Flavonoid Biosynthesis in Bayberry Fruit
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ABSTRACT:
PROVIDER: PRJEB20868 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: Tomato (Solanum lycopersicum) serves as a research model for fruit development; however, while it is an important dietary source of antioxidant nutrients, the transcriptional regulation of genes that determine nutrient levels remains poorly understood. The goals of this study are to investigate dynamic changes of tomato genes during fruit development at transcription level and provides insight into the regulatory mechanism of fruit development and presents candidate transcription factors involved in secondary metabolism. Methods: The transcriptomes of fruit at seven developmental stages (7, 14, 21, 28, 35, 42 and 49 days after flowering) from two tomato cultivars (Ailsa Craig and HG6-61) were evaluated using the Illumina sequencing platform. Raw sequences were filtered and the resulting sets of clean reads were used for the following analysis by tophat and edgeR software. qRT–PCR validation was performed using SYBR Green assays Results: The average number of reads produced for each sample was 9.5 million, with the number of clean reads per sample ranging from 3.3 to 10.9 million. The number of reads that were mapped to the S. lycopersicum genome ranged from 1,786,380 to 6,780,667. A total of 26,397 genes, which were expressed in at least one developmental stage, were detected in the two cultivars, and the expression patterns of those genes could be divided into 20 groups using a K-mean cluster analysis. Gene Ontology term enrichment analysis indicated that genes involved in RNA regulation, secondary metabolism, hormone metabolism and cell wall metabolism were the most highly differentially expressed genes during fruit development and ripening. A co-expression analysis revealed several transcription factors whose expression patterns correlated with those of genes associated with ascorbic acid, carotenoid and flavonoid biosynthesis and 15 of these were validated with qRT–PCR. Correlation analysis revealed a high degree of consistency between transcript abundance determined by qRT-PCR or RNA-seq. Conclusions: Using RNA-seq analysis, the transcript abundance of a total of 26,397 genes was revealed. A total of 823 transcription factors were identified and their expression levels were compared to those of genes encoding enzymes involved in flavonoid, ascorbic acid and carotenoid biosynthesis. This revealed 20, 34 and 37 transcription factors putatively involved in the biosynthesis of flavonoids, ascorbic acid and carotenoids, respectively. This transcriptome study provides insight into the regulatory mechanism of fruit development and presents candidate transcription factors involved in secondary metabolism.
2015-06-01 | GSE64981 | GEO
Project description:Our study demonstrated the fluctuation of flavonoid biosynthesis in the two pomelo cultivars and laid a theoretical foundation for pomelo breeding to generate fruits with high flavonoid content.
2021-02-01 | GSE162849 | GEO
Project description:Intervention group:High flavonoid content fruit and vegetable diet guidance;Control group:No
Primary outcome(s): Flavonoid markers;Salivary cortisol;Blood cortisol;Gut microbiota;Mental Health Assessment Questionnaire;Fecal short chain fatty acids;Changes in defecation habits and traits
Study Design: Parallel
| 2717029 | ecrin-mdr-crc
Project description:Rubus chingii Hu, indigenous to China, is very rich in flavonoids. With the exception of anthocyanin, fruit flavonoids were much higher than most berries including other raspberry species, which partly contributed to its high phenolics and antioxidant capability. In contrast to other raspberries, anthocyanin and other flavonoids decreased as fruit matured. We investigated four typical phases of fruit maturation using transcriptomics, proteomics and metabolomics. The results indicate that the down-regulation of phenylpropanoid, flavonoid and anthocyanin biosynthesis are responsible for the metabolic decrease. The down-regulation of RcCHS (CL6140.Contig5) and RcCHI (Unigene14858 and Unigene22344) at gene and protein levels were associated with decreases of naringenin/naringenin chalcone respectively. Down-regulation of RcLAR (CL9527.Contig3) at gene and protein levels was consistent with decreases of afzelechin/epiafzelechin, catechin/epicatechin, and gallocatechin/epigallocatechin. However, multiple genes/proteins involved in the enzymatic pathways were divergent and differently regulated, e.g. Rc4CL genes/proteins were down-regulated while Rc4CL-like was maintained at constantly low levels.
2021-08-05 | PXD021977 | Pride
Project description:Secondary cell wall thickening (SCW) has a significant effect in the growth and development of plants, as well as in the resistance to various biotic and abiotic stresses. It is regulated by a multilevel transcriptional regulatory network, in which VASCULAR-RELATED NAC-DOMAINs (VNDs) act as key regulators. Lignin is an important component of SCW, it has a cooperative regulation with the biosynthesis of flavonoids which also originate from phenylpropanoid pathway. However, there are few studies on SCW thickening and flavonoid biosynthesis in flesh fruits. We want to investigate the role of FvVNDs on cell wall and fruit color development in Fragaria vesca.
