Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis).
Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis).
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集成 RNA-Seq 和 sRNA-Seq 分析识别茶树（Camellia sinensis）中冷藏和冷冻响应的关键分子参与者和途径
DOI：
10.1371/journal.pone.0125031
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Ding Z
中科院分区：
文献类型：
--
作者：
Zheng C;Zhao L;Wang Y;Shen J;Zhang Y;Jia S;Li Y;Ding Z
茶树[Camellia sinensis（L）O. Kuntze，Theaceae）是全球最受欢迎的非酒精饮料之一。低温胁迫是限制茶树生长、存活和地理分布的最严重的非生物胁迫之一。然而，茶树冷胁迫反应的基因调控网络和信号通路仍然没有被发掘出来。利用RNA-Seq、DGE和sRNA-Seq技术，对低温（4℃）和冷冻（-5℃）胁迫下茶树的miRNA和mRNA表达谱及其调控网络进行了综合分析。基于倍数变化分析获得差异表达（DE）miRNA和mRNA谱，发现miRNA和靶mRNA在调控网络中显示出连贯和不连贯的关系。此外，我们比较了几个关键途径（例如，“光合作用”）、GO术语（例如，“对karrikin的应答”）和转录因子（TF，例如，DREB 1b/CBF 1），它们与茶树的早期低温和/或冷冻反应有关。有趣的是，我们发现一类新的植物生长调节剂karrikins和与茶叶香气形成相关的关键酶β-樱草糖苷酶（BPR）可能在茶树的早期低温和冷冻反应中发挥重要作用。定量逆转录酶-聚合酶链反应（qRT-PCR）分析进一步证实了RNA-Seq和sRNA-Seq分析的结果。这是第一个同时在全基因组范围内分析miRNA和mRNA表达模式的研究，以阐明茶树对冷胁迫早期反应的分子机制。除了更深入地了解茶树的抗寒特性外，我们还提供了一个很好的案例研究，利用下一代测序技术分析非模式植物物种的mRNA/miRNA表达和谱。
Tea [Camellia sinensis (L) O. Kuntze, Theaceae] is one of the most popular non-alcoholic beverages worldwide. Cold stress is one of the most severe abiotic stresses that limit tea plants’ growth, survival and geographical distribution. However, the genetic regulatory network and signaling pathways involved in cold stress responses in tea plants remain unearthed. Using RNA-Seq, DGE and sRNA-Seq technologies, we performed an integrative analysis of miRNA and mRNA expression profiling and their regulatory network of tea plants under chilling (4℃) and freezing (-5℃) stress. Differentially expressed (DE) miRNA and mRNA profiles were obtained based on fold change analysis, miRNAs and target mRNAs were found to show both coherent and incoherent relationships in the regulatory network. Furthermore, we compared several key pathways (e.g., ‘Photosynthesis’), GO terms (e.g., ‘response to karrikin’) and transcriptional factors (TFs, e.g., DREB1b/CBF1) which were identified as involved in the early chilling and/or freezing response of tea plants. Intriguingly, we found that karrikins, a new group of plant growth regulators, and β-primeverosidase (BPR), a key enzyme functionally relevant with the formation of tea aroma might play an important role in both early chilling and freezing response of tea plants. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-Seq and sRNA-Seq analysis. This is the first study to simultaneously profile the expression patterns of both miRNAs and mRNAs on a genome-wide scale to elucidate the molecular mechanisms of early responses of tea plants to cold stress. In addition to gaining a deeper insight into the cold resistant characteristics of tea plants, we provide a good case study to analyse mRNA/miRNA expression and profiling of non-model plant species using next-generation sequencing technology.
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影响因子：
5.6
作者：
Du H;Liu H;Xiong L
通讯作者：
Xiong L
影响因子：
3.7
作者：
Fahlgren N;Howell MD;Kasschau KD;Chapman EJ;Sullivan CM;Cumbie JS;Givan SA;Law TF;Grant SR;Dangl JL;Carrington JC
通讯作者：
Carrington JC
DOI：
10.1073/pnas.0406069101
发表时间：
2004-10-19
影响因子：
11.1
作者：
Cook, D;Fowler, S;Thomashow, MF
通讯作者：
Thomashow, MF
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
7.2
作者：
Gilmour, SJ;Zarka, DG;Thomashow, MF
通讯作者：
Thomashow, MF