Data_Sheet_1_Genome-Wide Identification and Characterization of Long Noncoding RNAs in Populus × canescens Roots Treated With Different Nitrogen Fertilizers.xlsx

Nitrate (NO3−) and ammonium (NH4+) are the primary forms of inorganic nitrogen acquired by plant roots. LncRNAs, as key regulators of gene expression, are a class of non-coding RNAs larger than 200 bp. However, knowledge about the regulatory role of lncRNAs in response to different nitrogen forms remains limited, particularly in woody plants. Here, we performed strand-specific RNA-sequencing of P. × canescens roots under three different nitrogen fertilization treatments. In total, 324 lncRNAs and 6,112 mRNAs were identified as showing significantly differential expression between the NO3− and NH4NO3 treatments. Moreover, 333 lncRNAs and 6,007 mRNAs showed significantly differential expression between the NH4+ and NH4NO3 treatments. Further analysis suggested that these lncRNAs and mRNAs have different response mechanisms for different nitrogen forms. In addition, functional annotation of cis and trans target mRNAs of differentially expressed lncRNAs indicated that 60 lncRNAs corresponding to 49 differentially expressed cis and trans target mRNAs were involved in plant nitrogen metabolism and amino acid biosynthesis and metabolism. Furthermore, 42 lncRNAs were identified as putative precursors of 63 miRNAs, and 28 differentially expressed lncRNAs were potential endogenous target mimics targeted by 96 miRNAs. Moreover, ceRNA regulation networks were constructed. MSTRG.6097.1, MSTRG.13550.1, MSTRG.2693.1, and MSTRG.12899.1, as hub lncRNAs in the ceRNA networks, are potential candidate lncRNAs for studying the regulatory mechanism in poplar roots under different nitrogen fertilization treatments. The results provide a basis for obtaining insight into the molecular mechanisms of lncRNA responses to different nitrogen forms in woody plants.

硝酸盐（Nitrate, NO3−）与铵态氮（ammonium, NH4+）是植物根系获取无机氮的主要存在形式。长链非编码RNA（long non-coding RNAs, LncRNAs）作为基因表达的关键调控因子，是一类长度超过200 bp的非编码RNA。然而，目前关于LncRNAs在响应不同氮素形态中的调控作用的相关认知仍较为有限，这一情况在木本植物中尤为突出。本研究针对三种不同氮肥处理下的银灰杨（P. × canescens）根系开展了链特异性RNA测序（strand-specific RNA-sequencing）。结果显示，在硝酸盐与硝酸铵（NH4NO3）处理组间，共鉴定得到324个差异表达LncRNAs与6112个差异表达mRNA；此外，在铵态氮与硝酸铵处理组间，共鉴定得到333个差异表达LncRNAs与6007个差异表达mRNA。进一步分析表明，上述LncRNAs与mRNA对不同氮素形态具有不同的响应机制。此外，对差异表达LncRNAs的顺式（cis）靶mRNA与反式（trans）靶mRNA进行功能注释后发现，对应49个差异表达顺式/反式靶mRNA的60个LncRNAs参与了植物氮代谢与氨基酸生物合成及代谢过程。此外，本研究还鉴定出42个LncRNAs可作为63个miRNAs的潜在前体，同时发现28个差异表达LncRNAs可作为96个miRNAs的潜在内源靶模拟物（endogenous target mimics）。同时，本研究构建了内源竞争RNA（competing endogenous RNA, ceRNA）调控网络。其中MSTRG.6097.1、MSTRG.13550.1、MSTRG.2693.1及MSTRG.12899.1作为ceRNA网络中的核心LncRNAs（hub lncRNAs），是探究不同氮肥处理下杨树根系调控机制的潜在候选LncRNAs。本研究结果为深入解析木本植物中LncRNAs响应不同氮素形态的分子机制提供了重要研究基础。