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

Abstract

Background Sophora 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. Results To 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. Conclusion This 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.

Deciphering Alkaloid and Flavonoid Biosynthesis in Different Tissues of Sophora tonkinensis via Transcriptomics and Metabolomics

“…This study identi ed 35 DEGs involved in alkaloid biosynthesis, including eight unigenes encoding CAO (Fig. 4A), aligning with previous research on CAO in S. tonkinensis under drought stress [29]. Among these, the eight CAO-encoding unigenes were expressed in all tissues, with four highly expressed in leaves, two in seeds, and two in stems.…”

Transcriptome Analysis on the Quality of Epimedium koreanum in Different Soil Moisture Conditions at Harvesting Stage

“…These DEGs were predominantly enriched in metabolic processes, cellular structure, stimulus response, binding, transcriptional regulator activity, and catalytic activity. This pattern was akin to the GO analysis findings for the transcriptome of Sophora tonkinensis under moderate drought stress [25].…”

Biosynthesis of quinolizidine alkaloids in lupins: mechanistic considerations and prospects for pathway elucidation

“…Combined with the curated understanding of the QA pathway presented in this review, the prospects for the full elucidation of the QA pathway are very good. The available resources include high-quality genome drafts for L. angustifolius 61–63 and L. albus , 64,65 a pan-genome for L. albus , 66 and transcriptomic data for a range of lupin species and tissues, as compiled by Kamphuis et al 67 Additionally, transcriptomic data has been generated for Sophora species, 68,69 and these are of interest to uncover the pathway towards the matrine-like tetracyclic QAs. However, equivalent resources do not exist for species that primarily accumulate α-pyridone QAs, such as Laburnum anagyroides , which produces the smoking cessation agent (−)-cytisine ( 12 ).…”