Long non-coding RNAs (lncRNAs) play important roles in the regulation of plant responses to environmental stress by acting as essential regulators of gene expression. However, whether and how lncRNAs are involved in cold acclimation-dependent freezing tolerance in plants remains largely unknown. Medicago truncatula is a prominent model for studies of legume genomics, and distinguished by its cold-acclimation characteristics. To determine the roles of lncRNAs in plant cold stress response, we conducted genome-wide high-throughput sequencing in the legume model plant M. truncatula. RNA-seq data were generated from twelve samples for the four treatments, i.e., non-cold treated leaves and roots, cold-treated leaves and roots of M. truncatula Jemalong A17 seedlings. A total of 1204 million raw reads were generated. Of them, 1150 million filtered reads after quality control (QC) were subjected to downstream analysis. A large number of 24,368 unique lncRNAs were identified from the twelve samples. Among these lncRNAs, 983 and 1288 were responsive to cold treatment in the leaves and roots, respectively. We further found that the intronic-lncRNAs were most sensitive to the cold treatment. The cold-responsive lncRNAs were unevenly distributed across the eight chromosomes in M. truncatula seedlings with obvious preferences for locations. Further analyses revealed that the cold-responsive lncRNAs differed between leaves and roots. The putative target genes of the lncRNAs were predicted to mainly involve the processes of protein translation, transport, metabolism and nucleic acid transcription. Furthermore, the networks of a tandem array of CBF/DREB1 genes that were reported to be located in a major freezing tolerance QTL region on chromosome 6 and their related lncRNAs were dissected based on their gene expression and chromosome location. We identified a comprehensive set of lncRNAs that were responsive to cold treatment in M. truncatula seedlings, and discovered tissue-specific cold-responsive lncRNAs in leaves and roots. We further dissected potential regulatory networks of CBF Intergenic RNA (MtCIR1) and MtCBFs that play critical roles in response and adaptation of M. truncatula to cold stress.

中文翻译：

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通过高通量RNA测序鉴定截叶苜蓿中组织特异性和冷应答的lncRNA

长的非编码RNA（lncRNA）通过充当基因表达的重要调节剂，在调节植物对环境胁迫的反应中发挥重要作用。然而，在植物中，lncRNAs是否以及如何参与冷驯化相关的耐冻性仍然未知。ca藜苜蓿是研究豆类基因组学的重要模型，并具有冷适应特性。为了确定lncRNA在植物冷胁迫反应中的作用，我们在豆科植物模型植物M. truncatula中进行了全基因组高通量测序。从四种处理的十二个样品中获得RNA-seq数据，这四个处理分别是未经冷处理的M. truncatula Jemalong A17幼苗的叶和根，冷处理的叶和根。总共产生了1.204亿个原始读取。在他们当中 对质量控制（QC）之后的11.5亿个经过过滤的读数进行了下游分析。从十二个样品中鉴定出大量24,368个独特的lncRNA。在这些lncRNA中，983和1288分别对叶片和根部的冷处理有反应。我们进一步发现内含子-lncRNA对冷处理最敏感。冷响应的lncRNAs在t.catula苗的八个染色体上分布不均，位置明显偏爱。进一步的分析表明，冷响应的lncRNA在叶和根之间有所不同。预测的lncRNA的假定靶基因主要涉及蛋白质翻译，转运，代谢和核酸转录的过程。此外，据报道，CBF / DREB1基因串联阵列的网络位于6号染色体的主要耐冻QTL区域，并根据其基因表达和染色体位置解剖了相关的lncRNA。我们确定了一套完整的lncRNA，它们对截叶芒幼苗的冷处理有反应，并在叶和根中发现了组织特异性的冷反应lncRNA。我们进一步剖析了CBF基因间RNA（MtCIR1）和MtCBFs的潜在调控网络，这些基因在t藜分支杆菌对冷胁迫的响应和适应中起关键作用。我们确定了一套完整的lncRNA，它们对截叶芒幼苗的冷处理有反应，并在叶和根中发现了组织特异性的冷反应lncRNA。我们进一步剖析了CBF基因间RNA（MtCIR1）和MtCBFs的潜在调控网络，这些基因在t藜分支杆菌对冷胁迫的响应和适应中起关键作用。我们确定了一套完整的lncRNA，它们对截叶芒幼苗的冷处理有反应，并在叶和根中发现了组织特异性的冷反应lncRNA。我们进一步剖析了CBF基因间RNA（MtCIR1）和MtCBFs的潜在调控网络，这些基因在t藜分支杆菌对冷胁迫的响应和适应中起关键作用。