Metabolomic and Transcriptomic Analyses Reveal the Molecular Mechanism Underlying the Massive Accumulation of Secondary Metabolites in Fenugreek (Trigonella foenum-graecum L.) Seeds
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Plant Pathogenic Microorganism Materials
2.3. Metabolomic Analysis
2.4. Liquid Chromatography–Mass Spectrometry (LC–MS)
2.5. Metabolic Information Analysis
2.6. Library Construction and Sequencing
2.7. Data Filtering
2.8. De Novo Assembly
2.9. Coding Sequence (CDS) Prediction
2.10. Gene Annotation
2.11. Gene Quantification
2.12. Differentially Expressed Gene (DEG) Analyses
2.13. Integrated Analysis of the Transcriptome and Metabolome
2.14. Preparation of the Crude Ethanol Extract of Fenugreek Seeds
2.15. Antifungal Activity Test of Fenugreek Seed Extracts
3. Results
3.1. Fenugreek Metabolome Analysis
3.2. Principal Component Analysis (PCA)
3.3. Cluster Heatmap Analysis
3.4. Enrichment Analyses of Differentially Accumulated Metabolites (DAMs) and Metabolites in Pathways Related to Flavonoids and Alkaloids
3.5. Analysis of Fenugreek Seed Transcriptome Data
3.6. Differential Expression Gene (DEG) Analysis
3.7. KEGG and GO Enrichment Analysis of DEGs
3.8. Integrated Metabolome and Transcriptome Analysis of Flavonoids and Alkaloids
3.9. Antifungal Activity Analyses
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Compounds | Fold Change | Pathway |
---|---|---|
Flavonoids: | ||
3,7-Di-O-methylquercetin | 36.862 | map00944 Flavone and flavonol biosynthesis |
Luteolin 7-O-β-D-diglucuronide | 27.739 | map00944 Flavone and flavonol biosynthesis |
Apigenin | 24.697 | map00941 Flavonoid biosynthesis |
Apigenin 7-O-β-D-glucoside | 21.996 | map00941 Flavonoid biosynthesis |
Naringin | 18.806 | map00941 Flavonoid biosynthesis |
Chrysoeriol | 16.954 | map00944 Flavone and flavonol biosynthesis |
Rutin | 16.662 | map00944 Flavone and flavonol biosynthesis |
Kaempferol 3-O-glucoside | 14.202 | map00944 Flavone and flavonol biosynthesis |
Luteolin 7-O-β-D-glucoside | 11.333 | map00944 Flavone and flavonol biosynthesis |
Dihydrokaempferol | 8.712 | map00941 Flavonoid biosynthesis |
Luteolin 7-O-[β-D-glucuronosyl-(1->2)-β-D-glucuronide]-4′-O-β-D-glucuronide | 8.27 | map00944 Flavone and flavonol biosynthesis |
Epigallocatechin 3-gallate | 7.897 | map04152 AMPK signaling pathway |
Phlorizin | 7.408 | map00941 Flavonoid biosynthesis |
Kaempferide | 6.491 | map00944 Flavone and flavonol biosynthesis |
(+)-Catechin | 2.936 | map00941 Flavonoid biosynthesis |
Naringenin | 2.463 | map00941 Flavonoid biosynthesis |
Isoflavonoids: | ||
Pseudobaptigenin | 36.652 | map00941 Flavonoid biosynthesis |
2′-Hydroxybiochanin A | 30.126 | map00943 Isoflavonoid biosynthesis |
2′-Hydroxygenistein | 19.097 | map00943 Isoflavonoid biosynthesis |
Pratensein | 16.954 | map00943 Isoflavonoid biosynthesis |
Alkaloids and derivatives: | ||
Ecgonine methyl ester | 24.183 | map00960 Tropane, piperidine, and pyridine alkaloid biosynthesis |
