Transcriptome Analysis of Differential Genes Related to Anthocyanin Synthesis in Red and Green Walnut
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ABSTRACT:
PROVIDER: PRJNA680307 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13114300_1.fastq.gz | Fastqsanger.gz | |||
| SRR13114300_2.fastq.gz | Fastqsanger.gz | |||
| SRR13114301_1.fastq.gz | Fastqsanger.gz | |||
| SRR13114301_2.fastq.gz | Fastqsanger.gz | |||
| SRR13114302_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the application of high-throughput analysis of genes related to anthocyanin synthesis in red and green walnuts based on transcriptome sequencing technology. By obtaining a sequence of more than 3 billion bases from mRNA, we found genes that are differentially expressed with anthocyanin synthesis in 4 leaf growth stages and 3 peel growth stages of red and green walnuts.
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Project description:The role of photosynthesis in fruits still challenges scientists. This is especially true in the case of mature grape berries of red varieties lined by an anthocyanin-enriched exocarp (skin) almost impermeable to gases. Although chlorophylls are degraded and replaced by carotenoids in several fruits, available evidence suggests that they may persist in red grapes at maturity. In the present study, chloroplasts were isolated from the skin of red grape berries (cv. Vinhão) to measure chlorophyll levels and the organelle proteome. The results showed that chloroplasts (and chlorophylls) are maintained in ripe berries masked by anthocyanin accumulation and that the proteome of chloroplasts from green and mature berries is distinct. Several proteins of the light reactions significantly accumulated in chloroplasts at the mature stage, including those of light-harvesting complexes of photosystems I (PSI) and II (PSII), redox chain, and ATP synthase, while chloroplasts at the green stage accumulated more proteins involved in the Calvin cycle and the biosynthesis of amino acids, including precursors of secondary metabolism. Taken together, results suggest that although chloroplasts are more involved in biosynthetic reactions in green berries, at the mature stage, they may provide ATP for energy-demanding processes such as anthocyanin biosynthesis or even O2 to feed the respiratory demand of inner tissues.
2022-10-25 | PXD037346 | Pride
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:The anthocyanin glycosides in potato tubers not only provide the plant with bright color and high nutritional value, but also have pharmacological effects such as antioxidant, hypotensive, lipid-lowering and immunity-boosting. However, the regulatory mechanism of anthocyanin in potato tubers is still unclear. In this study, the content of anthocyanin was measured in four potato varieties (B, R, Y and W) and genes regulating anthocyanin synthesis in different potato varieties were identified by comparing transcriptomic approaches. The results showed that 82.6G of filtered data were obtained in 12 sequencing libraries, of which 82.23-87.66% of clean fragments were covered to the reference genome. In total, 42,793 genes were found in the twelve libraries of which 3765 were new genes. Finally, 3638 (B), 4295 (R) and 3594 (Y) DEGs were obtained in the three groups by the strict threshold screening (FDR<0.05 and |log2FC|>1), respectively. GO analysis showed that DEGs were mainly enriched in entries such as cell (GO:0005623), metabolic process (GO:0008152), catalytic activity (GO:0003824), etc. KEGG analysis revealed that metabolic pathways (ko01100), phenylalanine metabolism (ko00360), photosynthesis (ko00195) were significantly enriched. In addition, some genes related to anthocyanin synthesis (e.g. CHS, bHLH and MYB) were highly induced or repressed in different varieties. In conclusion, the results of this study provide insight into the genes regulating anthocyanin formation in potato and provide a scientific reference for breeding better quality potato varieties.
2021-11-20 | GSE189082 | GEO
Project description:Fruit color is an important economic trait. The color of red walnut cultivars is mainly attributed to anthocyanins. The aim of this study was to explore the differences in the molecular mechanism of leaf and peel color change between red and green walnut. A reference transcriptome of walnut was sequenced and annotated to identify genes related to fruit color at the ripening stage. More than 290 million high-quality reads were assembled into 39,411 genes using a combined assembly strategy. Using Illumina digital gene expression profiling, we identified 4568 differentially expressed genes (DEGs) between red and green walnut leaf and 3038 DEGs between red and green walnut peel at the ripening stage. We also identified some transcription factor families (MYB, bHLH, and WD40) involved in the control of anthocyanin biosynthesis. The trends in the expression levels of several genes encoding anthocyanin biosynthetic enzymes and transcription factors in the leaf and peel of red and green walnut were verified by quantitative real-time PCR. Together, our results identified the genes involved in anthocyanin accumulation in red walnut. These data provide a valuable resource for understanding the coloration of red walnut.
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Project description:Anthocyanins are flavonoid compounds responsible for red/purple colours in the leaves, fruit and flowers of many plant species. They are produced through a multistep pathway which is controlled by MYB transcription factors. VvMYBA1 and VvMYBA2 activate anthocyanin biosynthesis in grapevine (Vitis vinifera) and are non-functional in white grapevine cultivars. In this study, transgenic grapevines with altered VvMYBA gene expression were developed, and transcript analysis was carried out on berries using a microarray technique. The results showed that VvMYBA is a positive regulator of the later stages of anthocyanin synthesis, modification and transport in Shiraz. One up-regulated gene ANTHOCYANIN 3- O-GLUCOSIDE-6”-O-ACYLTRANSFERASE (Vv3AT) encodes a BAHD acyltransferase protein, belonging to a clade separate from most anthocyanin acyltransferases. Functional studies (in planta and in vitro) show that Vv3AT has a broad anthocyanin substrate specificity and can also utilise both aliphatic and aromatic acyl donors, a novel activity for this enzyme family found in nature. In V. vinifera cv. Pinot Noir, a red-berried grapevine mutant lacking acylated anthocyanins, Vv3AT contains a nonsense mutation encoding a truncated protein that lacks two motifs required for BAHD protein activity. Promoter activation assays confirm that Vv3AT transcription is activated by VvMYBA1, which adds to the current understanding of the regulation of the BAHD gene family. The flexibility of Vv3AT to use both classes of acyl donors will be useful in the engineering of anthocyanins in planta or in vitro.
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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.
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