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Open AccessArticle
Integrated Metabolomics and Transcriptomics Analyses Reveal the Regulatory Mechanisms of Anthocyanin and Carotenoid Accumulation in the Peel of Coffea arabica
by
Zuquan Wang
Zuquan Wang †,
Chun Xie
Chun Xie †,
Yihong Wu
Yihong Wu ,
Haobo Liu
Haobo Liu ,
Xuesong Zhang
Xuesong Zhang ,
Huabo Du
Huabo Du ,
Xuejun Li
Xuejun Li * and
Chuanli Zhang
Chuanli Zhang *
College of Tropical Crops, Yunnan Agricultural University, Pu’er 665000, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2024, 25(19), 10754; https://doi.org/10.3390/ijms251910754 (registering DOI)
Submission received: 11 September 2024
/
Revised: 30 September 2024
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Accepted: 4 October 2024
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Published: 6 October 2024
Abstract
The color of coffee fruits is influenced by several factors, including cultivar, ripening stage, and metabolite composition. However, the metabolic accumulation of pigments and the molecular mechanisms underlying peel coloration during the ripening process of Coffea arabica L. remain relatively understudied. In this study, UPLC-MS/MS-based metabolomics and RNA sequencing (RNA-seq)-based transcriptomics were integrated to investigate the accumulation of anthocyanins and carotenoids in the peel of Coffea arabica at different ripening stages: green peel (GP), green-yellow peel (GYRP), red peel (RP), and red-purple peel (RPP). This integration aimed at elucidating the molecular mechanisms associated with these changes. A total of ten anthocyanins, six carotenoids, and thirty-five xanthophylls were identified throughout the ripening process. The results demonstrated a gradual decrease in the total carotenoid content in the peel with fruit maturation, while anthocyanin content increased significantly. Notably, the accumulation of specific anthocyanins was closely associated with the transition of peel colors from green to red. Integrated metabolomics and transcriptomics analyses identified the GYRP stage as critical for this color transition. A weighted gene co-expression network analysis (WGCNA) revealed that enzyme-coding genes such as 3AT, BZ1, and lcyE, along with transcription factors including MYB, NAC, and bHLH, which interact with PHD and SET TR, may regulate the biosynthesis of anthocyanins and carotenoids, thereby influencing peel pigmentation. These findings provide valuable insights into the molecular mechanisms underlying the accumulation of anthocyanins and carotenoids in Coffea arabica peel during fruit maturation.
Share and Cite
MDPI and ACS Style
Wang, Z.; Xie, C.; Wu, Y.; Liu, H.; Zhang, X.; Du, H.; Li, X.; Zhang, C.
Integrated Metabolomics and Transcriptomics Analyses Reveal the Regulatory Mechanisms of Anthocyanin and Carotenoid Accumulation in the Peel of Coffea arabica. Int. J. Mol. Sci. 2024, 25, 10754.
https://doi.org/10.3390/ijms251910754
AMA Style
Wang Z, Xie C, Wu Y, Liu H, Zhang X, Du H, Li X, Zhang C.
Integrated Metabolomics and Transcriptomics Analyses Reveal the Regulatory Mechanisms of Anthocyanin and Carotenoid Accumulation in the Peel of Coffea arabica. International Journal of Molecular Sciences. 2024; 25(19):10754.
https://doi.org/10.3390/ijms251910754
Chicago/Turabian Style
Wang, Zuquan, Chun Xie, Yihong Wu, Haobo Liu, Xuesong Zhang, Huabo Du, Xuejun Li, and Chuanli Zhang.
2024. "Integrated Metabolomics and Transcriptomics Analyses Reveal the Regulatory Mechanisms of Anthocyanin and Carotenoid Accumulation in the Peel of Coffea arabica" International Journal of Molecular Sciences 25, no. 19: 10754.
https://doi.org/10.3390/ijms251910754
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