Transcriptome and metabolome analysis reveals anthocyanin biosynthesis pathway associated with poplar (Populus deltoids) leaf color formation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA895328 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22077219_1.fastq.gz | Fastqsanger.gz | |||
| SRR22077219_2.fastq.gz | Fastqsanger.gz | |||
| SRR22077220_1.fastq.gz | Fastqsanger.gz | |||
| SRR22077220_2.fastq.gz | Fastqsanger.gz | |||
| SRR22077221_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:Colored-leaf plants are increasingly popular and have been attracting more and more attentions. However, studies about the anthocyanin components and molecular mechanisms of anthocyanin biosynthesis in QHP and ZSY was still unclear. In present study, an integrated metabolite and transcriptome profiling analysis was performed to explore the anthocyanin compositions and the specific regulatory network of anthocyanin biosynthesis in purple leaves of QHP and ZSY. A total of 39 anthocyanin compounds were detected based on the LC-MS/MS analysis. Of these, 12 cyanidins, 7 pelargonidins, 5 delphindins, and 5 procyanidins are the major anthocyanin compounds, which were significantly differentially accumulated in purple leaves of QHP and ZSY. The major genes associated with anthocyanin biosynthesis, including structural genes and TFs, were differentially expressed in the purple leaves of QHP and ZSY through RNA-seq data analysis, some of which were further assessed by qRT-PCR. Correlation between RNA-seq analysis and metabolite profiling showed that the expression pattern of some differentially expressed genes in anthocyanin biosynthes pathway were closely correlated with the differential accumulation of anthocyanins. In addition, one member of SG5 subgroup of R2R3-MYB TFs, Podel.04G021100, shows a similar expression pattern to some structure genes and closely correlates with sixteen anthocyanin compounds, indicating that the MBY TF (Podel.04G021100) may be involved in the regulation of anthocyanin biosynthesis. The above results not only make us systematic and comprehensive understand the anthocyanin components and corresponding molecular mechanisms of anthocyanin biosynthesis in purple leaves of QHP and ZSY, but also contribute to the promotion and application of anthocyanins in colored-leaf poplars.
2022-10-31 | GSE216754 | GEO
Project description:The grape color locus 2 affects anthocyanin pigmentation of vegetative organs.
2017-03-11 | GSE88765 | GEO
Project description:Purpose: The present study aimed to investigate the anthocyanin components and identify relevant regulatory genes in purple wheat grain by carrying out transcriptome analyses. Methods: The seeds of purple grain wheat and white grain wheat were collected 30 days after flowering, and three biological replicates were set. Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000. Then synthesizing the fragmented RNA into cDNA through the action of reverse transcriptase, and finally obtaining acDNA library. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol. Results: A total of 10440 diferentially expressed genes were signifcantly enriched by RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed signifcantly enriched flavonoid biosynthesis and anthocyanin biosynthesis in CW_S versus W_S. And the ANS and UFGT genes were predicted as core genes in anthocyanin biosynthesis. Conclusions: Our study represents the detailed analysis of wheat grain transcriptomes, with biologic replicates, generated by RNA-seq technology. Through this study, we speculated that ANS and UFGT genes are the core genes of anthocyanin biosynthesis.The significant differences of these genes affect the synthesis of anthocyanins in wheat grains, and thus affect the grain color of wheat.
2023-04-24 | GSE198515 | GEO
Project description:MicroRNA172 (miR172) plays a role in regulating a diverse range of plant developmental processes. However, its role in regulating anthocyanin biosynthesis is unclear. In this study, we show that transgenic apple plants over-expressing miR172 show a reduction in red colouration and anthocyanin accumulation in multiple tissue types. This reduction was consistent with decreased expression of APETALA2 homolog MdAP2_1a (a miR172 target gene), MdMYB10, and targets of MdMYB10, as demonstrated by both RNA-seq and RT-PCR analyses. During the onset of anthocyanin biosynthesis in apple fruit skin, miR172 transcript abundance was negatively correlated and MdAP2_1a mRNA concentration was positively correlated with fruit skin red-colouration. The positive role of MdAP2_1a in regulating anthocyanin biosynthesis was supported by the enhanced petal anthocyanin accumulation in transgenic tobacco plants overexpressing MdAP2_1a, and by the reduction in anthocyanin accumulation in apple and cherry fruits transfected with an MdAP2_1a virus-induced-gene-silencing construct. We demonstrated that MdAP2_1a could bind directly to the promoter and protein sequences of MdMYB10 in yeast and tobacco, and enhance MdMYB10 promotor activity. In Arabidopsis, over-expression of miR172 reduced anthocyanin concentration and RNA transcript abundance of anthocyanin genes in plantlets cultured on medium containing 7% sucrose. The anthocyanin content and RNA abundance of anthocyanin genes could be partially restored by using a synonymous mutant of MdAP2_1a, which had lost the miR172 target sequences at mRNA level, but not restored by using a WT MdAP2_1a. These results indicate that miR172 inhibits anthocyanin biosynthesis through suppressing the expression of an AP2 transcription factor that positively regulates MdMYB10.
