. Additionally, the 52 lncRNAs were predicted as target mimics for microRNAs (miRNAs) in C. songorica. RT-qPCR results suggested that MSTRG.43964.1 and MSTRG.4400.2 may regulate the expression of miRNA397 and miRNA166, respectively, as target mimics under water stress and during recovery. Finally, a co-expression network was constructed based on the lncRNAs, miRNAs, protein-coding genes (PCgenes) and transcription factors under water stress and during recovery in C. songorica.
In C. songorica, lncRNAs, miRNAs, PCgenes and transcription factors constitute a complex transcriptional regulatory network which lncRNAs can regulate PCgenes and miRNAs under water stress and recovery. This study provides fundamental resources to deepen our knowledge on lncRNAs during ubiquitous water stress.
水分胁迫严重制约植物生长和产量。长链非编码 RNA（lncRNA）在各种生物调控过程中作为多功能调节剂发挥作用。迄今为止，尚未对水分胁迫条件下的芨芨草进行系统的 lncRNA 筛选和潜在功能分析。
本研究通过基于 Illumina 的 RNA-seq 获得了不同程度水分胁迫和恢复处理的芨芨草幼根和幼茎转录组。通过生物信息学分析共鉴定出 3397 个 lncRNA。lncRNA 差异表达分析表明，水分胁迫和恢复过程中根的响应高于茎。我们进一步鉴定了 1644 个转录因子，其中 189 个与芨芨草中的 163 个 lncRNA 相对应。通过与主要禾本科物种的 blast 比较分析，鉴定出 81 个与水分胁迫相关的直系同源物调控 lncRNA，作为家族中重要的进化保守基因调控水分胁迫响应的核心。在这些靶基因中，发现两个基因参与脱落酸（ABA）信号通路，四个基因富集于淀粉和蔗糖代谢。此外，预测了 52 个 lncRNA 作为芨芨草中 miRNA（miRNA）的靶标模拟物。RT-qPCR 结果表明，MSTRG.43964.1 和 MSTRG.4400.2 可能作为靶标模拟物，在水分胁迫和恢复过程中分别调节 miRNA397 和 miRNA166 的表达。最后，基于水分胁迫和恢复过程中芨芨草中的 lncRNA、miRNA、蛋白编码基因（PCgene）和转录因子构建了一个共表达网络。
在芨芨草中，lncRNA、miRNA、PCgene 和转录因子构成了一个复杂的转录调控网络，lncRNA 可以在水分胁迫和恢复过程中调节 PCgene 和 miRNA。本研究为深入了解普遍存在的水分胁迫下的 lncRNA 提供了基础资源。
