Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of flavonoid biosynthesis in blackberry

Wu, Yaqiong; Zhang, Chunhong; Huang, Zhengjin; Lyu, Lianfei; Li, Weilin; Wu, Wenlong

doi:10.1016/j.foodres.2022.110948

Cited by 40 publications

(12 citation statements)

References 52 publications

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“…As the downstream metabolite of naringenin, kaempferol and quercetin have a significant influence on the scavenging ROS and the detoxification of free radicals, which strengthen tolerance to environmental changes ( Tattini et al., 2005 ; Belinha et al., 2007 ). In the present study, the expression of the genes encoding F3′,5′H and CYP75B were downregulated in G. uralensis by drought stress, which might affect the conversion of kaempferol into quercetin ( Wu et al., 2022b ). However, the content of 3- O -methylquercetin, a derivative of quercetin, was enhanced by G5 application.…”

Section: Discussionmentioning

confidence: 56%

Comprehensive physiological, transcriptomic, and metabolomic analyses reveal the synergistic mechanism of Bacillus pumilus G5 combined with silicon alleviate oxidative stress in drought-stressed Glycyrrhiza uralensis Fisch.

Lang

et al. 2022

Front. Plant Sci.

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Glycyrrhiza uralensis Fisch. is often cultivated in arid, semi-arid, and salt-affected regions that suffer from drought stress, which leads to the accumulation of reactive oxygen species (ROS), thus causing oxidative stress. Plant growth-promoting bacteria (PGPB) and silicon (Si) have been widely reported to be beneficial in improving the tolerance of plants to drought stress by maintaining plant ROS homeostasis. Herein, combining physiological, transcriptomic, and metabolomic analyses, we investigated the response of the antioxidant system of G. uralensis seedlings under drought stress to Bacillus pumilus (G5) and/or Si treatment. The results showed that drought stress caused the overproduction of ROS, accompanied by the low efficiency of antioxidants [i.e., superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), the ascorbate (AsA)–glutathione (GSH) pool, total carotenoids, and total flavonoids]. Inversely, supplementation with G5 and/or Si enhanced the antioxidant defense system in drought-stressed G. uralensis seedlings, and the complex regulation of the combination of G5 and Si differed from that of G5 or Si alone. The combination of G5 and Si enhanced the antioxidant enzyme system, accelerated the AsA–GSH cycle, and triggered the carotenoid and flavonoid metabolism, which acted in combination via different pathways to eliminate the excess ROS induced by drought stress, thereby alleviating oxidative stress. These findings provide new insights into the comparative and synergistic roles of PGPB and Si in the antioxidant system of plants exposed to drought and a guide for the application of PGPB combined with Si to modulate the tolerance of plants to stress.

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Section: Discussionmentioning

confidence: 56%

Comprehensive physiological, transcriptomic, and metabolomic analyses reveal the synergistic mechanism of Bacillus pumilus G5 combined with silicon alleviate oxidative stress in drought-stressed Glycyrrhiza uralensis Fisch.

Lang

et al. 2022

Front. Plant Sci.

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“…The biosynthesis of anthocyanins in grape skin is mainly carried out by the flavonoid pathway, a process controlled by structural genes that regulate the formation of multi-enzyme complexes by various structural enzymes downstream, which in turn catalyze anthocyanin biosynthesis 26 . One study observed a significant correlation between anthocyanin synthesis structural genes and plant color changes 27 . In ‘Summer Black’ grapes, it was found that increases in anthocyanin levels were mainly due to the upregulation of structural genes such as PAL , C4H , 4CL , CHS , DFR , and ANS 28 .…”

Section: Discussionmentioning

confidence: 99%

Influence of rootstock on endogenous hormones and color change in Cabernet Sauvignon grapes

Liu

Zhu

Sun

et al. 2023

Sci Rep

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Different rootstocks for grapes can significantly affect fruit color and quality, possibly by affecting hormone contents, related genetic pathways, and fruit coloring mechanisms in skin. ‘Cabernet Sauvignon’ was grafted to ‘5BB’, ‘SO4’, ‘140R’, ‘CS’, ‘3309M’ and ‘Vitis riparia’ rootstocks, with self-rooting seedlings as the control (CS/CS), and sampled from the early stage of veraison to the ripening stage. The effects of rootstock on the contents of gibberellin (GA3), auxin (IAA), and abscisic acid (ABA) in grape skin were determined alongside the expression levels of eight anthocyanin synthesis related genes using real-time fluorescence quantitative PCR methods. The rootstock cultivars exhibited accelerated fruit color change, and the CS/140R combination resulted in grapes with more color than the control group in the same period. With the development of fruit, the IAA and GA3 contents in the skin of different rootstock combinations showed trends of increasing initially, then decreasing, while the ABA content decreased initially and then increased. During the verasion (28 July), the various ‘Cabernet Sauvignon’ rootstock combinations exhibited varying degrees of increases in GA3, ABA, and IAA contents; correlation analysis showed that, at the start of veraison, the expression levels of the anthocyanin synthesis-related genes VvCHS, VvDFR, and VvUFGT had strong positive correlations with hormone contents, which indicated they are key genes involved in the endogenous hormone responsive anthocyanin biosynthesis pathway. The results of this study showed that rootstock regulates the fruit coloring process by influencing the metabolism level of peel hormones in the ‘Cabernet Sauvignon’ grape.

