Light is one the most important environmental factors regulating the accumulation of specific metabolites in plants, such as flavonoid. Chalcone synthase (CHS) is the key rate-limiting enzyme of the flavonoid biosynthesis pathway, while little is known about the CHS genes in mango (Mangifera indica L.). Therefore, the aim of the study was to obtain the genome-wide identification of the CHS genes in mango and screen the light-responsive family members. In this study, a total of 21 CHS genes were identified from the mango genome, and most of the members contained the Cys-His-Asn triad and the CHS/STS signature motif. Most of the MiCHS genes were located on chromosomes 2 and 4, and seven pairs of tandem duplication genes and five pairs of segmental duplication genes were detected among the MiCHS members. The expression of MiCHSs showed a tissue-specific pattern and was not correlated with the flavonoid or anthocyanin accumulation in cultivars with different peel colors. MiCHS4, MiCHS16 and MiCHS17 were found to respond to preharvest and postharvest UV-B plus visible light treatments, which exhibited no significant relationship with the light-responsive cis-acting element distribution in the promoter region. Our results are helpful and can be used to further study the function of MiCHS genes in light-induced flavonoid biosynthesis in mango.

Pomegranate (Punica granatum L.) is an ancient fruit crop that has been cultivated worldwide and is known for its attractive appearance and functional metabolites. Fruit color is an important index of fruit quality, but the color formation pattern in the peel of evergreen pomegranate and the relevant molecular mechanism is still unknown. In this study, the contents of pigments including anthocyanins, carotenoids, and chlorophyll in the peel of ‘Danruo No. 1’ pomegranate fruit during three developmental stages were measured, and RNA-seq was conducted to screen key genes regulating fruit color formation. The results show that pomegranate fruit turned from green to red during development, with a dramatic increase in a* value, indicating redness and anthocyanins concentration, and a decrease of chlorophyll content. Moreover, carotenoids exhibited a decrease–increase accumulation pattern. Through RNA-seq, totals of 30, 18, and 17 structural genes related to anthocyanin biosynthesis, carotenoid biosynthesis and chlorophyll metabolism were identified from differentially expressed genes (DEGs), respectively. Transcription factors (TFs) such as MYB, bHLH, WRKY and AP2/ERF were identified as key candidates regulating pigment metabolism by K-means analysis and weighted gene co-expression network analysis (WGCNA). The results provide an insight into the theory of peel color formation in evergreen pomegranate fruit.

Anthocyanins are important secondary metabolites in fruits, and anthocyanin accumulation in the flesh of peach exhibits a spatial pattern, but the relevant mechanism is still unknown. In this study, the yellow-fleshed peach, cv. ‘Jinxiu’, with anthocyanin accumulation in the mesocarp around the stone was used as the experimental material. Red flesh (RF) and yellow flesh (YF) were sampled separately for flavonoid metabolite (mainly anthocyanins), plant hormone, and transcriptome analyses. The results showed that the red coloration in the mesocarp was due to the accumulation of cyanidin-3-O-glucoside, with an up-regulation of anthocyanin biosynthetic genes (F3H, F3′H, DFR, and ANS), transportation gene GST, and regulatory genes (MYB10.1 and bHLH3). Eleven ERFs, nine WRKYs, and eight NACs were also defined as the candidate regulators of anthocyanin biosynthesis in peach via RNA-seq. Auxin, cytokinin, abscisic acid (ABA), salicylic acid (SA), and 1-aminocyclopropane-1-carboxylic acid (ACC, ethylene precursor) were enriched in the peach flesh, with auxin, cytokinin, ACC, and SA being highly accumulated in the RF, but ABA was mainly distributed in the YF. The activators and repressors in the auxin and cytokinin signaling transduction pathways were mostly up-regulated and down-regulated, respectively. Our results provide new insights into the regulation of spatial accumulation pattern of anthocyanins in peach flesh.

