Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators

Zhang, Zixuan; Ming, Tan; Zhang, Yingying; Jia, Yue; Zhu, Shuxian; Wang, Jiang; Jie, Zhao; Liao, Yueyue; Zhang, Xiang

doi:10.1186/s12864-021-07980-w

Cited by 14 publications

(6 citation statements)

References 33 publications

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“…Combined with the research on lignan biosynthesis of other species, we continued to excavate the enzyme genes related to lignan biosynthesis from the 26658 Unigenes annotated. Referring to the phenylpropane metabolic pathway (ko00940) and some other reported lignan biosynthesis pathways (ko00998) [10][11][12][13][14][15], a total of 13 classes of 137 transcriptome samples of Kadsura coccinea root, stem, and leaf (3 replicates in each part) and cluster-analyze the differential genes, as shown in Figure 4. Heat map analysis showed that the total expression and species of Kadsura coccinea lignan synthase gene in stems and leaves were closer to those in roots.…”

Section: Gene Analysis Of Enzymes Involved In Lignans Synthesismentioning

confidence: 99%

Kadsura coccinea Lignan Metabolism Based on Metabolome and Transcriptome Analysis

Liang¹,

Li²,

Li³

et al. 2022

Journal of Oncology

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Kadsura coccinea is an important resource of traditional Chinese medicine. We find out the gene information of enzymes related to lignan biosynthesis and metabolism of Kadsura coccinea, so as to provide a scientific basis for the breeding of new varieties of Kadsura coccinea. In this paper, 2-year-old Kadsura coccinea from Hunan Kadsura coccinea provincial germplasm resource bank was used as the material and its root, stem, and leaf were analyzed by extensive targeted metabolomics combined with transcriptome sequencing. The results showed the following: (1) 51 lignans were detected by metabolome analysis, and the content of lignans in roots was higher than that in stems and leaves. The high content of lignans in roots, stems, and leaves includes ring-opening isolarch phenol-4-o-glucoside, narrow leaf schisandrin E, and schisandrin B. (2) After transcriptome sequencing, 13 classes of 137 Unigenes related to lignan biosynthesis pathway were retrieved. The analysis of differential genes in different parts showed that the overall expression amount and species of Kadsura coccinea lignan synthase gene in stems and leaves were closer than those in roots. CCoAOMT, C3H, and SIDR gene families are mainly expressed in roots and stems. (3) Metabolome combined with transcriptome analysis further screened these genes and obtained 11 genes of enzyme gene families such as HCT, DIR, COMT, CAD, SIDR, and PLR, which are highly correlated in lignan synthesis. Therefore, there are many lignans and their synthase-related genes in Kadsura coccinea roots, stems, and leaves, but the content and expression of different lignans and their synthase-related genes are quite different in each part. In this study, the gene information of the Kadsura coccinea lignan biosynthesis enzyme was obtained for the first time, which laid a good foundation for the cloning and molecular breeding of the key enzyme gene of lignan biosynthesis.

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Section: Gene Analysis Of Enzymes Involved In Lignans Synthesismentioning

confidence: 99%

Kadsura coccinea Lignan Metabolism Based on Metabolome and Transcriptome Analysis

Liang¹,

Li²,

Li³

et al. 2022

Journal of Oncology

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“…4 D, Dataset S4 ). Previous researches have suggested that the most important hepatoprotective compounds in H. pedunculosum are lignans, primarily dehydrodiconiferyl alcohol, herpetrione, herpetin, herpetetrone and herpetotriol [ 9 , 33 ]. Most of these species-specific lignans were found in YM seeds but not in GM seeds (Fig.…”

Section: Discussionmentioning

confidence: 99%

Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of lignan biosynthesis in Herpetospermum pedunculosum (Cucurbitaceae)

