Integrated Metabolome and Transcriptome Analysis Reveals a Regulatory Network of Fruit Peel Pigmentation in Eggplant (Solanum melongena L.)
Abstract
:1. Introduction
2. Results
2.1. Variation in Fruit Peel Color and Total Anthocyanin and Chlorophyll Contents
2.2. Flavonoid Metabolic Differences
2.3. Comparison of Differentially Accumulated Metabolites among the Five Eggplant Varieties
2.4. Comparative Transcriptome of Fruit Peels among the Five Eggplant Varieties
2.5. Identification of DEGs Involved in Flavonoid Biosynthesis
2.6. Identification of DEGs Involved in Chlorophyll Metabolism
2.7. Identification of DEGs Involved in Hormone-Mediated Signaling Pathways
2.8. Identification of Coexpressed Gene Networks and Key Candidates
2.9. Validation of Differentially Expressed Genes by Quantitative Real-Time PCR
3. Discussion
3.1. Pigment Accumulation in Different Colors of Eggplant Fruit Peels
3.2. The Activation of Early Phenylpropanoid/Flavonoid Biosynthesis Genes for Anthocyanin Accumulation in Fruit Peels
3.3. Candidate Transcription Factors Modulated Anthocyanin Accumulation in Eggplant Fruit Peels
3.4. Plant Hormone Signaling Pathway for Color Variation in Eggplant Fruit Skins
4. Materials and Methods
4.1. Plant Materials
4.2. Total Anthocyanin and Chlorophyll Analysis
4.3. Fruit Peel Color Intensity Measurement
4.4. Flavonoid Identification and Quantification
4.5. RNA-Seq Analysis
4.6. Bioinformatic Analysis
4.7. Coexpression Network Analysis
4.8. Quantitative Real-Time PCR Analysis
4.9. Vector Construction and Transformation of Eggplant
4.10. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Samples | Clean Reads | Reads Mapped | Q20 (%) | Q30 (%) | GC Content (%) |
---|---|---|---|---|---|
A1–1 | 47409416 | 45993726 (97.01%) | 97.69 | 93.49 | 42.23 |
A1–2 | 46685604 | 45365789 (97.17%) | 97.77 | 93.64 | 42.46 |
A1–3 | 48592694 | 47236677 (97.21%) | 97.8 | 93.68 | 42.69 |
A2–1 | 48679876 | 47284281 (97.13%) | 97.75 | 93.59 | 42.33 |
A2–2 | 43769020 | 42395918 (96.86%) | 97.67 | 93.51 | 41.91 |
A2–3 | 49045732 | 47596182 (97.04) | 97.68 | 93.41 | 42.18 |
A3–1 | 46608676 | 45126433 (96.82) | 97.76 | 93.63 | 41.66 |
A3–2 | 45840606 | 44446440 (96.96%) | 97.8 | 93.73 | 41.9 |
A3–3 | 49665704 | 47998296 (96.64%) | 97.68 | 93.5 | 42.34 |
A4–1 | 47772226 | 46365463 (97.06%) | 97.79 | 93.67 | 42.50 |
A4–2 | 42518600 | 41148256 (96.78%) | 97.43 | 92.92 | 42.12 |
A4–3 | 49236290 | 47743262 (96.97%) | 97.77 | 93.64 | 42.22 |
A5–1 | 46807752 | 45518684 (97.25%) | 97.88 | 93.9 | 42.42 |
A5–2 | 47101278 | 46077478 (97.83%) | 98.15 | 94.37 | 42.34 |
A5–3 | 43808476 | 42891632 (97.91%) | 98.23 | 94.57 | 42.44 |
Comparison Groups | Total DEGs | Downregulated DEGs | Upregulated DEGs |
---|---|---|---|
A1 vs. A2 | 4265 | 1936 | 2329 |
A1 vs. A3 | 3987 | 2236 | 1751 |
A1 vs. A5 | 4005 | 2431 | 1574 |
A2 vs. A3 | 4253 | 2507 | 1746 |
A2 vs. A5 | 3837 | 2540 | 1297 |
A3 vs. A5 | 3629 | 2087 | 1542 |
A4 vs. A1 | 4456 | 1679 | 2777 |
A4 vs. A2 | 4095 | 1314 | 2781 |
A4 vs. A3 | 2881 | 1176 | 1705 |
A4 vs. A5 | 2152 | 1146 | 1006 |
Module | Gene | Annotation | Connectivity |
---|---|---|---|
Purple | Smechr0303487 | Homobox-leucine zipper protein GLABRA2 | 164.2872382 |
Purple | Smechr1201797 | Flavonoid 3′5′-hydroxylase | 163.1378627 |
Purple | Smechr0302054 | Uncharacterized protein | 163.0477793 |
Purple | Smechr0601814 | GATA transcription factor 26 | 162.7337461 |
Purple | Smechr1002540 | Anthocyanin 3-O-glucosyltransferase | 159.0606892 |
Purple | Smechr0500713 | Phenylalanine ammonia-lyase 2 | 157.7681631 |
Purple | Smechr1002420 | WRKY transcription factor 44 | 157.7222576 |
Purple | Smechr1102209 | Kirola | 157.0941481 |
Purple | Smechr0901701 | Anthocyanin-related transcription factor TT8 | 156.9502973 |
Purple | Smechr0302347 | 4-coumarate-CoA ligase 2 | 156.3548796 |
Violet | Smechr1000379 | Chlorophyll a-b binding protein | 103.30002 |
Violet | Smechr0902639 | 30S ribosomal protein S1 | 102.53807 |
Violet | Smechr0901976 | Uncharacterized protein | 101.83604 |
Violet | Smechr0502558 | Protein TIC55, chloroplastic | 101.50027 |
Violet | Smechr1100719 | ABC transporter F family member 5 | 98.330714 |
Violet | Smechr0900664 | Chlorophyll a-b binding protein | 97.539107 |
Violet | Smechr1001174 | Uncharacterized protein | 94.912891 |
Violet | Smechr1200635 | Chlorophyllide a oxygenase | 90.176381 |
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Zhou, X.; Liu, S.; Yang, Y.; Liu, J.; Zhuang, Y. Integrated Metabolome and Transcriptome Analysis Reveals a Regulatory Network of Fruit Peel Pigmentation in Eggplant (Solanum melongena L.). Int. J. Mol. Sci. 2022, 23, 13475. https://doi.org/10.3390/ijms232113475
Zhou X, Liu S, Yang Y, Liu J, Zhuang Y. Integrated Metabolome and Transcriptome Analysis Reveals a Regulatory Network of Fruit Peel Pigmentation in Eggplant (Solanum melongena L.). International Journal of Molecular Sciences. 2022; 23(21):13475. https://doi.org/10.3390/ijms232113475
Chicago/Turabian StyleZhou, Xiaohui, Songyu Liu, Yan Yang, Jun Liu, and Yong Zhuang. 2022. "Integrated Metabolome and Transcriptome Analysis Reveals a Regulatory Network of Fruit Peel Pigmentation in Eggplant (Solanum melongena L.)" International Journal of Molecular Sciences 23, no. 21: 13475. https://doi.org/10.3390/ijms232113475