Ontology highlight
ABSTRACT:
PROVIDER: PRJNA682781 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptomics Library Data of Chitosan-coated Cavendish Banana
| PRJNA579921 | ENA
Project description:We report the first RNA sequencing data of 1.25% chitosan-coated and uncoated (control) fruit of Musa acuminata (AAA Group, Subgroup Cavendish) at unripe (day 1) and ripe (day 7) stage
2019-11-21 | GSE139457 | GEO
Project description:Fleshy fruits evolved independently multiple times during angiosperm history, including the use of ethylene for the initiation and maintenance of ripening. ENCODE data of 355 transcriptome, 66 accessible chromatin, 160 histone and 45 DNA methylation profiles from eleven fleshy fruit species revealed three types of transcriptional feedback loops controlling ripening. Eudicots peach, papaya and melon evolved their circuits using carpel senescence NAC genes, whereas tomato, apple and pear utilized floral identity MADS genes derived from recent whole-genome-duplications. The monocot banana used both, forming a unique dual-loop circuit. Genes in these circuits and their tissue-specific H3K27me3 mark could be traced back to both dry fruits and ethylene-independent fleshy fruits, suggesting that the ethylene-dependent ripening mechanisms evolved from pre-existing genetic and epigenetic pathways in the ancestral angiosperms. FruitENCODE provides a comprehensive annotation of functional elements for fleshy fruit crops and new insight into the origins of climacteric fruit ripening.
2018-07-04 | GSE116581 | GEO
Project description:The fruit physiology of banana cultivars is poorly understood. To study the ripening of plantain, a high-throughput proteomics experiment was executed and compared to the better known Cavendish. The starch content in plantain was at the onset of ripening very high and decreased to undetectable levels. Multivariate analysis of the proteins was performed correlated to the starch dynamics. The drop in sucrose synthase and the raise of acid invertase during ripening indicated a change in the balance of the sucrose fate. During ripening, sugars may no longer be available for respiration since they are stored in the vacuoles, making citrate the preferred respiratory substrate. One isoform of alfa amylase acted during the early phases of starch breakdown while another acted during the later phases when the starch branches are simpler in structure. We found significant variety specific differences in granule-bound starch synthase, alpha- and beta amylases, cell wall invertase and sucrose synthase that corroborate the difference in starch content/structure between both bananas. Differences in small heat shock proteins and in the cell wall-modifying enzyme xyloglucan endotransglucosylase/hydrolase support respectively the presumed higher carotenoid content and the firmer fruit structure of plantains.
2020-06-08 | PXD013724 | Pride
Project description:DNA methylation is a conserved epigenetic mark that influences diverse biological processes in many eukaryotes. Recently, DNA methylation was proposed to regulate fleshy fruit ripening. Fleshy fruits can be distinguished by their ripening process as climacteric fruits, such as tomatoes, or non-climacteric fruits, such as strawberries. Tomatoes undergo a global decrease in DNA methylation during ripening, due to increased expression of a DNA demethylase gene. The dynamics and biological relevance of DNA methylation during ripening of non-climacteric fruits, or other climacteric fruits, are unknown. Here, we generated and characterized single-base resolution maps of the DNA methylome in strawberry fruit, from immature to ripe stages. We observed an overall loss of DNA methylation during strawberry fruit ripening. Thus, ripening-induced DNA hypomethylation occurs not only in climacteric fruit, but also in non-climacteric fruit. However, we discovered that the mechanisms underlying DNA hypomethylation during ripening of tomato and strawberry are distinct. Unlike in tomatoes, DNA demethylase genes were not up-regulated during ripening of strawberries. Instead, genes involved in RNA-directed DNA methylation were down-regulated during strawberry ripening. Further, ripening-induced DNA hypomethylation was associated with decreased siRNA levels, consistent with reduced RdDM activity. Therefore, we propose that DNA hypomethylation during strawberry ripening is caused by diminished RdDM activity. Finally, hundreds of ripening-related genes displayed altered expression that was associated with, and thus potentially regulated by, DNA hypomethylation during ripening. Our findings provide new insight into the DNA methylation dynamics during the ripening of non-climateric fruit and reveal a novel function of RdDM in regulating an important process in plant development.
2018-11-13 | GSE113084 | GEO
Project description:Using sRNA-Seq to provide small RNA status in fruit ripening stages in sweet orange DNA methylation is an important epigenetic mark involved in many biological processes. The genome of the climacteric tomato fruit undergoes a global loss of DNA methylation due to active DNA demethylation during the ripening process. It is unclear whether the ripening of other fruits is also associated with global DNA demethylation. We characterized the single-base resolution DNA methylomes of sweet orange fruits. Compared to immature orange fruits, ripe orange fruits gained DNA methylation at over 30,000 genomic regions and lost DNA methylation at about 1,000 genomic regions, suggesting a global increase in DNA methylation during orange fruit ripening. This increase in DNA methylation was correlated with decreased expression of DNA demethylase genes. The application of a DNA methylation inhibitor interfered with ripening, indicating that the DNA hypermethylation is critical for the proper ripening of orange fruits. We found that ripening-associated DNA hypermethylation was associated with the repression of several hundred genes, such as photosynthesis genes, and with the activation of hundreds of genes including genes involved in ABA responses. Our results suggest important roles of DNA methylation in orange fruit ripening.
2018-12-28 | GSE120025 | GEO
Project description:[original title] Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes A tomato MADS-box transcription factor, LeMADS-RIN, controls fruit ripening and mutation in this gene results in non-ripening phenotype of fruit. This mutation down-regulates certain ripening related ethylene responses, however, other ethylene responses are normal. A complete understanding of this mutation and its effect on fruit transcriptome during ripening is not clear. In this study, microarray analysis has been used to investigate the influence of rin mutation on fruit transcriptome at different stages of ripening. A total of 2,398 genes were found to be differentially expressed in wild type fruit pericarp, which on cluster analysis indicated a major shift in their expression profiles in rin mutant fruit. A total of 1,802 genes were found to be differentially expressed between wild type and rin mutant fruits and 17% of these genes encoded regulatory elements, suggesting that mutation in LeMADS-RIN results in disturbance in the regulatory transcriptional networks during ripening. Since LeMADS-RIN has been reported to bind to the CArG box of LeACS2 promoter, in-silico analysis of 51 putative promoter sequences of the genes, that showed ripening associated up-regulation in wild type but showed impairment in up-regulation in rin mutant fruit during ripening, were searched for presence of CArG box along with ethylene and auxin responsive elements. The study revealed that only 24 putative promoter sequences harbor LeMADS-RIN specific CArG box suggesting an alternative mode of regulation by LeMADS-RIN for CArG box deficient genes. Three chronological stages of tomato (Solanum lycopersicon) fruit ripening were compared between wild type and rin mutant
2012-02-29 | E-GEOD-20720 | biostudies-arrayexpress