Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

Ying Liang,Li Gu,Zhongyi Zhang,Chuanhua Deng,Fan Wei,Yang Lin,Jianhua Miao,Mingjie Li,Guili Wei,Shuangshuang Qin,Kunhua Wei

doi:10.1186/s12870-021-03334-6

Abstract

BackgroundSophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood.ResultsTo identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs.ConclusionThis is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.

Highlights

Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China
Physiological changes in S. tonkinensis under drought stress To study the physiological changes in S. tonkinensis under drought stress, plant roots were collected under three irrigation treatments: control treatment (CK), mild drought treatment (MDT), and severe drought treatment (SDT) (Fig. 1A)
To elucidate the genes and miRNAs involved in the drought response mechanisms of S. tonkinensis, the collected root samples were subjected to next-generation sequencing to identify differentially expressed unigenes (DEGs) and differentially expressed miRNAs (DEMs)

Summary

Introduction

Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Sophora tonkinensis is a traditional Chinese plant included in the “Pharmacopoeia of the People’s Republic of China (2020 edition)”, and the roots and rhizomes (known as “Shan-Dou-Gen” in Chinese) of this plant have been used as folk medicine for the treatment of fever, throat inflammation, and tumours [1]. S. tonkinensis is the main raw material of greater than 30 types of Chinese patent drugs. As a result of overexploitation and habitat degeneration, the wild resources of S. tonkinensis have decreased rapidly over recent years or even become extinct in many distribution areas. Cultivated S. tonkinensis has become the main source of S. tonkinensis-based drugs. As the demand for S. tonkinensis-based drugs is ever increasing, the price of S. tonkinensis roots increased from approximately 23.05 dollars/kg in 2016 [4] to approximately 31.73 dollars/kg in 2020

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