Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs
Ontology highlight
ABSTRACT: 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
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).
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.
Project description:Background miRNAs and their regulatory functions have been extensively characterized in model species but whether apple has evolved similar or unique regulatory features remains unknown. Results We performed deep sRNA-seq and identified 23 conserved, 10 less-conserved and 42 apple-specific miRNAs or families with distinct expression patterns. The identified miRNAs target 118 genes representing a wide range of enzymatic and regulatory activities. Apple also conserves two TAS gene families with similar but unique tasiRNA biogenesis profiles and target specificities. Importantly, we found that miR159, miR828 and miR858 can collectively target up to 81 MYB genes potentially involved in diverse aspects of plant growth and development. These miRNA target sites are differentially conserved among MYBs, which is largely influenced by the location and conservation of the encoded amino acid residues in MYB factors. Finally, we found that ten of the 19 miR828-targeted MYBs undergo siRNA biogenesis at the 3' cleaved, highly divergent transcript regions, generating over 100 sequence-distinct siRNAs that potentially target over 70 diverse genes as confirmed by degradome analysis. Conclusion Our work identified and characterized apple miRNAs, their expression patterns, targets and regulatory functions. We also discovered that three miRNAs and the ensuing siRNAs exploit both conserved and divergent sequence features of MYB genes to initiate distinct regulatory networks targeting a multitude of genes inside and outside the MYB family. Identification of apple miRNAs and their targets from four different tissues
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.
Project description:Background Field observations and a few physiological studies pointed out that peach embryogenesis and fruit development are strictly related. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools failed. Moreover, physiological disturbances during the early embryo development lead to seed abortion and fruitlet abscission. Later on, the interactions between seed and fruit development become less stringent. Genetic and molecular information about seed and fruit development in peach is limited. Results The isolation of 455 genes differentially expressed in seed and fruit was done by means of a comparative analysis of the transcription profiles carried out in peach (Prunus persica, cv Fantasia) seed and mesocarp throughout development by means of µPEACH 1.0, the first peach microarray. Genes differentially expressed in the two organs and specific of developmental stages had been identified, and some were validated as markers. Genes representative of the main functional categories are present, among which several transcription factors such as MADS-box, bZIP, Aux/IAA, AP2, WRKY, and HD. Some of these showed a similar transcription profile in the two organs, while others displayed an opposite pattern, being more expressed in embryo at early development and in mesocarp at ripening. Conclusions The µPEACH1.0, although developed from ripe fruit ESTs, resulted in being suitable for studying seed/mesocarp interactions. Among the differentially expressed genes, marker genes specific for organ and stage of development have been selected. Comparisons were carried out by pooling stage 1 and 2 (named early development, e) and stage 3 and 4 (named late development, l), separately for mesocarp (M) and seed (S) of cultivar Fantasia, and using a simple loop experimental design. RNA has been extracted from fruit harvest at above-mentioned stages of development. At least four hybridizations have been conducted for a total of four technical replicates (with dye-swap).
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).
Project description:Manipulating the crop load in peach trees determines carbon supply and optimum balance between fruit yield and quality potentials. The impact of carbon supply on peach fruit quality was assessed in three development stages (S2, S3, S4) on fruit of equal maturity from trees that were carbon (C) starved (unthinned) and sufficient (thinned). Previous studies determined that primary metabolites of peach fruit mesocarp are mainly linked with developmental processes, thus, the secondary metabolite profile was assessed using non-targeted liquid chromatography mass-spectrometry (LC-MS). Carbon sufficient (C-sufficient) fruit demonstrated superior quality attributes as compared to C-starved fruit. Early metabolic shifts in the secondary metabolome appear to prime quality at harvest. Enhanced C-availability facilitated the increased and consistent synthesis of flavonoids, like catechin, epicatechin and eriodyctiol, via the phenylpropanoid pathway, providing a link between the metabolome and fruit quality, and serving as signatures of C-sufficiency during peach fruit development.
Project description:Correlation analysis of the expression of bud dormancy-related genes in 10 peach cultivars, with different chilling requirements for dormancy release.
Project description:‘Crumbly’ fruit is a developmental disorder in red raspberry (Rubus idaeus) that results in malformed fruit with poor adherence of drupelets to one another. In terms of quality and yield, crumbly fruit has become a serious problem in the raspberry industry resulting in unsaleable fruit and waste. A microarray experiment, using pools of progeny from a segregating mapping population (Glen Moy x Latham) with either 'normal' or 'crumbly' fruit at three different fruit developmental stages ('closed'; 'open'; 'green'), identified several genes that were differentially expressed between the crumbly and non-crumbly phenotypes within three quantitative trait loci (QTL) identified. Analysis of gene function highlighted the importance of processes that compromise ovule fertilization as triggers of the crumbly fruit phenotype.
Project description:LC-MS/MS proteomic studies using in vitro peach cultures provided data on exoproteomes of the three isolates at equivalent stages of brown rot colonization