“…At present, more and more genes related to flavonoid biosynthesis pathway have been identified in some plant species: PsDFR , PsANS and PhCHS in peony [ 15 , 56 ]; CitCHS in citrus [ 47 , 57 ]; MiCHS , MiCHI and MiF3H in mango [ 58 ]; SbCHS , SbCHI and SbF3H in Selaginella officinalis [ 59 ]; CHS-A , CHS-B and AcFLSs in onion [ 60 ]; AgMYB1 in celery [ 61 ]; GbFLS in ginkgo biloba [ 62 , 63 ]; SmCHS , SmCHI and SmFNS in Salvia miltiorrhiza [ 50 ]; MaCHS in mulberry [ 64 ]; CtC4H2 , CtCHS3 , CtCHI3 , CtF3H3 and CtF3H1 in safflower [ 65 ]; CsMYB6A and CsUGT72AM1 in purple leaf tea [ 66 ]; AaFLS1 in Artemisia annua [ 67 ]. In order to explore the candidate genes that affecting cucumber peel yellowing, we further analyzed six DEGs involved in phenylpropionic acid, flavonoid, isoflavonoid, flavone and flavonol biosynthesis according to the relevant network map ( Figure 5 ).…”
Section: Discussionmentioning confidence: 99%
“…In recent years, joint analysis based on multifunctional “omics” data has been demonstrated to be a powerful tool to clarify different aspects of plant developmental biology as well as environmental responses [ 14 , 15 , 16 ], such as drought stress response [ 4 ], effects of grafting different rootstocks on fruit flavor [ 1 ] and astringency-related gene mining in cucumber [ 17 ]. Furthermore, transcriptome and metabolome analysis have been widely used to identify signal pathway and mechanisms controlling pigment accumulation in plant pulp or peel.…”
Section: Introductionmentioning confidence: 99%
See 1 more Smart Citation
Chen
1
,
Zhou
2
,
Chen
3
et al. 2021
IJMS
Yellow peel will adversely affect the appearance quality of cucumber fruit, but the metabolites and the molecular mechanism of pigment accumulation in cucumber peel remain unclear. Flavonoid metabolome and transcriptome analyses were carried out on the young peel and old peel of the color mutant L19 and the near-isogenic line L14. The results showed that there were 165 differential flavonoid metabolites in the old peel between L14 and L19. The total content of representative flavonoid metabolites in the old peel of L14 was 95 times that of L19, and 35 times that of young peel of L14, respectively. This might explain the difference of pigment accumulation in yellow peel. Furthermore, transcriptome analysis showed that there were 3396 and 1115 differentially expressed genes in the yellow color difference group (Young L14 vs. Old L14 and Old L14 vs. Old L19), respectively. These differentially expressed genes were significantly enriched in the MAPK signaling pathway–plant, plant–pathogen interaction, flavonoid biosynthesis and cutin, suberine and wax biosynthesis pathways. By analyzing the correlation between differential metabolites and differentially expressed genes, six candidate genes related to the synthesis of glycitein, kaempferol and homoeriodictyol are potentially important. In addition, four key transcription factors that belong to R2R3-MYB, bHLH51 and WRKY23 might be the major drivers of transcriptional changes in the peel between L14 and L19. Then, the expression patterns of these important genes were confirmed by qRT-PCR. These results suggested that the biosynthesis pathway of homoeriodictyol was a novel way to affect the yellowing of cucumber peel. Together, the results of this study provide a research basis for the biosynthesis and regulation of flavonoids in cucumber peel and form a significant step towards identifying the molecular mechanism of cucumber peel yellowing.