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“…At present, transcriptome and metabolome combined analysis has been widely used to explore the relationships between the expression of genes and metabolites related to biosynthetic pathways, so as to obtain metabolites-related functional genes and regulator networks ( Liu et al, 2020 ; Du et al, 2021 ; Fu et al, 2021 ; Hou et al, 2021 ; Zou et al, 2021 ; Wu et al, 2022 ). The transcriptome and metabolome association analysis results showed that some transporter genes were also obviously positively associated with various types of flavonoids.…”

Section: Discussionmentioning

confidence: 99%

Integrative Analysis of Metabolome and Transcriptome Identifies Potential Genes Involved in the Flavonoid Biosynthesis in Entada phaseoloides Stem

2022

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Entada phaseoloides stem is known for its high medicinal benefits and ornamental value. Flavonoids are one of the main active constituents in E. phaseoloides stem. However, the regulatory mechanism of flavonoids accumulation in E. phaseoloides is lacking. Here, phytochemical compounds and transcripts from stems at different developmental stages in E. phaseoloides were investigated by metabolome and transcriptome analysis. The metabolite profiling of the oldest stem was obviously different from young and older stem tissues. A total of 198 flavonoids were detected, and flavones, flavonols, anthocyanins, isoflavones, and flavanones were the main subclasses. The metabolome data showed that the content of acacetin was significantly higher in the young stem and older stem than the oldest stem. Rutin and myricitrin showed significantly higher levels in the oldest stem. A total of 143 MYBs and 143 bHLHs were identified and classified in the RNA-seq data. Meanwhile, 34 flavonoid biosynthesis structural genes were identified. Based on the expression pattern of structural genes involved in flavonoid biosynthesis, it indicated that flavonol, anthocyanin, and proanthocyanin biosynthesis were first active during the development of E. phaseoloides stem, and the anthocyanin or proanthocyanin biosynthesis branch was dominant; the flavone biosynthesis branch was active at the late developmental stage of the stem. Through the correlation analysis of transcriptome and metabolome data, the potential candidate genes related to regulating flavonoid synthesis and transport were identified. Among them, the MYBs, bHLH, and TTG1 are coregulated biosynthesis of flavonols and structural genes, bHLH and transporter genes are coregulated biosynthesis of anthocyanins. In addition, the WDR gene TTG1-like (AN11) may regulate dihydrochalcones and flavonol biosynthesis in specific combinations with IIIb bHLH and R2R3-MYB proteins. Furthermore, the transport gene protein TRANSPARENT TESTA 12-like gene is positively regulated the accumulation of rutin, and the homolog of ABC transporter B family member gene is positively correlated with the content of flavone acacetin. This study offered candidate genes involved in flavonoid biosynthesis, information of flavonoid composition and characteristics of flavonoids accumulation, improved our understanding of the MYBs and bHLHs-related regulation networks of flavonoid biosynthesis in E. phaseoloides stem, and provided references for the metabolic engineering of flavonoid biosynthesis in E. phaseoloides stem.

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Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of flavonoid biosynthesis in blackberry

Cited by 40 publications

References 52 publications

Comprehensive physiological, transcriptomic, and metabolomic analyses reveal the synergistic mechanism of Bacillus pumilus G5 combined with silicon alleviate oxidative stress in drought-stressed Glycyrrhiza uralensis Fisch.

Comprehensive physiological, transcriptomic, and metabolomic analyses reveal the synergistic mechanism of Bacillus pumilus G5 combined with silicon alleviate oxidative stress in drought-stressed Glycyrrhiza uralensis Fisch.

Influence of rootstock on endogenous hormones and color change in Cabernet Sauvignon grapes

Integrative Analysis of Metabolome and Transcriptome Identifies Potential Genes Involved in the Flavonoid Biosynthesis in Entada phaseoloides Stem

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