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Volume 25
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10.3390/ijms25189860
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Article

Integrated Metabolome, Transcriptome and Long Non-Coding RNA Analysis Reveals Potential Molecular Mechanisms of Sweet Cherry Fruit Ripening

by
Gangshuai Liu
1,2,
Daqi Fu
2,
Xuwei Duan
3,
Jiahua Zhou
1,
Hong Chang
1,
Ranran Xu
1,
Baogang Wang
1,* and
Yunxiang Wang
1,*
1
Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
2
College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
3
Institute of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2024, 25(18), 9860; https://doi.org/10.3390/ijms25189860
Submission received: 22 June 2024 / Revised: 29 August 2024 / Accepted: 10 September 2024 / Published: 12 September 2024
(This article belongs to the Special Issue Recent Advances in Plant Molecular Science in China 2024)
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Abstract

Long non-coding RNAs (lncRNAs), a class of important regulatory factors for many biological processes in plants, have received much attention in recent years. To explore the molecular roles of lncRNAs in sweet cherry fruit ripening, we conducted widely targeted metabolome, transcriptome and lncRNA analyses of sweet cherry fruit at three ripening stages (yellow stage, pink stage, and dark red stage). The results show that the ripening of sweet cherry fruit involves substantial metabolic changes, and the rapid accumulation of anthocyanins (cyanidin 3-rutinoside, cyanidin 3-O-galactoside, and cyanidin 3-O-glucoside) is the main cause of fruit coloration. These ripening-related alterations in the metabolic profile are driven by specific enzyme genes related to the synthesis and decomposition of abscisic acid (ABA), cell wall disintegration, and anthocyanin biosynthesis, as well as transcription factor genes, such as MYBs, bHLHs, and WD40s. LncRNAs can target these ripening-related genes to form regulatory modules, incorporated into the sweet cherry fruit ripening regulatory network. Our study reveals that the lncRNA-mRNA module is an important component of the sweet cherry fruit ripening regulatory network. During sweet cherry fruit ripening, the differential expression of lncRNAs will meditate the spatio-temporal specific expression of ripening-related target genes (encoding enzymes and transcription factors related to ABA metabolism, cell wall metabolism and anthocyanin metabolism), thus driving fruit ripening.
Keywords: Prunus avium L.; abscisic acid; cell wall; anthocyanin; transcription factor Prunus avium L.; abscisic acid; cell wall; anthocyanin; transcription factor

Share and Cite

MDPI and ACS Style

Liu, G.; Fu, D.; Duan, X.; Zhou, J.; Chang, H.; Xu, R.; Wang, B.; Wang, Y. Integrated Metabolome, Transcriptome and Long Non-Coding RNA Analysis Reveals Potential Molecular Mechanisms of Sweet Cherry Fruit Ripening. Int. J. Mol. Sci. 2024, 25, 9860. https://doi.org/10.3390/ijms25189860

AMA Style

Liu G, Fu D, Duan X, Zhou J, Chang H, Xu R, Wang B, Wang Y. Integrated Metabolome, Transcriptome and Long Non-Coding RNA Analysis Reveals Potential Molecular Mechanisms of Sweet Cherry Fruit Ripening. International Journal of Molecular Sciences. 2024; 25(18):9860. https://doi.org/10.3390/ijms25189860

Chicago/Turabian Style

Liu, Gangshuai, Daqi Fu, Xuwei Duan, Jiahua Zhou, Hong Chang, Ranran Xu, Baogang Wang, and Yunxiang Wang. 2024. "Integrated Metabolome, Transcriptome and Long Non-Coding RNA Analysis Reveals Potential Molecular Mechanisms of Sweet Cherry Fruit Ripening" International Journal of Molecular Sciences 25, no. 18: 9860. https://doi.org/10.3390/ijms25189860

APA Style

Liu, G., Fu, D., Duan, X., Zhou, J., Chang, H., Xu, R., Wang, B., & Wang, Y. (2024). Integrated Metabolome, Transcriptome and Long Non-Coding RNA Analysis Reveals Potential Molecular Mechanisms of Sweet Cherry Fruit Ripening. International Journal of Molecular Sciences, 25(18), 9860. https://doi.org/10.3390/ijms25189860

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