Sanguinarine | 19.123 | map00950 Isoquinoline alkaloid biosynthesis |
Compound | Gene Name | Correlation Coefficients | p-Values |
---|---|---|---|
Flavonoids: Apigenin | legumin B | 0.999397805 | 0.000000544 |
Chrysosplenol D | legumin B | 0.999574004 | 0.000000272 |
Cosmosiin | legumin J | 0.999622259 | 0.000000214 |
Resokaempherol | legumin J | 0.999758896 | 0.0000000872 |
seed linoleate 9S-lipoxygenase-3 | 0.9991967 | 0.000000968 | |
Kaempferitrin | H/ACA ribonucleoprotein complex | 0.999758896 | 0.0000000872 |
subunit 4 | |||
HMG (high mobility group) box protein | 0.9991967 | 0.000000968 | |
with ARID | |||
Isoflavonoids: 3,7-Di-O-methylquercetin | legumin J | 0.999412712 | 0.000000517 |
Apigenin dimethylether; | aldehyde decarbonylase | 0.999397805 | 0.000000544 |
Astragalin | legumin B | 0.999583385 | 0.00000026 |
Tangeretin | UPSTREAM OF FLC protein | 0.999001756 | 0.00000149 |
Pratensein | legumin J | 0.999724414 | 0.000000114 |
Dehydroferreirin; | legumin J | 0.999650167 | 0.000000184 |
Alkaloids and derivatives: | |||
Harmalol | (R)-mandelonitrile β-glucosyltransferase | 0.999715273 | 0.000000122 |
(+/−)-6-Acetonyldihydrosanguinarine | tetratricopeptide repeat (TPR)-containing protein | 0.99925841 | 0.000000825 |
Phytopathogenic Fungi | Treat (Diameter/cm) | CK (Diameter/cm) | Blank (Diameter/cm) | Inhibition Rate |
---|---|---|---|---|
M. oryzae | 3.85 ± 0.18 b | 6.13 ± 0.08 a | 5.63 ± 0.63 | 37.22% |
A. tenuissima (Kunze)Wiltshire | 3.77 ± 0.28 b | 6.52 ± 0.25 a | 6.67 ± 0.16 | 42.16% |
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Zhao, Q.; Wu, G.; Yang, P.; Shi, Y.; Fu, Z.; Mo, H.; Shi, C.; Yu, S. Metabolomic and Transcriptomic Analyses Reveal the Molecular Mechanism Underlying the Massive Accumulation of Secondary Metabolites in Fenugreek (Trigonella foenum-graecum L.) Seeds. Genes 2024, 15, 343. https://doi.org/10.3390/genes15030343
Zhao Q, Wu G, Yang P, Shi Y, Fu Z, Mo H, Shi C, Yu S. Metabolomic and Transcriptomic Analyses Reveal the Molecular Mechanism Underlying the Massive Accumulation of Secondary Metabolites in Fenugreek (Trigonella foenum-graecum L.) Seeds. Genes. 2024; 15(3):343. https://doi.org/10.3390/genes15030343
Chicago/Turabian StyleZhao, Qiuyu, Guoxing Wu, Pu Yang, Yuanchong Shi, Zuoyi Fu, Haifeng Mo, Chunlan Shi, and Shuhui Yu. 2024. "Metabolomic and Transcriptomic Analyses Reveal the Molecular Mechanism Underlying the Massive Accumulation of Secondary Metabolites in Fenugreek (Trigonella foenum-graecum L.) Seeds" Genes 15, no. 3: 343. https://doi.org/10.3390/genes15030343
APA StyleZhao, Q., Wu, G., Yang, P., Shi, Y., Fu, Z., Mo, H., Shi, C., & Yu, S. (2024). Metabolomic and Transcriptomic Analyses Reveal the Molecular Mechanism Underlying the Massive Accumulation of Secondary Metabolites in Fenugreek (Trigonella foenum-graecum L.) Seeds. Genes, 15(3), 343. https://doi.org/10.3390/genes15030343