“…At present, more and more genes related to flavonoid biosynthesis pathway have been identified in some plant species: PsDFR , PsANS and PhCHS in peony [ 15 , 56 ]; CitCHS in citrus [ 47 , 57 ]; MiCHS , MiCHI and MiF3H in mango [ 58 ]; SbCHS , SbCHI and SbF3H in Selaginella officinalis [ 59 ]; CHS-A , CHS-B and AcFLSs in onion [ 60 ]; AgMYB1 in celery [ 61 ]; GbFLS in ginkgo biloba [ 62 , 63 ]; SmCHS , SmCHI and SmFNS in Salvia miltiorrhiza [ 50 ]; MaCHS in mulberry [ 64 ]; CtC4H2 , CtCHS3 , CtCHI3 , CtF3H3 and CtF3H1 in safflower [ 65 ]; CsMYB6A and CsUGT72AM1 in purple leaf tea [ 66 ]; AaFLS1 in Artemisia annua [ 67 ]. In order to explore the candidate genes that affecting cucumber peel yellowing, we further analyzed six DEGs involved in phenylpropionic acid, flavonoid, isoflavonoid, flavone and flavonol biosynthesis according to the relevant network map ( Figure 5 ).…”
Section: Discussionmentioning confidence: 99%
“…In recent years, joint analysis based on multifunctional “omics” data has been demonstrated to be a powerful tool to clarify different aspects of plant developmental biology as well as environmental responses [ 14 , 15 , 16 ], such as drought stress response [ 4 ], effects of grafting different rootstocks on fruit flavor [ 1 ] and astringency-related gene mining in cucumber [ 17 ]. Furthermore, transcriptome and metabolome analysis have been widely used to identify signal pathway and mechanisms controlling pigment accumulation in plant pulp or peel.…”
Section: Introductionmentioning confidence: 99%
Chen
1
,
Zhou
2
,
Chen
3
et al. 2021
IJMS
Yellow peel will adversely affect the appearance quality of cucumber fruit, but the metabolites and the molecular mechanism of pigment accumulation in cucumber peel remain unclear. Flavonoid metabolome and transcriptome analyses were carried out on the young peel and old peel of the color mutant L19 and the near-isogenic line L14. The results showed that there were 165 differential flavonoid metabolites in the old peel between L14 and L19. The total content of representative flavonoid metabolites in the old peel of L14 was 95 times that of L19, and 35 times that of young peel of L14, respectively. This might explain the difference of pigment accumulation in yellow peel. Furthermore, transcriptome analysis showed that there were 3396 and 1115 differentially expressed genes in the yellow color difference group (Young L14 vs. Old L14 and Old L14 vs. Old L19), respectively. These differentially expressed genes were significantly enriched in the MAPK signaling pathway–plant, plant–pathogen interaction, flavonoid biosynthesis and cutin, suberine and wax biosynthesis pathways. By analyzing the correlation between differential metabolites and differentially expressed genes, six candidate genes related to the synthesis of glycitein, kaempferol and homoeriodictyol are potentially important. In addition, four key transcription factors that belong to R2R3-MYB, bHLH51 and WRKY23 might be the major drivers of transcriptional changes in the peel between L14 and L19. Then, the expression patterns of these important genes were confirmed by qRT-PCR. These results suggested that the biosynthesis pathway of homoeriodictyol was a novel way to affect the yellowing of cucumber peel. Together, the results of this study provide a research basis for the biosynthesis and regulation of flavonoids in cucumber peel and form a significant step towards identifying the molecular mechanism of cucumber peel yellowing.
“…So, too, must there be information at the level of the individual protein components, including reorganization of intracellular interaction networks and localization. Even the role of post-translational modifications, as in the case of the phenylpropanoid and flavonoid pathways, is just beginning to be uncovered 39,40,54,69 . Technologies to address these questions in a comprehensive manner are increasingly within reach and will help write a new understanding of the processes by which cells execute re-equilibration of their metabolic status, both as part of immediate responses and to achieve new long-term steady states.…”
Section: Resultsmentioning confidence: 99%
Hildreth
1
,
Foley
2
,
Muday
3
et al. 2020
Sci Rep
While the effects of phytohormones on plant gene expression have been well characterized, comparatively little is known about how hormones influence metabolite profiles. This study examined the effects of elevated auxin and ethylene on the metabolome of Arabidopsis roots using a highresolution 24 h time course, conducted in parallel to time-matched transcriptomic analyses. Mass spectrometry using orthogonal UPLC separation strategies (reversed phase and HILIC) in both positive and negative ionization modes was used to maximize identification of metabolites with altered levels. The findings show that the root metabolome responds rapidly to hormone stimulus and that compounds belonging to the same class of metabolites exhibit similar changes. The responses were dominated by changes in phenylpropanoid, glucosinolate, and fatty acid metabolism, although the nature and timing of the response was unique for each hormone. These alterations in the metabolome were not directly predicted by the corresponding transcriptome data, suggesting that post-transcriptional events such as changes in enzyme activity and/or transport processes drove the observed changes in the metabolome. These findings underscore the need to better understand the biochemical mechanisms underlying the temporal reconfiguration of plant metabolism, especially in relation to the hormone-metabolome interface and its subsequent physiological and morphological effects.are available in the supplementary materials (Table S1). Data mining for the specific metabolites rutin, IAA and ACC was performed by searching the detected masses of the features in the XCMS positive datasets for masses corresponding to [M + H] + ions and the negative XCMS datasets for masses corresponding to [M − H] − ions. Features were not observed that corresponded to either IAA or ACC, while the details regarding the assignment of rutin are included in Table S1. transcriptome data analysis. Microarray datasets for root samples generated under identical conditions 11,12 were examined for changes in the expression of genes associated with the synthesis, inactivation, or transport of hormone-responsive metabolites, identified from the KEGG database 78 or the recent literature (e.g., in the case of members of the GH, DAO, and PIN families). Results for genes exhibiting a SLR of ≥ 0.5 or ≤ −0.5 in all three biological replicates for at least one time point are presented in Tables 4 and 5, with the data for all examined genes provided in Datafile S5.
