Prunus persica
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ABSTRACT:
PROVIDER: PRJNA291517 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:The fruit of melting-flesh peach cultivars produce high levels of ethylene caused by high expression of PpACS1, resulting in rapid fruit softening at the late-ripening stage. In contrast, the fruit of stony hard peach cultivars do not soften and produce little ethylene due to low expression of PpACS1. To elucidate the mechanism for suppressing PpACS1 expression in stony hard peaches, a microarray analysis was performed. Several genes that displayed similar expression patterns as PpACS1 were identified and shown to be IAA-inducible genes. Change in gene expression according to growth of fruits in 'melting peach M-bM-^@M-^XAkatsukiM-bM-^@M-^Y fruit sampled at 92, 98, 104 and 106 day after full bloom (DAB). Propylene induced gene expression stony peach M-bM-^@M-^XManamiM-bM-^@M-^Y and M-bM-^@M-^XOdorokiM-bM-^@M-^Y harvested at commercial maturity (Tatsuki et al., 2006).
2013-03-27 | E-GEOD-45490 | biostudies-arrayexpress
Project description:Transcriptional changes associated with woolliness during fruit ripening in Prunus persica
| PRJNA98185 | ENA
Project description:The fruit of melting-flesh peach cultivars produce high levels of ethylene caused by high expression of PpACS1, resulting in rapid fruit softening at the late-ripening stage. In contrast, the fruit of stony hard peach cultivars do not soften and produce little ethylene due to low expression of PpACS1. To elucidate the mechanism for suppressing PpACS1 expression in stony hard peaches, a microarray analysis was performed. Several genes that displayed similar expression patterns as PpACS1 were identified and shown to be IAA-inducible genes.
2013-03-27 | GSE45490 | 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:In this study we performed a comprehensive analysis of miRNAs and their targets from peach fruit tissue using high-throughput sequencing combined with bioinformatics analysis and molecular experiments. A total of 557 known miRNAs and 275 putative novel miRNAs were predicted. 3959 and 1614 target genes for the 349 known and 193 novel miRNAs, respectively, were predicted where a single target gene could be targeted by different miRNAs, and a single miRNA can also have a large number of target genes. Proteins predicted to be targeted by the miRNAs in this study encompass a wide range of transcription factors and are involved in biological processes and pathways ranging from development, metabolism, and stress responses to signal transduction. Thirty conserved miRNAs and 27 novel miRNAs exhibited differential expression profiles in three tissues of peach, with expression patterns of some miRNAs appearing to be tissue or developmental-stage specific. A total of 115 and 101 target genes were identified to be cleaved by 61 known miRNAs and 27 novel miRNAs through degradome sequencing, respectively. These miRNAs induce cleavage of their targets precisely at the position between nucleotides 10 and 11 of the miRNA sequence from 5’ to 3’ end. The findings of this study provide an important basis for the analysis of miRNAs, their targets and the functions of these targets in peach fruit.
2017-02-11 | GSE83110 | 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.
2014-01-01 | GSE49579 | GEO
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:Trees with weeping shoot architectures are valued for their beauty and are a resource for understanding how plants regulate posture control. The Prunus persica (peach) weeping phenotype, which has elliptical downward arching branches, is caused by a homozygous mutation in the WEEP gene. Until now, little was known about the function of WEEP protein despite its high conservation throughout Plantae. Here, we present the results of anatomical, biochemical, biomechanical, physiological, and molecular experiments that provide insight into WEEP function. Our data suggest that weeping peach trees do not have defects in branch structure. Rather, transcriptomes from the adaxial (upper) and abaxial (lower) sides of standard and weeping branch shoot tips revealed flipped expression patterns for genes associated with early auxin response, tissue patterning, cell elongation, and tension wood development. This suggests that WEEP promotes polar auxin transport toward the lower side during shoot gravitropic response, leading to cell elongation and tension wood development. In addition, weeping peach trees exhibited steeper root systems and faster lateral root gravitropic response. This suggests that WEEP moderates root gravitropism and is essential to establishing the set-point angle of lateral roots from the gravity vector. Additionally, size-exclusion chromatography indicated that WEEP proteins self-oligomerize, like other proteins with sterile alpha motif domains. Collectively, our results from weeping peach provide new insight into polar auxin transport mechanisms associated with gravitropism and lateral shoot and root orientation.
2023-12-13 | GSE250141 | GEO