Comprehensive transcriptome analysis reveals genes potentially involved in isoflavone biosynthesis in Pueraria thomsonii Benth

Abstract

Pueraria thomsonii Benth is an important medicinal plant. Transcriptome sequencing, unigene assembly, the annotation of transcripts and the study of gene expression profiles play vital roles in gene function research. However, the full-length transcriptome of P . thomsonii remains unknown. Here, we obtained 44,339 nonredundant transcripts of P . thomsonii by using the PacBio RS II Isoform and Illumina sequencing platforms, of which 43,195 were annotated genes. Compared with the expression levels in the plant roots, those of transcripts with a |fold change| ≥ 4 and FDR < 0.01 in the leaves or stems were assigned as differentially expressed transcripts (DETs). In total, we found 9,225 DETs, 32 of which came from structural genes that were potentially involved in isoflavone biosynthesis. The expression profiles of 8 structural genes from the RNA-Seq data were validated by qRT-PCR. We identified 437 transcription factors (TFs) that were positively or negatively correlated with at least 1 of the structural genes involved in isoflavone biosynthesis using Pearson correlation coefficients (r) (r > 0.8 or r < -0.8). We also identified a total of 32 microRNAs (miRNAs), which targeted 805 transcripts. These miRNAs caused enriched function in ‘ATP binding’, ‘defense response’, ‘ADP binding’, and ‘signal transduction’. Interestingly, MIR156a potentially promoted isoflavone biosynthesis by repressing SBP , and MIR319 promoted isoflavone biosynthesis by repressing TCP and HB-HD-ZIP . Finally, we identified 2,690 alternative splicing events, including that of the structural genes of trans-cinnamate 4-monooxygenase and pullulanase, which are potentially involved in the biosynthesis of isoflavone and starch, respectively, and of three TFs potentially involved in isoflavone biosynthesis. Together, these results provide us with comprehensive insight into the gene expression and regulation of P . thomsonii .

The Role of Polyphenols in Abiotic Stress Response: The Influence of Molecular Structure

“…First, liquiritigenin and naringenin are hydroxylated by 2-hydroxyisoflavanone synthase (IFS) and 2-hydroxyisoflavone dehydrate (HID) to form daidzein, genistein ( Figure 6 ), and formononetin. These isoflavone scaffolds are then further modified by glycosyltransferases and methyltransferases, yielding diverse isoflavonoids [ 93 ]. Isoflavones have garnered much scientific attention due to their estrogen-like properties, but a critical evaluation of clinical studies has created some controversy regarding their efficacy [ 94 ].…”

Peer Review #1 of "Transcriptome sequencing and analysis reveals the molecular response to selenium stimuli in Pueraria lobata (willd.) Ohwi (v0.2)"

“…ROS can damage cell membranes and other components and harm plants (Nandini et al, 2016). Low selenium stress has been reported to activate the antioxidant system to scavenge ROS and enhance a plant's ability to withstand a variety of oxidative stresses (Wang et al, 2012).…”

Integrated Analysis of mRNA and microRNA Elucidates the Regulation of Glycyrrhizic Acid Biosynthesis in Glycyrrhiza uralensis Fisch

“…At that time, the temperature ranged from 20 to 32 • C. Total RNA from leaves and roots was extracted using the RNAprep Pure Plant Kit (DP171221) (TIANGEN Biotech (Beijing, China) Co., Ltd.) and TRIzol reagent (Invitrogen, Carlsbad, CA, USA), respectively, according to the manufacturer s instructions. Then, RNAs were assessed and quantified as described previously [57].…”

“…The poly(A) mRNAs of leaf and root samples (every organ with three replicates) were separated from the total RNA using oligo(dT) magnetic beads (Dynal, Oslo). Then, the mRNAs were used to construct strand-specific transcriptome libraries, as in our previous work [57]. Finally, these libraries were sequenced using the Illumina platform.…”