2022-12-24 | GSE173297 | GEO
Project description:Over recent decades the progression of natural autumnal senescence has been increasingly delayed across wide areas of the Northern Hemisphere and is thought to be caused by rising temperature. Recently this delay has been shown to be partly attributable to rising atmospheric carbon dioxide concentrations [CO2]. Here, for the first time, we present a possible mechanistic explanation for this phenomenon. Using a plantation of Populus x euramericana grown at elevated [CO2] (e[CO2]) using Free-Air CO2 Enrichment (FACE) technology, we investigated the molecular and biochemical basis underlying this response. Using a poplar cDNA microarray where late growing season and senescing leaves from ambient [CO2] (a[CO2]) and e[CO2] were compared, revealed unique increases and decreases in transcript abundance in the e[CO2] treatment. Growth at e[CO2]caused the greatest increase in the abundance of transcripts catalysing steps in the anthocyanin biosynthetic pathway and an increase in leaf anthocyanin content. Leaf sucrose and starch content were also increased during senescence in e[CO2] and associated with a higher abundance of transcripts in the sucrose and starch biosynthetic pathways. We propose that in e[CO2], autumnal photosynthesis and sugar accumulation results in changes in genes expression that include further investment in secondary carbon metabolism leading to anthocyanin production. This enables prolonged leaf longevity during natural autumnal senescence through increased availability of carbon and improved stress tolerance while in contrast this may also have a negative effect on the control of dormancy.
2010-02-01 | GSE15874 | GEO
Project description:Populus alba × Populus glandulosa (84K poplar) is model material with excellent genetic engineering resource and ornamental value. In our study, AmRosea1 (Antirrhinum majus) was overexpressed in 84K poplar, and the transgenic 84K (AM) poplar with high content of anthocyanin exhibited red pigmentation leaves. The transcriptome analysis between wild type (WT) and AM showed that 170 differentially expressed genes (DEGs) (86 up-regulated and 84 down-regulated) were found, and some DEGs were involved in flavone and flavonol biosynthesis, flavonoid biosynthesis and anthocyanin biosynthesis. The metabolome analysis showed that 13 anthocyanins-related differentially accumulated metabolites (DAMs) were detected in AM. The correlation analysis between DEGs and DAMs were performed, and the results revealed that 18 DEGs, including 11 MYB genes, two BZ1 genes, one FG2 gene, one ANS gene, and three IF7MAT genes, were negatively or positively correlated with 13 DAMs. The phylogenetic analysis demonstrated that there was high homology between AmRosea1 and PagMYB113, and MYB113 co-expressed with BZ1, ANS and DFR directly. Our results elucidated the molecular mechanism of plant color change mediated by anthocyanin biosynthesis pathway, which laid the foundation for the development and utilization of colorful woody plant.
| S-EPMC9207281 | biostudies-literature
Project description:Taproots of different carrot genotypes were used to identify the candidate genes related to anthocyanin synthesis with particular focus on R2R3MYB, bHLH transcription factors, and glutathione S-transferase gene (GST). The RNA-sequencing analysis (RNA-Seq) showed that DcMYB6 and DcMYB7 had genotypic dependent expressed and they are likely involved in the regulation of anthocyanin biosynthesis. They were specifically upregulated in solid black taproots, including both black phloem and xylem. DcbHLH3 (LOC108204485) was upregulated in all black samples compared with the orange ones. We also found that GST1 (LOC108205254) might be an important anthocyanin transporter, and its upregulated expression resulted in the increasing of vacuolar anthocyanin accumulation in black samples.