“…We suggest post-translational regulation as a possible mechanism for flavonoid accumulation because (i) a quantitative increase was detected simultaneously in a broad range of flavonoids, including colorless flavonoids by metabolic analysis in AD, implying the up-regulation of early biosynthetic gene(s) and (ii) the enrichment of genes encoding proteins involved in post-translational regulation (notably F-box proteins) among down-regulated DEGs, without the clear transcriptional up-regulation of flavonoid biosynthetic genes, was observed by transcriptome analysis. Increasing evidence for the involvement of the post-translational regulation of flavonoid biosynthetic genes, especially early flavonoid biosynthetic genes, in the determination of flavonoid content, has been reported for many crops [13][14][15]53,54]. Gu et al [54] reported that CHS, which catalyzes an early step in the flavonoid biosynthetic pathway, contained the largest number of ubiquitination sites among genes in the same pathway.…”
Section: Discussionmentioning confidence: 99%
“…Increasing evidence for the involvement of the post-translational regulation of flavonoid biosynthetic genes, especially early flavonoid biosynthetic genes, in the determination of flavonoid content, has been reported for many crops [13][14][15]53,54]. Gu et al [54] reported that CHS, which catalyzes an early step in the flavonoid biosynthetic pathway, contained the largest number of ubiquitination sites among genes in the same pathway. In addition, Zhang et al [14,15] showed that PAL, the enzyme responsible for the first step of the phenylpropanoid pathway, is a common target of four F-box proteins, thus the knock-out mutation of genes encoding these proteins results in the accumulation of a broad range of flavonoids.…”
Section: Discussionmentioning confidence: 99%
Jo
1
,
Ryu
2
,
Kim
3
et al. 2020
Genes
Anthocyanins (a subclass of flavonoids) and flavonoids are crucial determinants of flower color and substances of pharmacological efficacy, respectively, in chrysanthemum. However, metabolic and transcriptomic profiling regarding flavonoid accumulation has not been performed simultaneously, thus the understanding of mechanisms gained has been limited. We performed HPLC-DAD-ESI-MS (high-performance liquid chromatography coupled with photodiode array detection and electrospray ionization mass spectrometry) and transcriptome analyses using “ARTI-Dark Chocolate” (AD), which is a chrysanthemum mutant cultivar producing dark-purple ray florets, and the parental cultivar “Noble Wine” for metabolic characterization and elucidation of the genetic mechanism determining flavonoid content. Among 26 phenolic compounds identified, three cyanidins and eight other flavonoids were detected only in AD. The total amounts of diverse flavonoids were 8.0 to 10.3 times higher in AD. Transcriptome analysis showed that genes in the flavonoid biosynthetic pathway were not up-regulated in AD at the early flower stage, implying that the transcriptional regulation of the pathway did not cause flavonoid accumulation. However, genes encoding post-translational regulation-related proteins, especially F-box genes in the mutated gene, were enriched among down-regulated genes in AD. From the combination of metabolic and transcriptomic data, we suggest that the suppression of post-translational regulation is a possible mechanism for flavonoid accumulation in AD. These results will contribute to research on the regulation and manipulation of flavonoid biosynthesis in chrysanthemum.
