See the published version of this preprint at BMC Plant Biology.
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Research article
Hongyan Zhang
Huazhong Agriculture University
Corresponding Author
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Background: Carotenoids and flavonoids are important secondary metabolites in plants, which exert multiple bioactivities and benefits to human health. Although the genes that encode carotenogenesis and flavonoid biosynthetic enzymes are well characterized, the transcriptional regulatory mechanisms that are related to the pathway genes remain to be investigated. In this study, ‘Cara cara’ navel orange (CNO) fruit at four development stages were used to identify the key genes and TFs for carotenoids and flavonoids accumulation.
Results: In this study, CNO was used to investigate the profiles of carotenoids and flavonoids by a combination of metabolomic and transcriptomic analyses. The important stage for the accumulation of the major carotenoid, lycopene was found to be at 120 days after florescence (DAF). The transcripts of five carotenogenesis genes were highly correlated with lycopene contents, and 16, 40, 48, 24 and 18 transcription factors (TFs) were predicted to potentially bind 1-deoxy-D-xylulose-5-phosphate synthase (DXS1), deoxyxylulose 5-phosphate reductoisomerase (DXR), geranylgeranyl diphosphate synthase (GGPPS2), phytoene synthase (PSY1) and lycopene β-cyclase (LCYB) promoters, respectively. Narirutin was the most abundant flavonoid in the flesh at the early stages, 60 DAF was the most important stage for the accumulation of flavonoids, and 17, 22, 14, 25, 24 and 16 TFs could potentially bind phenylalanine ammonia-lyase (PAL-1 and PAL-4), 4-Coumarate-CoA ligase (4CL-2 and 4CL-5), chalcone synthase (CHS-1) and chalcone isomerase (CHI) promoters, respectively. Furthermore, both sets of fifteen candidate TFs might regulate at least three key genes and contribute to carotenoids/flavonoids accumulation in CNO fruit. Finally, a hierarchical model for the regulatory network among the pathway genes and TFs was proposed.
Conclusions: Collectively, our results suggest that DXS1, DXR, GGPPS2, PSY1 and LCYB genes were the most important genes for carotenoids accumulation, while PAL-1, PAL-4, 4CL-2, 4CL-5, CHS-1 and CHI for flavonoids biosynthesis. A total of 24 TFs were postulated as co-regulators in both pathways directly, which might play important roles in carotenoids and flavonoids accumulation in CNO fruit.
Keywords
Citrus, Carotenoid, Flavonoid, Transcription factor, Transcriptome, Metabolomics
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- FigureS1.tif
Figure S1. Differentially expressed genes in juice sacs of CNO fruit at different development stages. A, Numbers of differentially expressed genes at different developmental stages. B, KEGG analysis result of the differentially expressed genes in juice sacs between 90 DAF and 120 DAF.
- FigureS2.tif
Figure S2. A heatmap showing the expression levels of flavonoids biosynthesis-related genes in CNO fruit based on transcriptome data.
- FigureS3.tif
Figure S3. KEGG analysis result of the differentially expressed genes in juice sacs between 60 DAF and 90 DAF.
- FigureS4.tif
Figure S4. TFs that regulated the carotenoids and flavonoids biosynthesis genes.
- TableS15.xls
Table S1. Carotenoids identified in CNO at six developmental stages (μg/g, FW). U: undetectable. Table S2. Flavonoids identified in CNO at six developmental stages (ng/g, FW). U: undetectable. Table S3. Basic statistics of RNA-Seq clean-data mapped to the reference genome. Table S4. The expression levels of genes in CNO fruit (FPKM). Table S5. The expressed genes were clustered into nine groups by Mfuzz.
- TableS610.xls
Table S6. TFs were predicted in DXS1, DXR, GGPPS2, PSY1 and LCYB. Table S7. The TFs that showed high Pearson correlation coefficients with carotenoids synthesis-related genes. PCCa: Pearson correlation coefficient. Table S8. TFs predicted in PAL-1, PAL-4, 4CL-2, 4CL-5, CHS-1 and CHI genes. Table S9. The TFs that showed high Pearson correlation coefficients with flavonoids synthesis-related genes. PCCa: Pearson correlation coefficient. Table S10. TFs predicted in 30 most important TFs that regulate at least three carotenoid or flavonoids genes.
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View the published article at BMC Plant Biology.
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Editorial decision: Accept
On 18 Dec, 2020
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On 13 Dec, 2020
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Editor invited
On 13 Dec, 2020
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Received 02 Dec, 2020
Reviewer #2 agreed
On 08 Nov, 2020
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On 05 Nov, 2020
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On 01 Nov, 2020
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On 01 Nov, 2020
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On 01 Nov, 2020
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Editorial decision: Major revision
On 04 Oct, 2020
Review #2 received
Received 04 Oct, 2020
Reviewer #2 agreed
On 03 Sep, 2020
Review #1 received
Received 03 Sep, 2020
Reviewer #1 agreed
On 24 Aug, 2020
Reviewers invited
Invitations sent on 13 Aug, 2020
Editor assigned
On 29 Jul, 2020
First submitted
On 28 Jul, 2020
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On 28 Jul, 2020
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See the published version of this preprint at BMC Plant Biology.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Hongyan Zhang
Huazhong Agriculture University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Plant Biology.