2020-03-06 | GSE146419 | GEO
Project description:IntroductionColored-leaf plants are increasingly popular for their aesthetic, ecological, and social value, which are important materials for research on the regulation of plant pigments. However, anthocyanin components and the molecular mechanisms of anthocyanin biosynthesis in colored-leaf poplar remain unclear. Consequently, an integrative analysis of transcriptome and metabolome is performed to identify the key metabolic pathways and key genes, which could contribute to the molecular mechanism of anthocyanin biosynthesis in the colored-leaf cultivars poplar.MethodsIn this study, integrated metabolite and transcriptome analysis was performed to explore the anthocyanin composition and the specific regulatory network of anthocyanin biosynthesis in the purple leaves of the cultivars 'Quanhong' (QHP) and 'Zhongshanyuan' (ZSY). Correlation analysis between RNA-seq data and metabolite profiles were also performed to explore the candidate genes associated with anthocyanin biosynthesis. R2R3-MYB and bHLH TFs with differential expression levels were used to perform a correlation analysis with differentially accumulated anthocyanins.Results and discussionA total of 39 anthocyanin compounds were detected by LC-MS/MS analysis. Twelve cyanidins, seven pelargonidins, five delphinidins, and five procyanidins were identified as the major anthocyanin compounds, which were differentially accumulated in purple leaves of QHP and ZSY. The major genes associated with anthocyanin biosynthesis, including structural genes and transcription factors, were differentially expressed in purple leaves of QHP and ZSY through RNA-sequencing (RNA-seq) data analysis, which was consistent with quantitative real-time PCR analysis results. Correlation analysis between RNA-seq data and metabolite profiles showed that the expression patterns of certain differentially expressed genes in the anthocyanin biosynthesis pathway were strongly correlated with the differential accumulation of anthocyanins. One R2R3-MYB subfamily member in the SG5 subgroup, Podel.04G021100, showed a similar expression pattern to some structural genes. This gene was strongly correlated with 16 anthocyanin compounds, indicating that Podel.04G021100 might be involved in the regulation of anthocyanin biosynthesis. These results contribute to a systematic and comprehensive understanding of anthocyanin accumulation and to the molecular mechanisms of anthocyanin biosynthesis in QHP and ZSY.
| S-EPMC9998943 | biostudies-literature
Project description:Environmental factors play an important role in anthocyanin biosynthesis, and potassium, an essential nutrient for blueberry growth, can act as an enzyme activator. However, few reports exist on the transcriptional and anthocyanin metabolic changes in blueberries regulated by potassium. In this study, blueberries treated with potassium at different stages were compared for changes in enzyme activity, transcription, and metabolism related to anthocyanin synthesis. The results showed that potassium treatment significantly enhanced the activities of key enzymes F3H, F3'5'H, and UFGT in the anthocyanin synthesis pathway of blueberry fruit. Metabolomic results indicated that the contents of malvidin, petunidin, and delphinidin were higher with potassium fertilization, and potassium treatment promoted the early color change of blueberry fruit. The transcriptome analysis identified 102 glucose metabolism-related genes and 12 differential potassium transport genes potentially involved in potassium-regulated anthocyanin synthesis and accumulation. It was found that thirteen genes relate to anthocyanin synthesis. UFGT, F3H, CHI, HCT, C12RT1, DFR, and F3'5'H were all closely associated with potassium-controlled flavonoid and anthocyanin metabolite synthesis. It provides valuable insights into the molecular mechanisms that regulate the synthesis of anthocyanins in blueberries.
2025-03-05 | GSE277541 | GEO
Project description:Background: Pear is one of the most important fruit crops worldwide. Anthocyanins and procyanidins (PAs) are important secondary metabolites that affect the appearance and nutritive quality of pear. However, few studies have focused on the molecular mechanism underlying anthocyanin and PA accumulation in pear. Results: We conducted metabolome and transcriptome analyses to identify candidate genes involved in anthocyanin and PA accumulation in young fruits of the pear cultivar ‘Clapp Favorite’ (CF) and its red mutation cultivar ‘Red Clapp Favorite’ (RCF). Gene–metabolite correlation analyses revealed a ‘core set’ of 20 genes that were strongly correlated with 10 anthocyanin and seven PA metabolites. Of these, PcGSTF12 was confirmed to be involved in anthocyanin and PA accumulation by complementation of the tt19-7 Arabidopsis mutant. Interestingly, PcGSTF12 was found to be responsible for the accumulation of procyanidin A3, but not petunidin 3, 5-diglucoside, opposite to the function of AtGSTs in Arabidopsis. Transformation with PcGSTF12 greatly promoted or repressed genes involved in anthocyanin and PA biosynthesis, regulation, and transport. Electrophoretic mobility shift and luciferase reporter assays confirmed positive regulation of PcGSTF12 by PcMYB114. Conclusion: These findings identify a core set of genes for anthocyanin and PA accumulation in pear. Of these, PcGSTF12 was confirmed to be involved in anthocyanin and PA accumulation. Our results also identified an important anthocyanin and PA regulation node comprising two core genes, PcGSTF12 and PcMYB114. These results provide novel insights into anthocyanin and PA accumulation in pear and represent a valuable data set to guide future functional studies and pear breeding.
2020-03-12 | GSE146798 | GEO