Rambutan is a tropical tree and its fruit has several favorable characteristics. To understand how the color of the rambutan fruit peel develops, the transcriptome, flavonoid metabolome, and carotenoid metabolome data of two rambutan cultivars, ‘BY2’ and ‘BY7’, which show yellow and red peels at maturity, respectively, were comprehensively analyzed at three developmental stages. We identified 26 carotenoid components and 53 flavonoid components in these cultivars. Anthocyanins were the main component contributing to the red color of ‘BY7’ after reaching ripeness. The carotenoid content decreased sharply as the fruit matured. Hence, we speculated that flavonols were the main contributors to the yellow color of the ‘BY2’ peel. In total, 6805 differentially expressed genes were screened by transcriptome analysis; the majority of them were enriched in metabolic pathways and the biosynthesis of secondary metabolites. Weighted gene co-expression network analysis results revealed that in addition to MYB and bHLH, ERF, WRKY, MYB-related, and C3H were the main potential transcription factors regulating the color of the rambutan peel. In addition, we also identified 12 structural genes associated with flavonoid biosynthesis. The research findings shed light on the molecular mechanisms of color acquisition in rambutan fruit peels, laying the foundation for the quality control of rambutan and the cultivation of differently colored cultivars of rambutan.

The biosynthesis of anthocyanins and proanthocyanidins (PAs), components of two main flavonoids in plants, is regulated by environmental factors such as light. We previously found that bagging significantly repressed the biosynthesis of anthocyanins in red ‘Ruby’ mango fruit peel, but induced the accumulation of PAs. However, the molecular mechanism remains unclear. In the current study, transcriptome sequencing was used for screening the essential genes responsible for the opposite accumulation pattern of anthocyanins and PAs by bagging treatment. According to weighted gene co-expression network analysis (WGCNA), structural genes and transcription factors highly positively correlated to anthocyanins and PAs were identified. One flavanone 3-hydroxylase (F3H) and seven structural genes, including one chalcone synthase (CHS), one flavonoid 3’-hydroxylase (F3’H), one anthocyanidin synthesis (ANS), three leucoanthocyanidin reductase (LARs), and one UDP glucose: flavonoid 3-O-glucosyltransferase (UFGT), are crucial for anthocyanin and PA biosynthesis, respectively. In addition to MYB and bHLH, ERF, C2H2, HD-ZIP, and NAC are important transcription factors that participate in the regulation of anthocyanin and PA biosynthesis in ‘Ruby’ mango fruit peel by bagging treatment. Our results are helpful for revealing the transcription regulation mechanism of light-regulated mango anthocyanin and PA biosynthesis, developing new technologies for inducing flavonoid biosynthesis in mangos, and breeding mango cultivars containing high concentrations of flavonoids.

Anthocyanins are important secondary metabolites that impart color to fruits, and their biosynthesis is regulated by light. AP2/ERF transcription factors represent one of the largest TF families in plants and play pivotal roles in regulating plant growth and development, secondary metabolism, and stress responses. However, their comprehensive profile in mango (Mangifera indica L.) and their role in mango anthocyanin biosynthesis remain largely unclear. In this study, genome-wide identification and analysis of the AP2/ERF gene family in mango were conducted. A total of 240 family members were identified and classified into five subfamilies. Phylogenetic tree, conserved motif, and gene structure analyses revealed high conservation within the same subfamily and significant divergence among different subfamilies. Synteny analysis indicated that segmental and tandem duplication events played a major role in the expansion of the MiAP2/ERF family. Organ-specific expression profiles based on RNA-seq data uncovered the expression patterns of MiAP2/ERF genes in different plant organs. Furthermore, RNA-seq analyses related to light-induced anthocyanin accumulation, including preharvest “bagging–debagging” treatment and postharvest UV-B/white light and blue light treatments, identified a subset of MiAP2/ERF genes with significant light-responsive trends. The expression patterns of six blue-light-induced MiAP2/ERF genes were validated by means of qPCR. In summary, this study provides a comprehensive theoretical characterization of the AP2/ERF family in mango and reveals its potential role in light-induced anthocyanin accumulation, thereby establishing a solid theoretical foundation for subsequent investigations into gene functions and molecular mechanisms.