Ontology highlight
ABSTRACT:
PROVIDER: PRJNA533973 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8936180_1.fastq.gz | Fastqsanger.gz | |||
| SRR8936180_2.fastq.gz | Fastqsanger.gz | |||
| SRR8936172_1.fastq.gz | Fastqsanger.gz | |||
| SRR8936172_2.fastq.gz | Fastqsanger.gz | |||
| SRR8936173_1.fastq.gz | Fastqsanger.gz |
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Project description:In the present study, we employed the high-throughput sequencing technology to profile miRNAs in blueberry fruits. A total of 9,992,446 small RNA tags with sizes ranged from 18 to 30 nt were obtained, indicating that blueberry fruits have a large and diverse small RNA population. Bioinformatic analysis has identified 412 conserved miRNAs, which belong to 20 families, and 57 predicted novel miRNAs likely unique to blueberries. Among them, expression profiles of 5 conserved miRNAs were validated by stem loop qRT-PCR. Furthermore, the potential target genes of the abundant conserved and novel miRNAs were predicted and subjected for Gene Ontology (GO) annotation. Enrichment analysis of the GO-represented biological processes and molecular functions revealed that these target genes were involved in a wide range of metabolic and developmental processes. This study is the first report on genome-wide miRNA profile analysis in blueberry and it provides a useful resource for further elucidation of the functional roles of miRNAs during fruit development and ripening.
2017-06-29 | GSE94411 | 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: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.
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Project description:Characterization of WGBS and RNA-seq in blueberry fruits
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Project description:Blueberry is one of the most desirable and nutritious fruits. During fruit development, the blueberry’s organoleptic properties and phytonutrient composition are ever-changing [1]. Blueberry fruit development is typically described in five phases: pads, cups, green, pink, and blue (ripe) [2]. The former two phases are referred to as the initial “expansion”. During expansion, young fruit is generally hard, dark green and distinguishable by size [3]. The latter three phases are referred to as maturation. Green fruit are hard and fully rounded green berries; pink berries are partially pigmented; blue (ripe) berries are fully colored and soft. Fruit maturation has attracted considerable research attention, and typically, the characteristics fruit softening, coloring, and sweetening are assessed [4].
2019-05-13 | PXD011815 | Pride
Project description:Strawberry is an ideal model for studying the molecular biology of the development and ripening of non-climacteric fruits. By using a custom-made and high quality oligo microarray platform done with over 32000 probes including all of the genes actually described in the strawberry genome, we have analyzed the expression of genes during the development and ripening in the receptacles of these fruits.
2019-10-18 | GSE126220 | GEO
Project description:Strawberry is an ideal model for studying the molecular biology of the development and ripening of non-climacteric fruits. By using a custom-made and high quality oligo microarray platform done with over 32000 probes including all of the genes actually described in the strawberry genome, we have analyzed the expression of genes during the development and ripening in the receptacles of these fruits.
2018-05-09 | GSE95300 | 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 tomato (Solanum lycopersicum) MADS-box transcription factor RIPENING INHIBITOR (RIN) acts as a master regulator of tomato fruit ripening. We previously identified a direct RIN target gene Solyc07g052960, which encodes a putative GRAS family protein belonging to the SHORT-ROOT (SHR) branch, but its role was unknown. RNA interference (RNAi)-mediated gene silencing reduced Solyc07g052960 expression in transgenic fruits, but the fruits appeared to ripen normally. However, the transgenic fruits at the ripening stage showed a marked decrease of the expression levels of several ripening-induced genes, especially involved in cell wall modification and secondary metabolism. This suggests that Solyc07g052960 participates in the regulation of these processes as one component of the RIN-activated transcriptional cascade regulating fruit ripening in tomato.
2014-03-01 | GSE45658 | GEO
Project description:Fruit ripening is a very important physiological process which gains relevance in crop species due to their economical and nutritional repercussions. During fruit ripening enormous metabolic changes occur in a genetically-controlled scenario affecting the physiology of most cell compartments. Peroxisomes are single-membrane bounded organelles present in all eukaryotes which display a noteworthy nitro-oxidative metabolism, and harbor catalase as one of the major antioxidant enzymes in cells. Quantitative proteomics analysis by isobaric tags for relative and absolute quantification (iTRAQ) was used to investigate the ripening process in sweet pepper (Capsicum annuum L.) fruits. Out of 2,574 quantified proteins, 692 were found to be significantly more abundant in immature green fruits compared to red ones, but 497 showed a lower expression as the ripening proceeded. Overall, about 50% of the detectable proteins were estimated to modify their expression due to the ripening process. Data obtained from the Gene Ontology algorithms (AgriGO platform) showed that from all the identified proteins, 46 (2%) were only predicted to have a peroxisomal origin, with a high number of them displaying up-expression tendency during ripening. Catalase was framed within the group which showed lower expression in ripe fruits, but this enzyme was also susceptible to undergo posttranslational modifications (PTMs) promoted by reactive nitrogen and oxygen species (RNS and ROS) through nitration, S-nitrosylation and oxidation events which provoked its inhibition. The biochemical characterization of catalase indicates that it has atypical native molecular mass (125-135 kDa), since it behaves as a homodimer, and isoelectric point of 7.4, which is higher than that of the majority of plant catalases reported so far. Taking together, these data suggest that ROS and RNS could be essential to modulate the role of catalase for the maintenance of basic cellular peroxisomal functions during pepper fruit ripening where nitro-oxidative stress occur.
2022-05-19 | PXD010457 | Pride