Abstract

Isatis indigotica Fort. is extremely widely planted and used for the source of the traditional Chinese medicine Radix Isatidis (Ban-Lan-Gen), which had pharmacological activities such as anti-endotoxic, antibacterial, antinociceptive, anti-inflammatory and antipyretic. In the cultivation, salt stress could affect the yields of Radix Isatidis, and activate the secondary metabolism, eg. the contents of epigoitrin in root and indigo in leaf increased after a period of salt stress, which was possibly regulated by related genes. But in early salt stress, the molecular response of I. indigotica and expression of related genes are also worthy of our attention, which it helps us to more fully understand the molecular response mechanism of I. indigotica, so that we can make better use of “salt stress” to stimulate its secondary metabolism. To determine the molecular changes of I. indigotica in salt stress, the RNA-seq was carried out for the expression profile with NGS QC Toolkit (v2.3.2) software, the Illumina HiSeqTM 2000 in Biomarker Technologies Co., Ltd and ESTScan program. The de novo assembly resulted in 33109 unigenes from more than 18.71 Gb data. Of these, 28868 unigenes were annotated using KOG, KEGG, Nr, Nt, Swiss-Prot and TrEMBL databases. Then, 11829 simple sequence repeats were found in unigenes and 7725 primers were designed. After detecting the expression value, the edgeR package found 135 DEG, of those 48 were up-regulated and 87 were down-regulated. The expression pattern of genes that was validated by qPCR indicated that mitochondrial transcription termination factor, non-LTR retroelement reverse transcriptase and CYP79F1 which involved in the first step in biosynthesis of core short-chain aliphatic glucosinolates might play a vital role in coping with salt stress. Although one assembly of I. indigotica unigenes were obtained before, this study would provide more molecular data for further analysis, and facilitate studies on the functions of genes involved in the salt related signal pathways.

中文翻译：

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转录组表达的表征：板蓝根对盐胁迫的响应

摘要

板蓝靛蓝堡。广泛种植并用作中药板蓝根（Ban-Lan-Gen）的来源，该药具有抗内毒素，抗菌，抗伤害感受，消炎和退烧的药理活性。在耕作过程中，盐胁迫可能会影响板蓝根的产量，并激活次生代谢。盐胁迫一段时间后，根和叶中靛蓝的表皮生长素含量增加，这可能受相关基因调控。但是在早期盐胁迫下，靛蓝的分子反应和相关基因的表达也值得我们关注，这有助于我们更充分地了解靛蓝的分子反应机理。，以便我们可以更好地利用“盐胁迫”来刺激其次级代谢。确定靛蓝肠杆菌的分子变化在盐胁迫下，使用NGS QC Toolkit（v2.3.2）软件，Biomarker Technologies Co.，Ltd.的Illumina HiSeqTM 2000和ESTScan程序对RNA-seq进行表达分析。从头组装从超过18.71 Gb数据中产生了33109个单基因。其中，使用KOG，KEGG，Nr，Nt，Swiss-Prot和TrEMBL数据库注释了28868个单基因。然后，在单基因中发现了11829个简单的重复序列，并设计了7725个引物。检测表达值后，edgeR软件包发现上调了48个蛋白中的135度，下调了87个蛋白。经qPCR验证的基因表达模式表明线粒体转录终止因子，非LTR逆转录酶和CYP79F1参与了核心短链脂肪族芥子油苷生物合成的第一步，可能在应对盐胁迫中起着至关重要的作用。虽然一个组装之前已经获得了I. indigotica unigenes，该研究将为进一步的分析提供更多的分子数据，并有助于研究与盐相关的信号通路中涉及的基因的功能。