Zhu,

Chen,

Sun

et al. 2024

BMC Genomics

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Background Herpetospermum pedunculosum (Ser.) C. B. Clarke is a traditional Chinese herbal medicine that heavily relies on the lignans found in its dried ripe seeds (Herpetospermum caudigerum), which have antioxidant and hepatoprotective functions. However, little is known regarding the lignan biosynthesis in H. pedunculosum. In this study, we used metabolomic (non-targeted UHPLC-MS/MS) and transcriptome (RNA-Seq) analyses to identify key metabolites and genes (both structural and regulatory) associated with lignan production during the green mature (GM) and yellow mature (YM) stages of H. pedunculosum. Results The contents of 26 lignan-related metabolites and the expression of 30 genes involved in the lignan pathway differed considerably between the GM and YM stages; most of them were more highly expressed in YM than in GM. UPLC-Q-TOF/MS confirmed that three Herpetospermum-specific lignans (including herpetrione, herpetotriol, and herpetin) were found in YM, but were not detected in GM. In addition, we proposed a lignan biosynthesis pathway for H. pedunculosum based on the fundamental principles of chemistry and biosynthesis. An integrated study of the transcriptome and metabolome identified several transcription factors, including HpGAF1, HpHSFB3, and HpWOX1, that were highly correlated with the metabolism of lignan compounds during seed ripening. Furthermore, functional validation assays revealed that the enzyme 4-Coumarate: CoA ligase (4CL) catalyzes the synthesis of hydroxycinnamate CoA esters. Conclusion These results will deepen our understanding of seed lignan biosynthesis and establish a theoretical basis for molecular breeding of H. pedunculosum.

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“…This suggests a higher lignan content in the autopolyploids than in the diploids. A higher lignan content is also observed in Isatidis radix , a common herb used in traditional Chinese medicine, post polyploidization [ 31 ].…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies have mainly reported the accumulation of phenylpropanoids in several plants, following polyploidization [ 30 , 31 , 50 – 52 ]. However, our results show that polyploidization had a complicated influence on the phenylpropanoid biosynthesis pathway in industrial hemp.…”

Section: Discussionmentioning

confidence: 99%

“…Past studies in the field of polyploidy have mainly focused on elucidating the relationship between polyploidization and gene expression using transcriptomic techniques [ 27 – 29 ]. However, combined metabolomic and transcriptomic analysis has been used to elucidate gene expression and metabolic differences in polyploids [ 30 , 31 ]. Although preliminary studies have shown that polyploidization can induce phenotypic and metabolic changes in cannabis plants, the mechanisms of these changes have yet to be elucidated.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptomic and metabolomic analyses reveal the differential accumulation of phenylpropanoids and terpenoids in hemp autotetraploid and its diploid progenitor

Tang,

Xu,

Gao

et al. 2023

BMC Plant Biol

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Background Cannabis sativa, a dioecious plant that has been cultivated worldwide for thousands of years, is known for its secondary metabolites, especially cannabinoids, which possess several medicinal effects. In this study, we investigated the autopolyploidization effects on the biosynthesis and accumulation of these metabolites, transcriptomic and metabolomic analyses were performed to explore the gene expression and metabolic variations in industrial hemp autotetraploids and their diploid progenitors. Results Through these analyses, we obtained 1,663 differentially expressed metabolites and 1,103 differentially expressed genes. Integrative analysis revealed that phenylpropanoid and terpenoid biosynthesis were regulated by polyploidization. No substantial differences were found in the cannabidiol or tetrahydrocannabinol content between tetraploids and diploids. Following polyploidization, some transcription factors, including nine bHLH and eight MYB transcription factors, affected the metabolic biosynthesis as regulators. Additionally, several pivotal catalytic genes, such as flavonol synthase/flavanone 3-hydroxylase, related to the phenylpropanoid metabolic pathway, were identified as being modulated by polyploidization. Conclusions This study enhances the overall understanding of the impact of autopolyploidization in C. sativa and the findings may encourage the application of polyploid breeding for increasing the content of important secondary metabolites in industrial hemp.

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Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators

Cited by 14 publications

References 33 publications

Kadsura coccinea Lignan Metabolism Based on Metabolome and Transcriptome Analysis

Kadsura coccinea Lignan Metabolism Based on Metabolome and Transcriptome Analysis

Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of lignan biosynthesis in Herpetospermum pedunculosum (Cucurbitaceae)

Transcriptomic and metabolomic analyses reveal the differential accumulation of phenylpropanoids and terpenoids in hemp autotetraploid and its diploid progenitor

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