Characterization of Transcriptome Expression: The Response of Isatis indigotica to Salt Stress
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Characterization of Transcriptome Expression: The Response of Isatis indigotica to Salt Stress X.-Q. Tanga,*, H.-W. Tana, S.-L. Shia, L.-L. Wanga, F.-Q. Wangb, K.-C. Wanga, and J. Yangb aCollege bInstitute
of Horticulture, Nanjing Agricultural University, Nanjing, 210095 PR China of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 PR China *e-mail: [email protected] Received February 21, 2020; revised May 17, 2020; accepted May 17, 2020
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. Keywords: Isatis indigotica, de novo assembly, expression profile, RNA-seq, salt stress DOI: 10.1134/S1021443720060163
INTRODUCTION Isatis indigotica Fort. (Chinese woad) is a biennial herbaceous plant species in the family Brassicaceae, which is widely distributed and cultivated in China. As one of the important traditional Chinese medicine plants, I. indigotica is an economical crop with large market share of Chinese essential medicine of Far East for many centuries. The dry root and leaf of I. indigotica is Radix Isatidis (Ban-Lan-Ge
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