Integrative analyses of metabolome and transcriptome reveals metabolomic variations and candidate genes involved in sweet cherry (Prunus avium L.) fruit quality during development and ripening

Yang, Haiying; Tian, Changping; Ji, Shujun; Ni, Fengzhu; Fan, Xinguang; Yang, Yanqing; Sun, Chanchan; Gong, Hansheng; Zhang, Aidi

doi:10.1371/journal.pone.0260004

Cited by 31 publications

(16 citation statements)

References 67 publications

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“…As shown in Figure 9(a), the heat map graphics revealed that many genes and metabolites were negatively or positively correlated, suggesting that the metabolism was likely affected by the transcriptome. The nine-quadrant diagrams [20] were consistent with the result of the heat map and provided more detailed information (Figure 9(b)). The correlation coefficient data (jrj > 0:80) were divided into 1-9 quadrants: the 1 and 9 quadrants indicated the negative correlation between the genes and metabolites; while the quadrants 3 and 7 suggested that they were positively correlated; the 5 quadrant meant no significance, and the rest of quadrants suggested a partial correlation.…”

Section: Integrative Analysis Of the Transcriptome Andsupporting

confidence: 80%

Integrative Analysis of Transcriptome and Metabolome to Illuminate the Protective Effects of Didymin against Acute Hepatic Injury

Pang

Xiong

Feng

et al. 2023

Mediators of Inflammation

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Based on the multiomics analysis, this study is aimed at investigating the underlying mechanism of didymin against acute liver injury (ALI). The mice were administrated with didymin for 2 weeks, followed by injection with lipopolysaccharide (LPS) plus D-galactosamine (D-Gal) to induce ALI. The pathological examination revealed that didymin significantly ameliorated LPS/D-Gal-induced hepatic damage. Also, it markedly reduced proinflammatory cytokines release by inhibiting the TLR4/NF-κB pathway activation, alleviating inflammatory injury. A transcriptome analysis proved 2680 differently expressed genes (DEGs) between the model and didymin groups and suggested that the PI3K/Akt and metabolic pathways might be the most relevant targets. Meanwhile, the metabolome analysis revealed 67 differently expressed metabolites (DEMs) between the didymin and model groups that were mainly clustered into the glycerophospholipid metabolism, which was consistent with the transcriptome study. Importantly, a comprehensive analysis of both the omics indicated a strong correlation between the DEGs and DEMs, and an in-depth study demonstrated that didymin alleviated metabolic disorder and hepatocyte injury likely by inhibiting the glycerophospholipid metabolism pathway through the regulation of PLA2G4B, LPCAT3, and CEPT1 expression. In conclusion, this study demonstrates that didymin can ameliorate LPS/D-Gal-induced ALI by inhibiting the glycerophospholipid metabolism and PI3K/Akt and TLR4/NF-κB pathways.

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Section: Integrative Analysis Of the Transcriptome Andsupporting

confidence: 80%

Integrative Analysis of Transcriptome and Metabolome to Illuminate the Protective Effects of Didymin against Acute Hepatic Injury

Pang

Xiong

Feng

et al. 2023

Mediators of Inflammation

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“…Moreover, color is one of the most efficient indicators for evaluating fruit quality and maturity. In the mature stage, the color of cherry fruits mainly present as dark red, such as in “Hong Deng” ( P. avium ), “Black Pearl” ( P. avium ), “Santina” ( P. avium ), “Kitayanka” ( P. avium ), “Irema BS” ( P. avium ), “Werdersche braune” ( P. avium ), “Erdi bottermo” ( P. cerasus ), and “Aode” ( P. cerasus ; Liu et al, 2013 ; Cao et al, 2015 ; Starkevič et al, 2015 ; Zhang et al, 2021 ; Yang et al, 2021b ); bright red, such as in “Lapins” ( P. avium ), “Duan bing” ( P. cerasus ), and “Black peel” ( P. cerasus ; Cao et al, 2015 ; Starkevič et al, 2015 ); yellow-and-bright-red bicolor, such as in “Caihong” ( P. avium ) and “Rainier” ( P. avium ; Liu et al, 2013 ; Jin et al, 2016 ); or yellow, such as in “Big Dragon” ( P. avium ) and “Belobokaya rannyaya” ( P. avium ; Starkevič et al, 2015 ; Jin et al, 2016 ). Interestingly, mature P. tomentosa fruits present as orange–red or creamy white ( Figure 1A ), greatly different from other cherries ( Cao et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

“…Usually, red pigment accumulation and anthocyanin content increase reach their deepest and the highest at the mature stage ( Liu et al, 2013 ; Shen et al, 2014 ; Starkevič et al, 2015 ; Jin et al, 2016 ; Yang et al, 2021a ). These suggest that anthocyanin may also play an important role in fruit ripening ( Carbone et al, 2019 ; Yang et al, 2021b ). In this study, the a */ b * value ratio was significantly higher in RP than WP fruits at mature stage, which is consistent with the color difference in the appearance of red and white P. tomentosa cherries ( Figures 1A , C ).…”

Section: Discussionmentioning

confidence: 99%

Metabolome and Transcriptome Analyses of Anthocyanin Accumulation Mechanisms Reveal Metabolite Variations and Key Candidate Genes Involved in the Pigmentation of Prunus tomentosa Thunb. Cherry Fruit

Zhang

Yang

et al. 2022

Front. Plant Sci.

