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

Abstract

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.

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]

“…Generally, pelargonidin is reportedly as indicating an orange-red color, while cyanidin and peonidin indicate a deep red or purplish-red color [ 42 ]. Cyanidin and its glycoside derivatives have been reported as the primary anthocyanins in red-colored cherries [ 21 , 26 , 43 ]. Cyanidin 3- O -rutinoside and cyanidin 3- O -glucoside are the major anthocyanin components in sweet cherry [ 24 , 44 , 45 ] and sour cherry fruits [ 46 , 47 ].…”

“…Cyanidin 3-rutinoside and cyanidin 3-glucosyl-rutinoside were the major components in both C. pseudocerasus and C. vulgaris [ 22 ], and cyanidin 3-rutinoside was predominant in C. avium [ 22 , 23 , 24 , 25 ]. Pelargonidin 3- O -glucoside, cyanidin 3- O -rutinoside, and pelargonidin 3- O -rutinoside were the chief compounds in the red C. tomentosa compared with the white fruit [ 26 ]. In C. avium and C. tomentosa , a large number of structural and regulatory genes involved in anthocyanin biosynthesis, transport and degradation pathway, have been identified by previous studies [ 26 , 27 , 28 , 29 ].…”

“…Pelargonidin 3- O -glucoside, cyanidin 3- O -rutinoside, and pelargonidin 3- O -rutinoside were the chief compounds in the red C. tomentosa compared with the white fruit [ 26 ]. In C. avium and C. tomentosa , a large number of structural and regulatory genes involved in anthocyanin biosynthesis, transport and degradation pathway, have been identified by previous studies [ 26 , 27 , 28 , 29 ]. It is worth noting that the major anthocyanin component and the related genes/transcription factors (TFs) regulating anthocyanin biosynthesis varied from different cherry species.…”

“…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.…”

The Integration of Metabolomics and Transcriptomics Provides New Insights for the Identification of Genes Key to Auxin Synthesis at Different Growth Stages of Maize

“…Transcriptome analysis is an important method to monitor gene expression in organisms, and the metabolome is the basis and direct embodiment of the biological phenotype [ 46 ]. Transcriptome sequencing generates substantial information on DEGs and the regulators of metabolic pathways, but has difficulty in determining the key signaling pathways because the genes and phenotypes are weakly correlated with each other.…”