Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L.
We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate (Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis (WGCNA) to describe the functionality and complexity of the physiological and morphogenetic...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-01-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311920633998 |
| _version_ | 1819000061101604864 |
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| author | Fang-fang FU Ying-shu PENG Gui-bin WANG Yousry A. EL-KASSABY Fu-liang CAO |
| author_facet | Fang-fang FU Ying-shu PENG Gui-bin WANG Yousry A. EL-KASSABY Fu-liang CAO |
| author_sort | Fang-fang FU |
| collection | DOAJ |
| description | We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate (Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis (WGCNA) to describe the functionality and complexity of the physiological and morphogenetic processes as well as gene expression and metabolic differences during seed germination stages. In total, 489 metabolites were detected, including 40 differentially accumulated metabolites. The transcriptomic analysis showed the expression of 6 984 genes changed significantly throughout the whole germination process. Using WGCNA, we identified modules related to the various seed germination stages and hub genes. In the initial imbibition stage (stage 1), the pivotal genes involved in RNA transduction and the glycolytic pathway were most active, while in the sprouting stage (stage 4), the pivotal genes were involved in multiple metabolic pathways. In terms of secondary metabolic pathways, we found flavonoid 4-reductase genes of anthocyanin biosynthesis pathway are most significantly affected during pomegranate seed germination, while the flavonol synthase gene was mainly involved in the regulation of isoflavonoid biosynthesis. |
| first_indexed | 2024-12-20T22:27:19Z |
| format | Article |
| id | doaj.art-44b29a7baf6e4fac88b95f8f4054accf |
| institution | Directory Open Access Journal |
| issn | 2095-3119 |
| language | English |
| last_indexed | 2024-12-20T22:27:19Z |
| publishDate | 2021-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj.art-44b29a7baf6e4fac88b95f8f4054accf2022-12-21T19:24:47ZengElsevierJournal of Integrative Agriculture2095-31192021-01-01201132146Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L.Fang-fang FU0Ying-shu PENG1Gui-bin WANG2Yousry A. EL-KASSABY3Fu-liang CAO4Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, P.R.ChinaCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, P.R.China; Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, B.C., V6T 1Z4, CanadaCo-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, P.R.ChinaDepartment of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, B.C., V6T 1Z4, Canada; Yousry A. EL-KASSABY, Tel: + 1-604-8221821, Fax: +1-604-8229102Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, P.R.China; Correspondence CAO Fu-liang, Tel/Fax: +86-25-85427921We conducted an integrative system biology of metabolome and transcriptome profile analyses during pomegranate (Punica granatum L.) seed germination and utilized a weighted gene co-expression network analysis (WGCNA) to describe the functionality and complexity of the physiological and morphogenetic processes as well as gene expression and metabolic differences during seed germination stages. In total, 489 metabolites were detected, including 40 differentially accumulated metabolites. The transcriptomic analysis showed the expression of 6 984 genes changed significantly throughout the whole germination process. Using WGCNA, we identified modules related to the various seed germination stages and hub genes. In the initial imbibition stage (stage 1), the pivotal genes involved in RNA transduction and the glycolytic pathway were most active, while in the sprouting stage (stage 4), the pivotal genes were involved in multiple metabolic pathways. In terms of secondary metabolic pathways, we found flavonoid 4-reductase genes of anthocyanin biosynthesis pathway are most significantly affected during pomegranate seed germination, while the flavonol synthase gene was mainly involved in the regulation of isoflavonoid biosynthesis.http://www.sciencedirect.com/science/article/pii/S2095311920633998seed germination stagesweighted gene co-expression network analysis (WGCNA)metabolometranscriptomeflavonoid pathway |
| spellingShingle | Fang-fang FU Ying-shu PENG Gui-bin WANG Yousry A. EL-KASSABY Fu-liang CAO Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L. Journal of Integrative Agriculture seed germination stages weighted gene co-expression network analysis (WGCNA) metabolome transcriptome flavonoid pathway |
| title | Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L. |
| title_full | Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L. |
| title_fullStr | Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L. |
| title_full_unstemmed | Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L. |
| title_short | Integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in Punica granatum L. |
| title_sort | integrative analysis of the metabolome and transcriptome reveals seed germination mechanism in punica granatum l |
| topic | seed germination stages weighted gene co-expression network analysis (WGCNA) metabolome transcriptome flavonoid pathway |
| url | http://www.sciencedirect.com/science/article/pii/S2095311920633998 |
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