Transcriptome and carotenoid profiling of different varieties of Coffea arabica provides insights into fruit color formation

Hu, Faguang; Bi, Xiaofei; Li, Hongming; Fu, Xingfei; Li, Yanan; Yang, Yang; Zhang, Xiaofang; Wu, Runlong; Li, Guiping; YuLan, Lv; Huang, Jiaxiong; Luo, Xinping; Shi, Rui

doi:10.1016/j.pld.2021.11.005

Cited by 11 publications

(7 citation statements)

References 92 publications

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“…Statistical analysis was performed using Microsoft Office Excel 2013 and SPSS 20.0 (IBM Corporation, Armonk, NY, USA), GraphPad Prism 9.0 (GraphPad Software, Inc., 7825 Fay Avenue, Suite 230, La Jolla, CA, USA), and R (http://www.r-project.org/) [44].…”

Section: Discussionmentioning

confidence: 99%

Transcriptomics and Metabolomics Reveal the Critical Genes of Carotenoid Biosynthesis and Color Formation of Goji (Lycium barbarum L.) Fruit Ripening

Feng

Wan

et al. 2023

Plants

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Carotenoids in goji (Lycium barbarum L.) have excellent health benefits, but the underlying mechanism of carotenoid synthesis and color formation in goji fruit ripening is still unclear. The present study uses transcriptomics and metabolomics to investigate carotenoid biosynthesis and color formation differences in N1 (red fruit) and N1Y (yellow fruit) at three stages of ripening. Twenty-seven carotenoids were identified in N1 and N1Y fruits during the M1, M2, and M3 periods, with the M2 and M3 periods being critical for the difference in carotenoid and color between N1 and N1Y fruit. Weighted gene co-expression network analysis (WGCNA), gene trend analysis, and correlation analysis suggest that PSY1 and ZDS16 may be important players in the synthesis of carotenoids during goji fruit ripening. Meanwhile, 63 transcription factors (TFs) were identified related to goji fruit carotenoid biosynthesis. Among them, four TFs (CMB1-1, WRKY22-1, WRKY22-3, and RAP2-13-like) may have potential regulatory relationships with PSY1 and ZDS16. This work sheds light on the molecular network of carotenoid synthesis and explains the differences in carotenoid accumulation in different colored goji fruits.

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Section: Discussionmentioning

confidence: 99%

Transcriptomics and Metabolomics Reveal the Critical Genes of Carotenoid Biosynthesis and Color Formation of Goji (Lycium barbarum L.) Fruit Ripening

Feng

Wan

et al. 2023

Plants

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“…At present, many data are available related to the molecular characterization of genes involved in carotenoid biosynthesis. Hu explained that one LCYE gene (LOC113688784) was expressed 2.21 times higher in matured seeds of red coffee (Coffea arabica) than that in yellow coffee seeds [17]. Li found that the imbalanced regulation of HYE and HYB resulted in an increase in zeaxanthin and a decrease in lutein in Chinese raspberry (Rubus chingii) [18].…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic Analysis of Anthocyanin and Carotenoid Biosynthesis in Red and Yellow Fruits of Sweet Cherry (Prunus avium L.) during Ripening

Wang

Jing

et al. 2023

Horticulturae

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The diversity of fruit color in sweet cherry (Prunus avium L.) has been attributed to the presence of either anthocyanin or carotenoid. We profiled the anthocyanin and carotenoid metabolites to investigate the different pigments and the underlying regulatory mechanisms of differential expression genes (DEGs) between red and yellow fruits of sweet cherry. We profiled two cultivars, ‘Jiangnanhong’(JNH, red fruits) and ‘Chaoyang’(CY, yellow fruits) to establish their anthocyanin and carotenoid metabolites by LC-MS/MS and transcriptome analysis by RNA-seq to test the difference in gene expression and metabolic substances between the two varieties. Cyanidin-3-O-rutinoside was the most different pigment between two cultivars, the content of which in red fruit was significantly higher than in the yellow one during the whole ripening stage (stage 3 and stage 4). The total carotenoid content in the two color types of fruits was close, but the content in yellow fruit was shown to be more stable after harvest. Based on the transcriptome data, the heatmap of selected structural DEGs showed that all of the anthocyanin genes expressed significantly higher levels in red fruits than that in yellow fruits. Two unigenes encoding chalcone synthase (CHS) and UDP glucose-flavonoid 3-O-glucosyltransferase (UFGT) were expressed 1134.58 and 1151.24 times higher in red than in yellow fruits at stage 4, respectively. Correlation analysis showed that anthocyanin genes in JNH were negatively correlated with those in CY; by contrast, there were some strong correlations observed between the two cultivars in carotenoid genes. Thus, the coloration of sweet cherry was mainly attributed to anthocyanin-related genes.

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“…It serves as a significant source of livelihood for millions of individuals residing in coffee-growing nations [ 1 ]. C. arabica and C. canephora are the most important commercial coffee varieties, accounting for about 70% and 30% of the world production, respectively, in agricultural coffee production [ 2 ]. The coffee-consuming population in China is growing at an annual rate of 15%, which is more than 7.5 times the global average growth rate.…”

Section: Introductionmentioning

confidence: 99%

A Systematic Analysis of the Correlation between Flavor Active Differential Metabolites and Multiple Bean Ripening Stages of Coffea arabica L.

Bi,

Yu,

et al. 2023

Molecules

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Coffee cherries contain a crucial flavor-precursor and chemical substances influencing roasted bean quality, yet limited knowledge exists on metabolite changes during cherry ripening. Our study identified 1078 metabolites, revealing 46 core differential metabolites using a KEGG pathway analysis. At the GF vs. ROF stage, amino acid synthesis dominated; ROF vs. BRF featured nucleotide catabolism; BRF vs. PRF exhibited glycoside and flavonoid synthesis; and PRF vs. PBF involved secondary metabolite synthesis and catabolism. The PRF stage emerged as the optimal cherry-harvesting period. A correlation analysis identified core differential metabolites strongly linked to taste indicators, suggesting their potential as taste markers. Notably, nucleotides and derivatives exhibited significant negative correlations with glycosides and flavonoids during ripening. This research systematically analyzed flavor and active substances in green coffee beans during cherry ripening, offering valuable insights into substance formation in Coffea arabica L.

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Transcriptome and carotenoid profiling of different varieties of Coffea arabica provides insights into fruit color formation

Cited by 11 publications

References 92 publications

Transcriptomics and Metabolomics Reveal the Critical Genes of Carotenoid Biosynthesis and Color Formation of Goji (Lycium barbarum L.) Fruit Ripening

Transcriptomics and Metabolomics Reveal the Critical Genes of Carotenoid Biosynthesis and Color Formation of Goji (Lycium barbarum L.) Fruit Ripening

Transcriptomic Analysis of Anthocyanin and Carotenoid Biosynthesis in Red and Yellow Fruits of Sweet Cherry (Prunus avium L.) during Ripening

A Systematic Analysis of the Correlation between Flavor Active Differential Metabolites and Multiple Bean Ripening Stages of Coffea arabica L.

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