Transcriptome sequencing and characterization of Astragalus membranaceus var. mongholicus root reveals key genes involved in flavonoids biosynthesis

Liang, Jianping; Li, Wenqian; Jia, Xiaoyun; Zhang, Ying; Zhao, Jianping

doi:10.1007/s13258-020-00953-5

Cited by 13 publications

(14 citation statements)

References 28 publications

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“…Bunge. Currently, transcriptome studies of A. mongholicus are mainly based on NGS [ 32 , 34 , 40 ]. Previous RNA-Seq investigations reported unigenes with an average length < 1000 bp.…”

Section: Discussionmentioning

confidence: 99%

Full-length transcriptome sequences by a combination of sequencing platforms applied to isoflavonoid and triterpenoid saponin biosynthesis of Astragalus mongholicus Bunge

et al. 2021

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Background Astragalus mongholicus Bunge is an important medicinal plant used in traditional Chinese medicine. It is rich in isoflavonoids and triterpenoid saponins. Although these active constituents of A. mongholicus have been discovered for a long time, the genetic basis of isoflavonoid and triterpenoid saponin biosynthesis in this plant is virtually unknown because of the lack of a reference genome. Here, we used a combination of next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing to identify genes involved in the biosynthetic pathway of secondary metabolites in A. mongholicus. Results In this study, NGS, SMRT sequencing, and targeted compound analysis were combined to investigate the association between isoflavonoid and triterpenoid saponin content, and specific gene expression in the root, stem, and leaves of A. mongholicus. Overall, 643,812 CCS reads were generated, yielding 121,107 non-redundant transcript isoforms with an N50 value of 2124 bp. Based on these highly accurate transcripts, 104,756 (86.50%) transcripts were successfully annotated by any of the seven databases (NR, NT, Swissprot, KEGG, KOG, Pfam and GO). Levels of four isoflavonoids and four astragalosides (triterpenoid saponins) were determined. Forty-four differentially expressed genes (DEGs) involved in isoflavonoid biosynthesis and 44 DEGs from 16 gene families that encode enzymes involved in triterpenoid saponin biosynthesis were identified. Transcription factors (TFs) associated with isoflavonoid and triterpenoid saponin biosynthesis, including 72 MYBs, 53 bHLHs, 64 AP2-EREBPs, and 11 bZIPs, were also identified. The above transcripts showed different expression trends in different plant organs. Conclusions This study provides important genetic information on the A. mongholicus genes that are essential for isoflavonoid and triterpenoid saponin biosynthesis, and provides a basis for developing the medicinal value of this plant.

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“…Bunge. Currently, transcriptome studies of A. mongholicus are mainly based on NGS [ 32 , 34 , 40 ]. Previous RNA-Seq investigations reported unigenes with an average length < 1000 bp.…”

Section: Discussionmentioning

confidence: 99%

Full-length transcriptome sequences by a combination of sequencing platforms applied to isoflavonoid and triterpenoid saponin biosynthesis of Astragalus mongholicus Bunge

et al. 2021

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“…Some studies have employed transcriptome sequencing (Illumina sequencing) technologies and expressed sequence tag (EST) library methods to analyze the metabolic mechanisms ( Liang et al, 2020 ; Wu P. et al, 2021 ). Jaakola et al (2002) and Zifkin et al (2012) analyzed the correlation between expression of genes related to flavonoid synthesis at different developmental stages and flavonoid content in highbush blueberries ( V. corymbosum “Rubel”) and wild blueberries ( Vaccinium myrtillus ), respectively.…”

