Prunus persica
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ABSTRACT:
PROVIDER: PRJNA291281 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptome analysis of peach cultivars with different harvest date under cold storage
| PRJNA327908 | ENA
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: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:Cold storage (CS) is widely used to extend fruit postharvest. In peach, chilling injuries may cause intense juice loss leading to a dry âwoollyâ texture of the fruit flesh. The disturbance, named woolliness, is associated to abnormal pectin metabolism and results in anatomical and physiological alterations. Application of gibberellic acid (GA) at the initial stages of pit hardening has been shown to impair woolliness incidence, however the mechanisms controlling the response remain unknown. We have employed genome wide transcription analyses to investigate the effects of GA application and CS of peaches. Approximately half (48.26%, 13846) of the investigated genes exhibited significant differential expression in response to the treatments. Gene ontology classes associated to cellular and developmental processes were overrepresented among the differentially regulated genes, whereas sequences classified in cell death and immune response categories were underrepresented. Gene set enrichment analyses demonstrated a predominant role of CS in repressing the transcription of genes associated to cell wall metabolism. In contrast, genes involved in hormone metabolism and signaling exhibited a more complex transcriptional response to the factors, indicating an extensive network of crosstalk between GA and low temperatures. Time course transcriptional profiling analyses also confirmed the involvement of cell wall metabolism genes in woolliness onset in peach. Overall, our results provide further insights on the mechanisms controlling the complex phenotypes associated to postharvest textural changes in peach. Four samples (CONT, CONTcs, GA3, GA3cs), each with three biological replicates (R1, R2 and R3), were analyzed. Control samples (CONT and CONTcs) consist of peach mesocarp not treated with GA3 at pit hardening, and either assayed at harvest (CONT) or after 15 days of cold storage (CONTcs). GA3 samples (GA3 and GA3cs) consist of peach mesocarp treated with GA3 at pit hardening, and either assayed at harvest (GA3) or after 15 days of cold storage (GA3cs).
2015-10-29 | E-GEOD-71460 | biostudies-arrayexpress
Project description:Transcriptomic analysis reveals cold responsive genes implicated in peach low temperature tolerance
| PRJNA117957 | ENA
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:Spring frost is a growing risk to temperate fruit production as warmer winter conditions can lead to earlier bloom, increasing the chance of damaging cold temperatures. One strategy to minimize the impacts of frost is to breed late-flowering cultivars to avoid the frost risk period. In this study, we analyzed Late-Flowering Peach (LFP) germplasm and showed its floral buds require longer chilling and warming periods during dormancy than the control cultivar, ‘John Boy’ (JB). We identified a 983-bp deletion in an AP2 gene, dubbed euAP2a, present only in LFP but not in 14 other peach genomes analyzed. This mutation eliminates an miR172 binding site, possibly allowing the euAP2a transcript to accumulate preferentially during chilling. These findings together with an early report that a deletion in the same euAP2a causes increasing floral petals, a morphological mark that also occurs in LFP, implies that the 983-bp deletion may contribute to the late-flowering phenotype. Furthermore, RNAseq data revealed that that two chilling- and three warm-responsive co-expression modules, which were collectively composed of 2,931 genes, were differentially activated at four of 13 dormancy stages. This activation was concurrent with a transient, stage-specific down-regulation of euAP2a. However, the mutated euAP2a in LFP did not exhibit the periodic downregulation events observed in JB and the concurrent activation of the five modules, leading to potential loss of activation of two chilling-responsive modules and an 8–12-day delay of three warm-responsive modules, which corresponds to the longer chilling requirement and delayed flowering time in the LFP buds. These findings support euAP2a as a potential regulator to control both floral development and bloom time in peach. Our findings provide important insight into the mechanisms underlying flowering time in peach, as well as a novel regulatory pathway that may operate in other plants. The results provide new insights to facilitate the breeding of new cultivars with late-flowering frost-avoidance traits.
2024-02-09 | GSE244570 | GEO
Project description:Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs
| PRJNA168085 | ENA