Version 3
Posted 05 Jan, 2021
No community comments so far
Editorial decision: Accept
On 18 Dec, 2020
Editor assigned
On 13 Dec, 2020
Submission checks complete
On 13 Dec, 2020
Editor invited
On 13 Dec, 2020
No comments provided
Review #2 received
Received 02 Dec, 2020
Reviewer #2 agreed
On 08 Nov, 2020
Reviewer #1 agreed
On 05 Nov, 2020
Reviewers invited
Invitations sent on 04 Nov, 2020
Editor assigned
On 01 Nov, 2020
Submission checks complete
On 01 Nov, 2020
Editor invited
On 01 Nov, 2020
No comments provided
Editorial decision: Major revision
On 04 Oct, 2020
Review #2 received
Received 04 Oct, 2020
Reviewer #2 agreed
On 03 Sep, 2020
Review #1 received
Received 03 Sep, 2020
Reviewer #1 agreed
On 24 Aug, 2020
Reviewers invited
Invitations sent on 13 Aug, 2020
Editor assigned
On 29 Jul, 2020
First submitted
On 28 Jul, 2020
Submission checks complete
On 28 Jul, 2020
Editor invited
On 28 Jul, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Plant Biology.
Background: Carotenoids and flavonoids are important secondary metabolites in plants, which exert multiple bioactivities and benefits to human health. Although the genes that encode carotenogenesis and flavonoid biosynthetic enzymes are well characterized, the transcriptional regulatory mechanisms that are related to the pathway genes remain to be investigated. In this study, ‘Cara cara’ navel orange (CNO) fruit at four development stages were used to identify the key genes and TFs for carotenoids and flavonoids accumulation.
Results: In this study, CNO was used to investigate the profiles of carotenoids and flavonoids by a combination of metabolomic and transcriptomic analyses. The important stage for the accumulation of the major carotenoid, lycopene was found to be at 120 days after florescence (DAF). The transcripts of five carotenogenesis genes were highly correlated with lycopene contents, and 16, 40, 48, 24 and 18 transcription factors (TFs) were predicted to potentially bind 1-deoxy-D-xylulose-5-phosphate synthase (DXS1), deoxyxylulose 5-phosphate reductoisomerase (DXR), geranylgeranyl diphosphate synthase (GGPPS2), phytoene synthase (PSY1) and lycopene β-cyclase (LCYB) promoters, respectively. Narirutin was the most abundant flavonoid in the flesh at the early stages, 60 DAF was the most important stage for the accumulation of flavonoids, and 17, 22, 14, 25, 24 and 16 TFs could potentially bind phenylalanine ammonia-lyase (PAL-1 and PAL-4), 4-Coumarate-CoA ligase (4CL-2 and 4CL-5), chalcone synthase (CHS-1) and chalcone isomerase (CHI) promoters, respectively. Furthermore, both sets of fifteen candidate TFs might regulate at least three key genes and contribute to carotenoids/flavonoids accumulation in CNO fruit. Finally, a hierarchical model for the regulatory network among the pathway genes and TFs was proposed.
Conclusions: Collectively, our results suggest that DXS1, DXR, GGPPS2, PSY1 and LCYB genes were the most important genes for carotenoids accumulation, while PAL-1, PAL-4, 4CL-2, 4CL-5, CHS-1 and CHI for flavonoids biosynthesis. A total of 24 TFs were postulated as co-regulators in both pathways directly, which might play important roles in carotenoids and flavonoids accumulation in CNO fruit.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- FigureS1.tif
Figure S1. Differentially expressed genes in juice sacs of CNO fruit at different development stages. A, Numbers of differentially expressed genes at different developmental stages. B, KEGG analysis result of the differentially expressed genes in juice sacs between 90 DAF and 120 DAF.
- FigureS2.tif
Figure S2. A heatmap showing the expression levels of flavonoids biosynthesis-related genes in CNO fruit based on transcriptome data.
- FigureS3.tif
Figure S3. KEGG analysis result of the differentially expressed genes in juice sacs between 60 DAF and 90 DAF.
- FigureS4.tif
Figure S4. TFs that regulated the carotenoids and flavonoids biosynthesis genes.
- TableS15.xls
Table S1. Carotenoids identified in CNO at six developmental stages (μg/g, FW). U: undetectable. Table S2. Flavonoids identified in CNO at six developmental stages (ng/g, FW). U: undetectable. Table S3. Basic statistics of RNA-Seq clean-data mapped to the reference genome. Table S4. The expression levels of genes in CNO fruit (FPKM). Table S5. The expressed genes were clustered into nine groups by Mfuzz.
- TableS610.xls
Table S6. TFs were predicted in DXS1, DXR, GGPPS2, PSY1 and LCYB. Table S7. The TFs that showed high Pearson correlation coefficients with carotenoids synthesis-related genes. PCCa: Pearson correlation coefficient. Table S8. TFs predicted in PAL-1, PAL-4, 4CL-2, 4CL-5, CHS-1 and CHI genes. Table S9. The TFs that showed high Pearson correlation coefficients with flavonoids synthesis-related genes. PCCa: Pearson correlation coefficient. Table S10. TFs predicted in 30 most important TFs that regulate at least three carotenoid or flavonoids genes.
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