Plant metagenome
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR125859.fastq.gz | Fastqsanger.gz | |||
| DRR125860.fastq.gz | Fastqsanger.gz | |||
| DRR125861.fastq.gz | Fastqsanger.gz | |||
| DRR125862.fastq.gz | Fastqsanger.gz | |||
| DRR125863.fastq.gz | Fastqsanger.gz |
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Project description:Small RNA sequencing was performed in woodland strawberry fruits for study of chromatin structure.
2024-09-25 | GSE208609 | GEO
Project description:Histone modifications mediate between genes and environment in plant growth and developmental events. To characterize the histone modification signatures in strawberry, we performed ChIP-seq experiments for seven histone marks in the immature and mature fruits, and leaves of the woodland strawberry F. vesca ('Ruegen'). The seven histone marks include H3K9/K14ac, H3K27ac, H3K4me1, H3K4me3, H3K36me3, H3K27me3 and H3K9me2. In addition, to reveal the effect of the histone deacetylase FvHDA6, H3K9/K14a was profiled in FvHDA6-OE fruits.
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Project description:To identify miRNAs involved in senescence of strawberry fruit, two independent small RNA libraries and one degradome library from strawberry fruits stored at 20 M-BM-0C for 0 and 24 h were constructed. A total of 18,759,735 and 20,293,492 mappable small RNA sequences were generated in the two small RNA libraries, respectively, and 88 known and 1224 new candidate miRNAs were obtained. Among them, 94 miRNAs were up-regulated and 64 were down-regulated in the senescence of strawberry fruit. Through degradome sequencing, 103 targets cleaved by 19 known miRNAs families and 55 new candidate miRNAs were identified. 14 targets, including NAC transcription factor, Auxin response factors (ARF) and Myb transcription factors, cleaved by 6 known miRNA families and 6 predicted candidates, were found to be involved in regulating fruit senescence. sample 1: Examination of small RNA in strawberry fruits stored at 20 M-BM-0C for 0; sample 2: Examination of small RNA in strawberry fruits stored at 20 M-BM-0C for 24 h
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Project description:For exploring the influence of the m6A methyltransferase gene MTA silencing in the global m6A mRNA methylomes of strawberry fruits, we performed m6A-seq in the MTA RNAi strawberry fruits (RNAi-MTA) and the controls with three independently biological replicates. Results showed that MTA silencing induces the m6A hypomethylation of thousands of transcripts, including those of ripening and ABA pathway genes.
2021-05-20 | GSE174703 | GEO
Project description:Many Trichoderma spp. are successful plant beneficial microbial inoculants due to their ability to act as biocontrol agents with direct antagonistic activities to phytopathogens, and as biostimulants capable of promoting plant growth. This work investigates the effects of treatments with three selected Trichoderma (strains T22, TH1 and GV41) to strawberry plants on the productivity and proteome of the formed fruit. Proteomic analysis of fruits,harvested from the plants previously treated with Trichoderma and control plants was performed by using a TMT-based protein quantification strategy. Bioinformatic analysis of the differential proteins accumulation in fruits, harvested from the treated plants, revealed a central network of interacting molecular species, that demonstrated the modulation of different plant physiological processes following the microbial inoculation.
2020-06-09 | PXD016951 | 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.
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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.
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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:Red and white strawberry fruits, were dipped for 1 min in the C.acutatum conidial suspension or in distilled water as control.
2010-12-31 | E-MEXP-2274 | biostudies-arrayexpress
Project description:In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a non-climacteric fruit, is still limited. NAC transcription factors mediate different developmental processes in plants. Here, we identified and characterized FaRIF (Ripening Inducing Factor), a NAC transcription factor that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid (ABA) biosynthesis and signaling, cell wall degradation and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.
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