Ontology highlight
ABSTRACT:
PROVIDER: PRJNA477414 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7410690_1.fastq.gz | Fastqsanger.gz | |||
| SRR7410690_2.fastq.gz | Fastqsanger.gz | |||
| SRR7410682_1.fastq.gz | Fastqsanger.gz | |||
| SRR7410682_2.fastq.gz | Fastqsanger.gz | |||
| SRR7410683_1.fastq.gz | Fastqsanger.gz |
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Project description:MicroRNAs play critical roles in various biological and metabolic processes. The function of miRNAs has been widely studied in model plants such as Arabidopsis and rice. However, the number of identified miRNAs and related miRNA targets in peach (Prunus persica) is limited. To understand further the relationship between miRNAs and their target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three tissues for deep sequencing. We identified 117 conserved miRNAs and 186 novel miRNA candidates in peach by deep sequencing and 19 conserved miRNAs and 13 novel miRNAs were further evaluated for their expression by RT-qPCR. The number of gene targets that were identified for 26 conserved miRNA families and 38 novel miRNA candidates, were 172 and 87, respectively. Some of the identified miRNA targets were abundantly represented as conserved miRNA targets in plant. However, some of them were first identified and showed important roles in peach development. Our study provides information concerning the regulatory network of miRNAs in peach and advances our understanding of miRNA functions during tissue development.
2014-01-01 | GSE49579 | GEO
Project description:We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development.
2012-07-03 | GSE38535 | GEO
Project description:MicroRNAs play critical roles in various biological and metabolic processes. The function of miRNAs has been widely studied in model plants such as Arabidopsis and rice. However, the number of identified miRNAs and related miRNA targets in peach (Prunus persica) is limited. To understand further the relationship between miRNAs and their target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three tissues for deep sequencing. We identified 117 conserved miRNAs and 186 novel miRNA candidates in peach by deep sequencing and 19 conserved miRNAs and 13 novel miRNAs were further evaluated for their expression by RT-qPCR. The number of gene targets that were identified for 26 conserved miRNA families and 38 novel miRNA candidates, were 172 and 87, respectively. Some of the identified miRNA targets were abundantly represented as conserved miRNA targets in plant. However, some of them were first identified and showed important roles in peach development. Our study provides information concerning the regulatory network of miRNAs in peach and advances our understanding of miRNA functions during tissue development. To identify more conserved and peach-speciM-oM-,M-^Ac miRNAs and their target genes and to understand further the mechanism of miRNA-regulated target genes during tissue development in peach, a small RNA library and three degradome libraries were constructed from three different tissues for deep sequencing.
2014-01-01 | E-GEOD-49579 | biostudies-arrayexpress
Project description:We performed small RNA deep sequencing and identified 47 peach-specific and 47 known miRNAs or families with distinct expression patterns. Together, the identified miRNAs targeted 80 genes, many of which have not been reported previously. Like the model plant systems, peach has two of the three conserved trans-acting siRNA biogenesis pathways with similar mechanistic features and target specificity. Unique to peach, three of the miRNAs collectively target 49 MYBs, 19 of which are known to regulate phenylpropanoid metabolism, a key pathway associated with stone hardening and fruit color development, highlighting a critical role of miRNAs in regulation of peach fruit development and ripening. We also found that the majority of the miRNAs were differentially regulated in different tissues, in part due to differential processing of miRNA precursors. Up to 16% of the peach-specific miRNAs were differentially processed from their precursors in a tissue specific fashion, which has been rarely observed in plant cells. The miRNA precursor processing activity appeared not to be coupled with its transcriptional activity but rather acted independently in peach. Collectively, the data characterizes the unique expression pattern and processing regulation of peach miRNAs and demonstrates the presence of a complex, multi-level miRNA regulatory network capable of targeting a wide variety of biological functions, including phenylpropanoid pathways which play a multifaceted spatial-temporal role in peach fruit development. Identification of peach miRNAs and their targets from four different tissues
2012-07-02 | E-GEOD-38535 | biostudies-arrayexpress
Project description:Plum pox virus (PPV) causes the serious sharka disease in Prunus trees. Peach [P. persica (L.) Batsch] trees are severely affected by PPV and no definitive source of genetic resistance has been identified at this moment. Previous results showed, however, that PPV-resistant ‘Garrigues’ almond [P. dulcis (Mill.) D.A. Webb] was able to transfer its resistance to ‘GF305’ peach through grafting, preventing these trees from PPV infection and reducing symptomatology and viral load in PPV-infected plants. A recent study tried to identify genes responsible for this effect by studying mRNA expression through RNAseq data in peach and almond plants, before and after grafting, and before and after PPV infection. In this work, we used the same peach and almond samples, but focused the high-throughput analyses on small RNAs (sRNAs) expression. We studied massive sequencing data and found an interesting pattern of sRNAs overexpression linked to antiviral defense genes that suggested activation of these genes followed by downregulation to basal levels. We also discovered that ‘Garrigues’ almond plants were infected by different plant viruses that were transferred to peach plants. The large amounts of viral sRNAs found in grafted peaches indicated a strong RNA silencing antiviral response and led us to postulate that these plant viruses could be collaborating by cross-protection in the observed ‘Garrigues’ effect.
2022-11-02 | GSE188935 | GEO
Project description:Using whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in peach fruits (Prunus persica) in six different stages.
2025-12-11 | GSE165094 | GEO
Project description:Purpose: This study was to explore the underlying molecular mechanism of temperature effects on fruit quality during shelf life. The transcriptome data of peach fruits stored in high temperature (HT, 35 °C) and common temperature (CT, 25 °C) conditions were measured and compared. Methods: Red flesh peach (Prunus persica L. Batsch cv. Tianxianhong) fruits with consistent color, shape and weight were selected and kept at 5 °C for 2 days after the day of harvest. Then, these fruits were randomly divided into two groups. One group was stored at CT for 7 days, and the other was stored at HT for 7 days. During storage, fruits were sampled at day 1, 2 and 3 as early stage as well as day 5, 6 and 7 as later stage. Total RNA of each sample was extracted and used to construct 24 RNA libraries. RNA sequencing was performed on an Illumina HiSeq 2500 platform. The differences in transcriptome, ethylene production, pulp softening of postharvest peach fruits were compared between CT and HT storage conditions Results: Our results showed that HT conditioning after 5 °C is better than CT to maintaining fruit quality during shelf life due to MEKK1-MKK2-MPK4/6 signal transduction and low level of ethylene and auxin biosynthesis enzymes which may affect genes related to softening and membrane stability through ethylene response factors (ERFs) and auxin response factors (ARFs).
2020-06-27 | GSE122868 | GEO