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ABSTRACT:
PROVIDER: PRJNA826346 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pyrus sinkiangensis cultivar:Yu Raw sequence reads
| PRJNA303067 | ENA
Project description:Korla fragrant pear (Pyrus sinkiangensis Yu) Transcriptome
| PRJNA869204 | ENA
Project description:‘Kuerlexiangli’ (Pyrus sinkiangensis Yu) is an important market pear in China. The shape and quality of the fruit is negatively affected by the presence of a persistent calyx. Here, to explore the molecular mechanism of calyx abscission, we designed an experiment to compare protein expression at two critical stages of the calyx abscission process under three treatments: a calyx abscising treatment (6000 × Flusilazole + 300 × PBO), a calyx persisting treatment (50 mg L−1 GA3), and a water control. We investigated the collected protein fragments using isobaric tags for relative and absolute protein quantitation (iTRAQ) to identify candidate proteins and perform relative quantification. We identified 378,078 spectra and 3,873 proteins, of which there were 2,371 differentially abundant proteins (DAPs) having Gene Ontology terms and associating with 124 defined pathways from the Kyoto Encyclopedia of Genes and Genomes. The DAPs that were correlated with calyx abscission were mainly those known to be involved in photosynthesis, plant hormone signal transduction, cell-wall modification, and carbohydrate metabolism. Quantitative real-time PCR was used to confirm the results of the digital transcript abundance measurements. Among the isolated candidate proteins, polygalacturonase and chitinase appear to play key roles during the process of calyx abscission. We identified candidate proteins that exhibit highly dynamic expression changes during the calyx abscission progress. These proteins are potential targets for future functional identification and should be valuable to explore the mechanism of the calyx abscission, and finally for the development of a method for inducing calyx abscission in fruit production based on the use of small molecules.
2020-06-17 | PXD012499 | Pride
Project description:To investigate the functions of TRANSPARENT TESTA 19 (TT19) on anthocyanin accumulation and stabilization using forward genetic screening approach. EMS mutagenized tt19 mutant to screen tt19 mutant suppressors that could restore the anthocyanin accumulation and the causative mutations were identified as point mutations in the RDR6/SGS3/DCL4 siRNA biogenesis pathway using whole genome re-sequencing. The idea for RNA-Seq and small RNA-Seq analysis is to illustrate the connection between siRNA biogenesis, TT19, and anthocyanin restoration. RNA's of 4 Arabidopsis lines (col-0, tt19 and two TT19 suppressors, all in triplicate) which were under AIC (3% sucrose shaking four days under 24h light) for four days was extracted. Small RNA libraries were prepared by BGI company and sequenced using BGISEQ-500 as 50SE.
2020-04-20 | GSE136901 | 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
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:Sugarcane established industrial crop providing sugar, ethanol and biomass-derived electricity around the world. Cane sugar content is an important, breeding target, but its improvement remains very slow in many breeding programmes. Biotechnology strategies to improve sucrose accumulation made little progress at crop level, mainly due to the limited understanding of its regulation. MiRNAs regulate many metabolic processes in plants. However, their roles and target genes associated with sugarcane sucrose accumulation remains unknown. Here, we conducted high-throughput sequencing of transcriptome, small RNAs and degradome of leaves and stem of two sugarcane genotypes with contrasting sucrose content from the early to late stages of sucrose accumulation stages, which provided more insights into miRNA-associated gene regulation during sucrose accumulation. Transcriptome analysis identified 18,722 differentially expressed genes (DEGs) between both genotypes during sucrose accumulation. The major DEGs identified were involved in starch and sucrose metabolism, and photosynthesis etc. miRNA sequencing identified 563 known and 281 novel miRNAs from both genotypes during sucrose accumulation. Of these, 311 miRNAs were differentially expressed.752 targets of 368 miRNAs (609 targets for 260 known miRNAs and 168 targets for 108 novel miRNAs) were identified by degradom sequencing.Several known and novel miRNAs and their target genes associated with sugar metabolism, sugar transport and sucrose storage were identified in this study.This new insight into the complex network of sucrose accumulation in sugarcane will help identify candidate targets for sucrose improvement in sugarcane through molecular means.
2021-12-30 | GSE188303 | GEO