Section: Introductionmentioning

confidence: 99%

Single-Molecule Real-Time and Illumina Sequencing to Analyze Transcriptional Regulation of Flavonoid Synthesis in Blueberry

et al. 2021

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Blueberries (Vaccinium corymbosum) contain large amounts of flavonoids, which play important roles in the plant’s ability to resist stress and can also have beneficial effects on human health when the fruits are eaten. However, the molecular mechanisms that regulate flavonoid synthesis in blueberries are still unclear. In this study, we combined two different transcriptome sequencing platforms, single-molecule real-time (SMRT) and Illumina sequencing, to elucidate the flavonoid synthetic pathways in blueberries. We analyzed transcript quantity, length, and the number of annotated genes. We mined genes associated with flavonoid synthesis (such as anthocyanins, flavonols, and proanthocyanidins) and employed fluorescence quantitative PCR to analyze the expression of these genes and their correlation with flavonoid synthesis. We discovered one R2R3 MYB transcription factor from the sequencing library, VcMYB1, that can positively regulate anthocyanin synthesis in blueberries. VcMYB1 is mainly expressed in colored (mature) fruits. Experiments showed that overexpression and transient expression of VcMYB1 promoted anthocyanin synthesis in Arabidopsis, tobacco (Nicotiana benthamiana) plants and green blueberry fruits. Yeast one-hybrid (Y1H) assay, electrophoretic mobility shift assay, and transient expression experiments showed that VcMYB1 binds to the MYB binding site on the promoter of the structural gene for anthocyanin synthesis, VcMYB1 to positively regulate the transcription of VcDFR, thereby promoting anthocyanin synthesis. We also performed an in-depth investigation of transcriptional regulation of anthocyanin synthesis. This study provides background information and data for studying the synthetic pathways of flavonoids and other secondary metabolites in blueberries.

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“…The biosynthesis of flavonoids has been reported in many other medicinal plants such as Astragalus membranaceus var. mongholicus, Apocynum venetum, and Eucommia ulmoides , and phenylpropanoid biosynthesis is the common core pathway for the synthesis of flavonoids [ 27 – 29 ]. The first step in flavonoid biosynthesis is regulated by enzymes (PAL, C4H, and 4CL) in the phenylpropanoid pathway.…”

Section: Discussionmentioning

confidence: 99%

Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes

Yuan

Pan

et al. 2021

BMC Genom Data

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Background Alpinia oxyphylla Miq. is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. Flavonoids are one of the main chemical compounds in A. oxyphylla; however, the genetic and molecular mechanisms of flavonoid biosynthesis are not well understood. We performed transcriptome analysis in the fruit, root, and leaf tissues of A. oxyphylla to delineate tissue-specific gene expression and metabolic pathways in this medicinal plant. Results In all, 8.85, 10.10, 8.68, 6.89, and 8.51 Gb clean data were obtained for early-, middle-, and late-stage fruits, leaves, and roots, respectively. Furthermore, 50,401 unigenes were grouped into functional categories based on four databases, namely Nr (47,745 unigenes), Uniprot (49,685 unigenes), KOG (20,153 unigenes), and KEGG (27,285 unigenes). A total of 3110 differentially expressed genes (DEGs) and five distinct clusters with similar expression patterns were obtained, in which 27 unigenes encoded 13 key enzymes associated with flavonoid biosynthesis. In particular, 9 DEGs were significantly up-regulated in fruits, whereas expression of 11 DEGs were highly up-regulated in roots, compared with those in leaves. Conclusion The DEGs and metabolic pathway related to flavonoids biosynthesis were identified in root, leaf, and different stages of fruits from A. oxyphylla. These results provide insights into the molecular mechanism of flavonoid biosynthesis in A. oxyphylla and application of genetically engineered varieties of A. oxyphylla.

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Transcriptome sequencing and characterization of Astragalus membranaceus var. mongholicus root reveals key genes involved in flavonoids biosynthesis

Cited by 13 publications

References 28 publications

Full-length transcriptome sequences by a combination of sequencing platforms applied to isoflavonoid and triterpenoid saponin biosynthesis of Astragalus mongholicus Bunge

Full-length transcriptome sequences by a combination of sequencing platforms applied to isoflavonoid and triterpenoid saponin biosynthesis of Astragalus mongholicus Bunge

Single-Molecule Real-Time and Illumina Sequencing to Analyze Transcriptional Regulation of Flavonoid Synthesis in Blueberry

Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes

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