Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation
Proanthocyanidin (PA) is an important bioactive compound with multiple physiological benefits in jujube (Ziziphus jujube Mill.). However, the molecular mechanisms underlying PA biosynthesis in jujube fruit have not been investigated. Here, the profiling of PA, (+)-catechin and (–)-epicatechin and tr...
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Tsinghua University Press
2023-09-01
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| Series: | Food Science and Human Wellness |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213453023000034 |
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| author | Wenqiang Wang Yunfeng Pu Hao Wen Dengyang Lu Min Yan Minzhe Liu Minyu Wu Hongjin Bai Lirong Shen Cuiyun Wu |
| author_facet | Wenqiang Wang Yunfeng Pu Hao Wen Dengyang Lu Min Yan Minzhe Liu Minyu Wu Hongjin Bai Lirong Shen Cuiyun Wu |
| author_sort | Wenqiang Wang |
| collection | DOAJ |
| description | Proanthocyanidin (PA) is an important bioactive compound with multiple physiological benefits in jujube (Ziziphus jujube Mill.). However, the molecular mechanisms underlying PA biosynthesis in jujube fruit have not been investigated. Here, the profiling of PA, (+)-catechin and (–)-epicatechin and transcriptome sequencing of three jujube cultivars from Xinjiang Uyghur Autonomous Region of China at five developmental stages were analyzed. The levels of total PAs and catechin exhibited a decreased trend over jujube ripening, and epicatechin content of two jujube cultivars increased first and then declined. Transcriptome analysis revealed that the differentially expressed genes (DEGs) were mainly enriched in ribosome, glycolysis/gluconeogenesis, fructose and mannose metabolism. 17 DEGs encoding PAL, CHS, CHI, CHS, F3’H, LAR, ANR, C4Hs, 4CLs, FLSs, DFRs and UFGTs involved in PA biosynthesis were relatively abundant. The highly transcribed LAR gene may greatly contribute to epicatechin accumulation. A weighted gene co-expression network analysis (WGCNA) was performed, and a network module including 1620 genes highly correlated with content of Pas and catechin was established. We identified 58 genes including 9 structural genes and 49 regulatory genes related to PA biosynthesis and regulation in the WGCNA module. Sixteen genes encoding 9 families of transcriptional factors (i.e., MYB, bHLH, ERF, bZIP, NAC, SBP, MIKC, HB, WRKY) were considered as hub genes. The results of qRT-PCR analysis validating 10 genes were well consistent with the transcriptome data. These findings provide valuable knowledge to facilitate its genetic studies and molecular breeding. |
| format | Article |
| id | doaj-art-2e810cd8b7854a23a74384e697e88ea5 |
| institution | Kabale University |
| issn | 2213-4530 |
| language | English |
| publishDate | 2023-09-01 |
| publisher | Tsinghua University Press |
| record_format | Article |
| series | Food Science and Human Wellness |
| spelling | doaj-art-2e810cd8b7854a23a74384e697e88ea52025-02-03T05:13:48ZengTsinghua University PressFood Science and Human Wellness2213-45302023-09-0112515571570Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulationWenqiang Wang0Yunfeng Pu1Hao Wen2Dengyang Lu3Min Yan4Minzhe Liu5Minyu Wu6Hongjin Bai7Lirong Shen8Cuiyun Wu9Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, ChinaCollege of Horticulture and Forestry, Tarim University, Alar 843300, ChinaDepartment of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, ChinaCollege of Horticulture and Forestry, Tarim University, Alar 843300, ChinaCollege of Horticulture and Forestry, Tarim University, Alar 843300, ChinaCollege of Horticulture and Forestry, Tarim University, Alar 843300, ChinaDepartment of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, ChinaCollege of Horticulture and Forestry, Tarim University, Alar 843300, ChinaDepartment of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, China; Corresponding authors.College of Horticulture and Forestry, Tarim University, Alar 843300, China; Corresponding authors.Proanthocyanidin (PA) is an important bioactive compound with multiple physiological benefits in jujube (Ziziphus jujube Mill.). However, the molecular mechanisms underlying PA biosynthesis in jujube fruit have not been investigated. Here, the profiling of PA, (+)-catechin and (–)-epicatechin and transcriptome sequencing of three jujube cultivars from Xinjiang Uyghur Autonomous Region of China at five developmental stages were analyzed. The levels of total PAs and catechin exhibited a decreased trend over jujube ripening, and epicatechin content of two jujube cultivars increased first and then declined. Transcriptome analysis revealed that the differentially expressed genes (DEGs) were mainly enriched in ribosome, glycolysis/gluconeogenesis, fructose and mannose metabolism. 17 DEGs encoding PAL, CHS, CHI, CHS, F3’H, LAR, ANR, C4Hs, 4CLs, FLSs, DFRs and UFGTs involved in PA biosynthesis were relatively abundant. The highly transcribed LAR gene may greatly contribute to epicatechin accumulation. A weighted gene co-expression network analysis (WGCNA) was performed, and a network module including 1620 genes highly correlated with content of Pas and catechin was established. We identified 58 genes including 9 structural genes and 49 regulatory genes related to PA biosynthesis and regulation in the WGCNA module. Sixteen genes encoding 9 families of transcriptional factors (i.e., MYB, bHLH, ERF, bZIP, NAC, SBP, MIKC, HB, WRKY) were considered as hub genes. The results of qRT-PCR analysis validating 10 genes were well consistent with the transcriptome data. These findings provide valuable knowledge to facilitate its genetic studies and molecular breeding.http://www.sciencedirect.com/science/article/pii/S2213453023000034JujubeProanthocyanidinTranscriptome analysisWGCNAHub genes |
| spellingShingle | Wenqiang Wang Yunfeng Pu Hao Wen Dengyang Lu Min Yan Minzhe Liu Minyu Wu Hongjin Bai Lirong Shen Cuiyun Wu Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation Food Science and Human Wellness Jujube Proanthocyanidin Transcriptome analysis WGCNA Hub genes |
| title | Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation |
| title_full | Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation |
| title_fullStr | Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation |
| title_full_unstemmed | Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation |
| title_short | Transcriptome and weighted gene co-expression network analysis of jujube (Ziziphus jujuba Mill.) fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation |
| title_sort | transcriptome and weighted gene co expression network analysis of jujube ziziphus jujuba mill fruit reveal putative genes involved in proanthocyanin biosynthesis and regulation |
| topic | Jujube Proanthocyanidin Transcriptome analysis WGCNA Hub genes |
| url | http://www.sciencedirect.com/science/article/pii/S2213453023000034 |
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