De novo Transcriptome Assembly of Chinese Kale and Global Expression Analysis of Genes Involved in Glucosinolate Metabolism in Multiple Tissues.
De novo Transcriptome Assembly of Chinese Kale and Global Expression Analysis of Genes Involved in Glucosinolate Metabolism in Multiple Tissues.
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DOI：
10.3389/fpls.2017.00092
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发表时间：
2017
影响因子：
5.6
通讯作者：
Chen C
中科院分区：
文献类型：
--
作者：
Wu S;Lei J;Chen G;Chen H;Cao B;Chen C
羽衣甘蓝是十字花科的一种蔬菜，由于其高硫代葡萄糖苷含量和营养品质，在中国南部和东南亚是一种受欢迎的作物。然而，对芥蓝中硫代葡萄糖苷代谢及其调控的分子遗传学和相关基因研究较少。在本研究中，我们对芥蓝11个组织中表达基因的转录组和表达谱进行了测序和鉴定。利用rna测序技术共生成了2.16亿个150-bp的clean reads。从这些序列中，整个植物共组装了98,180个unigenes，每个组织共组装了49,582~98,423个unigenes。Blast分析表明，共有80,688个（82.18%）单基因与已知蛋白相似。本研究使用的功能注释和分类工具表明，主要在芥蓝中表达的基因主要参与细胞和分子功能、信号转导和次生代谢产物的生物合成等基本过程。分析了芥蓝各组织中各基因的表达水平。我们发现了大量参与硫代葡萄糖苷代谢及其调控的候选基因，并分析了这些基因的表达模式。研究发现，参与硫代葡萄糖苷生物合成的大部分基因在根、叶柄和衰老叶片中高度表达。采用定量RT-PCR验证了RNA-seq中10个硫代葡萄糖苷生物合成基因在不同组织中的表达模式。这些结果为芥蓝基因在不同组织中的功能和表达活性提供了初步和全面的概述。
Chinese kale, a vegetable of the cruciferous family, is a popular crop in southern China and Southeast Asia due to its high glucosinolate content and nutritional qualities. However, there is little research on the molecular genetics and genes involved in glucosinolate metabolism and its regulation in Chinese kale. In this study, we sequenced and characterized the transcriptomes and expression profiles of genes expressed in 11 tissues of Chinese kale. A total of 216 million 150-bp clean reads were generated using RNA-sequencing technology. From the sequences, 98,180 unigenes were assembled for the whole plant, and 49,582~98,423 unigenes were assembled for each tissue. Blast analysis indicated that a total of 80,688 (82.18%) unigenes exhibited similarity to known proteins. The functional annotation and classification tools used in this study suggested that genes principally expressed in Chinese kale, were mostly involved in fundamental processes, such as cellular and molecular functions, the signal transduction, and biosynthesis of secondary metabolites. The expression levels of all unigenes were analyzed in various tissues of Chinese kale. A large number of candidate genes involved in glucosinolate metabolism and its regulation were identified, and the expression patterns of these genes were analyzed. We found that most of the genes involved in glucosinolate biosynthesis were highly expressed in the root, petiole, and in senescent leaves. The expression patterns of ten glucosinolate biosynthetic genes from RNA-seq were validated by quantitative RT-PCR in different tissues. These results provided an initial and global overview of Chinese kale gene functions and expression activities in different tissues.