State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
Research Network of Global Change Biology, Beijing Institutes of Life Science, the Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
BMC Plant Biol. 2020 Mar 6;20(1):99. doi: 10.1186/s12870-020-2301-1.
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.
长非编码 RNA（lncRNA）通过作为基因表达的重要调控因子，在植物对环境胁迫的反应调控中发挥重要作用。然而，lncRNA 是否以及如何参与植物的冷驯化相关的抗冻性仍然知之甚少。蒺藜苜蓿是豆科基因组研究的重要模式植物，其特点是具有冷驯化特性。为了确定 lncRNA 在植物冷胁迫反应中的作用，我们对豆科模式植物蒺藜苜蓿进行了全基因组高通量测序。
从非冷处理的叶片和根系、冷处理的叶片和根系的 12 个 M. truncatula Jemalong A17 幼苗样本中生成了 RNA-seq 数据。共产生了 1.2 亿条原始读数。其中，经过质量控制（QC）后有 1.15 亿条过滤后的读数用于下游分析。从这 12 个样本中鉴定出了 24368 个独特的 lncRNA。其中，叶片和根系中分别有 983 个和 1288 个 lncRNA 对冷处理有响应。我们进一步发现，内含子-lncRNA 对冷处理最敏感。冷响应 lncRNA 在 M. truncatula 幼苗的 8 条染色体上不均匀分布，位置偏好明显。进一步分析表明，叶片和根系中的冷响应 lncRNA 不同。lncRNA 的假定靶基因主要涉及蛋白质翻译、运输、代谢和核酸转录过程。此外，基于基因表达和染色体位置，我们对位于第 6 号染色体上主要抗冻性 QTL 区域的一组串联的 CBF/DREB1 基因及其相关的 lncRNA 进行了网络剖析。
我们鉴定了蒺藜苜蓿幼苗中对冷处理有响应的一组全面的 lncRNA，并在叶片和根系中发现了组织特异性的冷响应 lncRNA。我们进一步剖析了在蒺藜苜蓿对冷胁迫的响应和适应中发挥关键作用的 CBF 基因间 RNA（MtCIR1）和 MtCBFs 的潜在调控网络。