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Prunus tomentosa Thunb. has excellent nutritional, economic, and ornamental values with different fruit color. The red coloration of fruit is determined by anthocyanin pigmentation, which is an attractive trait for consumers. However, the mechanisms underlying fruit color formation in the P. tomentosa cherry are not well understood. In this research, the pigmentation patterns in red-color P. tomentosa (RP) fruit and white-color P. tomentosa (WP) were evaluated. Anthocyanin content in matured RP fruit was significantly abundant compared with WP fruit. Metabolomic profiling revealed that pelargonidin 3-O-glucoside, cyanidin 3-O-rutinoside, and pelargonidin 3-O-rutinoside were the predominant anthocyanin compounds in the RP fruit, while, WP fruit had less anthocyanin compositions and lower level. Then, integrative analyses of transcriptome and metabolome identified 285 significant differentially expressed genes (DEGs) closely related to anthocyanin differentially expressed metabolites (DEMs). Among them, nine genes were involved in anthocyanin biosynthesis, transport and degradation pathway, including four biosynthesis genes (PtPAL1, PtDFR, PtANS, and PtUFGT), two transport genes (PtGST11, PtABC10), and three degradation genes (PtPOD1, PtPOD16, PtPOD73). Transcriptome data and real-time PCR showed that the transcript levels of biosynthesis and transport genes were significantly higher in RP than in WP, especially PtANS, PtUFGT, and PtGST11, suggesting they may play key roles in red-colored fruit formation. Meanwhile, the degradation-related genes PtPOD1/16/73 took on exactly opposite trend, suggesting their potential effects on anthocyanin degradation. These results provide novel insights into color patterns formation mechanisms of cherries fruit, and the candidate key genes identified in anthocyanin biosynthesis, transport and degradation may provide a valuable resource for cherry breeding research in future.

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“…With the recent advancements in transcriptome and metabolome, the integrative analysis has provide an effective approach to illustrate the metabolic pathways and regulatory genes in fruit crops, such as sweet cherry [ 30 ], tomentosa cherry [ 26 ], strawberry [ 11 ], and longan [ 31 ]. In this study, integrative analysis of transcriptome and metabolome data were conducted to (i) analyze the color differences between dark-red and yellow Chinese cherry fruits, (ii) identify the differential expressed genes associated with anthocyanin biosynthesis during fruit development, and (iii) identify the key differential expressed metabolites related to anthocyanins and proanthocyanidins between mature dark-red and yellow fruits.…”

Section: Introductionmentioning

confidence: 99%

Integrated Transcriptome and Metabolome Analyses Provide Insights into the Coloring Mechanism of Dark-red and Yellow Fruits in Chinese Cherry [Cerasus pseudocerasus (Lindl.) G. Don]

Wang

Zhang

et al. 2023

IJMS

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Chinese cherry [Cerasus pseudocerasus (Lindl.) G. Don] is an important fruit tree from China that has excellent ornamental, economic, and nutritional values with various colors. The dark-red or red coloration of fruit, an attractive trait for consumers, is determined by anthocyanin pigmentation. In this study, the coloring patterns during fruit development in dark-red and yellow Chinese cherry fruits were firstly illustrated by integrated transcriptome and widely-targeted metabolome analyses. Anthocyanin accumulation in dark-red fruits was significantly higher compared with yellow fruits from the color conversion period, being positively correlated to the color ratio. Based on transcriptome analysis, eight structural genes (CpCHS, CpCHI, CpF3H, CpF3’H, CpDFR, CpANS, CpUFGT, and CpGST) were significantly upregulated in dark-red fruits from the color conversion period, especially CpANS, CpUFGT, and CpGST. On contrary, the expression level of CpLAR were considerably higher in yellow fruits than in dark-red fruits, especially at the early stage. Eight regulatory genes (CpMYB4, CpMYB10, CpMYB20, CpMYB306, bHLH1, CpNAC10, CpERF106, and CpbZIP4) were also identified as determinants of fruit color in Chinese cherry. Liquid chromatography-tandem mass spectrometry identified 33 and 3 differential expressed metabolites related to anthocyanins and procyanidins between mature dark-red and yellow fruits. Cyanidin-3-O-rutinoside was the predominant anthocyanin compound in both fruits, while it was 6.23-fold higher in dark-red than in yellow fruits. More accumulated flavanol and procyanidin contents resulted in less anthocyanin content in flavonoid pathway in yellow fruits due to the higher expression level of CpLAR. These findings can help understand the coloring mechanism of dark-red and yellow fruits in Chinese cherry, and provide genetic basis for breeding new cultivars.

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Integrative analyses of metabolome and transcriptome reveals metabolomic variations and candidate genes involved in sweet cherry (Prunus avium L.) fruit quality during development and ripening

Cited by 31 publications

References 67 publications

Integrative Analysis of Transcriptome and Metabolome to Illuminate the Protective Effects of Didymin against Acute Hepatic Injury

Integrative Analysis of Transcriptome and Metabolome to Illuminate the Protective Effects of Didymin against Acute Hepatic Injury

Metabolome and Transcriptome Analyses of Anthocyanin Accumulation Mechanisms Reveal Metabolite Variations and Key Candidate Genes Involved in the Pigmentation of Prunus tomentosa Thunb. Cherry Fruit

Integrated Transcriptome and Metabolome Analyses Provide Insights into the Coloring Mechanism of Dark-red and Yellow Fruits in Chinese Cherry [Cerasus pseudocerasus (Lindl.) G. Don]

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