Transcriptome Profiling Reveals Candidate Genes Involved in Stem Swelling of Tumorous Stem Mustard
Transcriptome Profiling Reveals Candidate Genes Involved in Stem Swelling of Tumorous Stem Mustard
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转录组分析揭示了与瘤茎芥菜茎肿胀有关的候选基因
DOI：
10.1016/j.hpj.2020.03.002
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发表时间：
2020-05-01
影响因子：
5.7
通讯作者：
Lai, Biao
中科院分区：
文献类型：
--
作者：
Du, Lina;Li, Changman;Lai, Biao
茎瘤芥以其膨大的茎而闻名，用其制成的酱菜“涪陵榨菜”。目前，对这种改性膨胀茎形成的分子机制还知之甚少。本文旨在确定参与膨大茎发育调控的候选基因。我们试图映射先前发表的芥菜转录组数据集，包括来自四个不同发育阶段的肿胀茎和没有肿胀茎的突变品种。通过对5个数据集的成对比较，我们确定了31 368个差异表达基因（DEG）。利用基因本体（GO）分析技术，共鉴定出55个与植物激素信号转导相关的DEG和259个在茎发育过程中持续上调或下调的转录因子。实时定量PCR（qRT-PCR）结果显示，12个重要候选DEG的表达与RNA-seq结果一致。我们的研究提供了数字化基因表达谱和肿胀茎发育过程的动态视图。此外，我们确定了候选基因，为进一步研究在非模式物种的修改茎发育的机制。
Tumorous stem mustard is well known for its swollen stem from which pickled "Fuling Mustard" is made. The molecular mechanisms governing the formation of the modified swollen stems are still poorly understood. This paper aims to identify candidate genes involved in the developmental regulation of the swollen stems. We sought to map previously published transcriptome datasets for Brassica juncea, including those derived from swollen stems at four different developmental stages and a mutant variety without swollen stems. Using pairwise comparisons of the five datasets, we identified 31 368 differentially expressed genes (DEGs). A total of 55 DEGs related to plant hormone signal transduction and 259 continuously up- or down regulated transcription factors were identified during stem development using Gene Ontology (GO) analysis. Quantitative real-time PCR (qRT-PCR) results showed that the expressions of 12 important candidate DEGs were consistent with RNA-seq results. Our study provided digital gene expression profiling and a dynamic view of the swollen stem development process. Furthermore, we identified candidate genes for further studies on mechanisms of modified stem development in non-model species.