2023-05-01 | GSE225542 | GEO
Project description:Abscisic acid (ABA) regulates plant development and adaptation to environmental conditions. The ABA biosynthesis pathway in plants has been thoroughly elucidated; however, very few transcription factors directly regulating the expression of ABA biosynthetic genes have been identified. Here we show that the tomato (Solanum lycopersicum) zinc finger transcription factor SlZFP2, which is mainly expressed in developing fruits and axillary buds, negatively regulates ABA biosynthesis. Overexpression of SlZFP2 resulted in multiple phenotypic changes, including more branches, early flowering, delayed fruit ripening, lighter seeds and faster seed germination, whereas gene silencing by RNA interference (RNAi) caused poor fruit set and inhibited seed germination. Gene expression analysis showed that SlZFP2 represses ABA biosynthesis mainly through downregulation of the ABA biosynthetic genes SITIENS (SIT), FLACCA (FLC) and aldehyde oxidase SlAO1. SlZFP2 delays the onset of ripening through suppression of the ripening regulator COLORLESS NON-RIPENING (CNR). Using bacterial one hybrid screening and a selected amplification and binding assay we identified the (A/T)(G/C)TT repeat as the core binding sequence of SlZFP2. We further identified a large number of tomato genes containing putative SlZFP2 binding sites in their promoter regions. Chromatin immunoprecipitation and electrophoretic mobility shift assays demonstrated that SIT, FLC and SlAO1 are direct targets of SlZFP2 through binding to their promoter regions. We propose that SlZFP2 represents a novel negative regulator for fine tuning ABA biosynthesis during fruit development and provides a potentially valuable tool for dissecting the role of ABA in fruit ripening.To gain further insight on transcriptome changes regulated by SlZFP2, we sequenced a representative SlZFP2 RNAi line in LA1589 background and its nontransgenic sibling (WT) on a Miseq platform. The RNAi line 207 showed defected fruit set and ABA biosynthesis were chosen for profiling gene expression via RNA sequencing. Its nontransgenic sibling was served as controls. Three biological replicates were conducted.
2015-11-23 | E-GEOD-63838 | biostudies-arrayexpress
Project description:We have performed a transcriptome analysis of genes at three different ripening stages of the pink-white fruits and the ripe stage of the red fruits of Chinese bayberry. This analysis provided a total of 119,701 unigenes, of which 41.43% were annotated in the Nr database. Our results showed that the formation of the pink-white color in Chinese bayberry fruits depended on the anthocyanin metabolic pathway, regulated by MYB1. Downregulated expression of key anthocyanin biosynthetic pathway genes, such as UFGT, F3’H, and ANS at the late stage of fruits development compared with DK3 fruits resulted in the failure to form red fruits. Our findings shed light on the regulatory mechanisms and metabolic processes that control color development in the fruits of Chinese bayberry.
2018-10-09 | GSE120925 | GEO
Project description:Background: The complex and dynamic changes during grape berry development have been studied in Vitis vinifera, but little is known about these processes in other Vitis species. The grape variety âNortonâ, with a major portion of its genome derived from Vitis aestivalis, maintains high levels of malic acid and phenolic acids in the ripening berries in comparison with V. vinifera varieties such as Cabernet Sauvignon. Furthermore, Norton berries develop a remarkably high level of resistance to most fungal pathogens while Cabernet Sauvignon berries remain susceptible to those pathogens. The distinct characteristics of Norton and Cabernet Sauvignon merit a comprehensive analysis of transcriptional regulation and metabolite pathways. Results: A microarray study was conducted on transcriptome changes of Norton berry skin during the period of 37 to 127 days after bloom, which represents berry developmental phases from herbaceous growth to full ripeness. Samples of six berry developmental stages were collected. Analysis of the microarray data revealed that a total of 3,352 probe sets exhibited significant differences at transcript levels, with two-fold changes between at least two developmental stages. Expression profiles of defense-related genes showed a dynamic modulation of nucleotide-binding site-leucine-rich repeat (NBS-LRR) resistance genes and pathogenesis-related (PR) genes during berry development. Transcript levels of PR-1 in Norton berry skin clearly increased during the ripening phase. As in other grapevines, genes of the phenylpropanoid pathway were up-regulated in Norton as the berry developed. The most noticeable was the steady increase of transcript levels of stilbene synthase genes. Transcriptional patterns of six MYB transcription factors and eleven structural genes of the flavonoid pathway and profiles of anthocyanins and proanthocyanidins (PAs) during berry skin development were analyzed comparatively in Norton and Cabernet Sauvignon. Transcriptional patterns of MYB5A and MYB5B were similar during berry development between the two varieties, but those of MYBPA1 and MYBPA2 were strikingly different, demonstrating that the general flavonoid pathways are regulated under different MYB factors. The data showed that there were higher transcript levels of the genes encoding flavonoid-3´-O-hydroxylase (F3´H), flavonoid-3´,5´-hydroxylase (F3´5´H), leucoanthocyanidin dioxygenase (LDOX), UDP-glucose:flavonoid 3´-O-glucosyltransferase (UFGT), anthocyanidin reductase (ANR), leucoanthocyanidin reductase (LAR) 1 and LAR2 in berry skin of Norton than in those of Cabernet Sauvignon. It was also found that the total amount of anthocyanins was markedly higher in Norton than in Cabernet Sauvignon berry skin at harvest, and five anthocyanin derivatives and three PA compounds exhibited distinctive accumulation patterns in Norton berry skin. Conclusions: This study provides an overview of the transcriptome changes and the flavonoid profiles in the berry skin of Norton, an important North American wine grape, during berry development. The steady increase of transcripts of PR-1 and stilbene synthase genes likely contributes to the developmentally regulated resistance during ripening of Norton berries. More studies are required to address the precise role of each stilbene synthase gene in berry development and disease resistance. Transcriptional regulation of MYBA1, MYBA2, MYB5A and MYBPA1 as well as expression levels of their putative targets F3´H, F3´5´H, LDOX, UFGT, ANR LAR1, and LAR2 are highly correlated with the characteristic anthocyanin and PA profiles of Norton berry skin. These results reveal a unique pattern of the regulation of transcription and biosynthesis pathways underlying the viticultural and enological characteristics of Norton grape, and yield new insights into the understanding of the flavonoid pathway in non-vinifera grape varieties. At each of six developmental stages, three biological replicates of berry samples were collected, each consists of ten randomly selected vines, a total of 18 samples were proccessed for analysis
2010-10-08 | E-GEOD-24561 | biostudies-arrayexpress
Project description:Papaya (Carica papaya L.) is a typical climacteric fruit, undergoing massive physico-chemical changes during ripening. Although papaya is widely cultivated and consumed, few studies have characterized the variations in metabolism during its ripening process at the proteasome level. Using an integrated approach involving Tandem Mass Tag labeling and liquid chromatography–mass spectrometry analysis, proteomes of papaya fruit at different ripening stages were investigated. A total of 3220 proteins were identified, of which 2818 were quantified. The differential accumulated proteins (DAPs) exhibited various biological functions and diverse subcellular localizations. Among the DEPs, most of the pathogen defense-related proteins were down-regulated, suggesting that disease resistance decreased during the ripening process. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that various metabolic pathways were significantly altered, particularly in flavonoid and fatty acid metabolisms. The up-regulation of several flavonoid biosynthesis-related proteins may provide more raw materials for pigment biosynthesis, accelerating the color variation of papaya fruit. Thus, variations in the fatty acid metabolism-related enzymes were investigated. For example, a lipoxygenase, which catalyzes the conversion of ACC to ethylene, was significantly induced, suggesting a cross-talk between the lipoxygenase-mediated fatty acid metabolism and the hormone-controlled fruit ripening in papaya. Furthermore, the contents of several important fatty acids were determined, and increased unsaturated fatty acids may be associated with papaya fruit volatile formation. Our data may give an intrinsic explanation of the variations in metabolism during the ripening process of papaya fruit and serve as a comprehensive resource for investigating the regulation mechanism involved.
2019-11-12 | PXD008871 | Pride
Project description:Abscisic acid (ABA) regulates plant development and adaptation to environmental conditions. The ABA biosynthesis pathway in plants has been thoroughly elucidated; however, very few transcription factors directly regulating the expression of ABA biosynthetic genes have been identified. Here we show that the tomato (Solanum lycopersicum) zinc finger transcription factor SlZFP2, which is mainly expressed in developing fruits and axillary buds, negatively regulates ABA biosynthesis. Overexpression of SlZFP2 resulted in multiple phenotypic changes, including more branches, early flowering, delayed fruit ripening, lighter seeds and faster seed germination, whereas gene silencing by RNA interference (RNAi) caused poor fruit set and inhibited seed germination. Gene expression analysis showed that SlZFP2 represses ABA biosynthesis mainly through downregulation of the ABA biosynthetic genes SITIENS (SIT), FLACCA (FLC) and aldehyde oxidase SlAO1. SlZFP2 delays the onset of ripening through suppression of the ripening regulator COLORLESS NON-RIPENING (CNR). Using bacterial one hybrid screening and a selected amplification and binding assay we identified the (A/T)(G/C)TT repeat as the core binding sequence of SlZFP2. We further identified a large number of tomato genes containing putative SlZFP2 binding sites in their promoter regions. Chromatin immunoprecipitation and electrophoretic mobility shift assays demonstrated that SIT, FLC and SlAO1 are direct targets of SlZFP2 through binding to their promoter regions. We propose that SlZFP2 represents a novel negative regulator for fine tuning ABA biosynthesis during fruit development and provides a potentially valuable tool for dissecting the role of ABA in fruit ripening.To gain further insight on transcriptome changes regulated by SlZFP2, we sequenced a representative SlZFP2 RNAi line in LA1589 background and its nontransgenic sibling (WT) on a Miseq platform.
2015-11-23 | GSE63838 | GEO