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Identification of miRNAs and Their Target Genes in Peach (Prunus persica L.) Using High-Throughput Sequencing and Degradome Analysis

ABSTRACT: 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.

ORGANISM(S): Prunus persica

PROVIDER: GSE49579 | GEO | 2014/01/01

SECONDARY ACCESSION(S): PRJNA214326

REPOSITORIES: GEO

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Identification of miRNAs and Their Target Genes in Peach (Prunus persica L.) Using High-Throughput Sequencing and Degradome Analysis

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

Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs

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

The identification of known and novel microRNAs and their targets in peach (Prunus persica) fruit by high-throughput sequencing

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

Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs

2012-07-03 | GSE38535 | GEO

Prunus persica

Project description:Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs

| PRJNA168085 | ENA

Prunus persica

Project description:The identification of known and novel microRNAs and their targets in peach (Prunus persica) fruit by high-throughput sequencing

| PRJNA324775 | ENA

Identification and differential expression of microRNAs during metamorphosis in the Japanese flounder (Paralichthys olivaceus)

Project description:The 987 probes (Japanese flounder conserved miRNAs and candidates, fish conserved miRNAs, and contro) were hybridized with two stages during Japanese flounder metamorphosis by miRNA microarray. We validated 92 miRNAs using miRNA microarray in the 17 dph and 29 dph of Japanese flounder development, and obtained 66 differertially expressed miRNAs by comparison miRNA expression patterns of the two stages. These results indicate that miRNAs might play key roles in regulating gene expression during Japanese flounder metamorphosis. Using miRNA microarray, the flounder conserved miRNAs and candidates were identified, and 92 conserved miRNAs were detected in the 17 dph and 29 dph during metamorphosis. Meanwhile, 66 conserved miRNAs were differertially expressed by comparison miRNA expression patterns of the two stages. We further identified flounder miRNAs during metamorphosis.

2013-03-10 | E-GEOD-27986 | biostudies-arrayexpress

Prunus persica cultivar:Hujingmilu

Project description:Peach （Prunus persica） Raw sequence reads

| PRJNA576753 | ENA

Defying Gravity: WEEP promotes negative gravitropism in Prunus persica by establishing asymmetric auxin gradients

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

Deep sequencing of organ- and stage-specific microRNAs in the evolutionarily basal insect Blattella germanica (L.) (Dictyoptera, Blattellidae)

Project description:microRNAs (miRNAs) have been reported as key regulators in the post-transcriptional process in eukaryotic cells. In insects most of the studies have been reported in holometabolans while only recently two hemimetabolansM-BM- (Locusta migratoria and Acyrthosiphonpisum) have had their miRNAs identified. Therefore, the study on miRNAs of the evolutionarily basal hemimetabolanM-BM- Blattella germanica, may provide valuable insights on the structural and functional evolution of miRNAs. Small RNA libraries of the cockroach B. germanica were built from the whole body of the last instar nymph, and the adult ovaries. The high throughput Solexa sequencing resulted in approximately 11 and 8 million reads for the whole-body andM-BM- ovaries, respectively. Bioinformatic analyses identified 38 known miRNAs as well as 11 known miRNA*s. We also found 411 miRNA candidates conserved in other insects and 1017 candidates specific of B. germanica. The positive correlation between Solexa data and real-time quantitative PCR showed that reads can be used as quantitative method. Novel miRNA candidates were validated by decreasing levels of expression in dicer-1 RNAi knockdown individuals. The comparison of the two libraries indicates that whole-body nymph contain more known miRNAs than ovaries, whereas the adult ovaries are enriched with novel miRNA candidates. Our study has identified many known miRNAs and novel miRNA candidates in the basal hemimetabolan insect B. germanica, and most of the specific sequences were found in ovaries. Deep sequencing data reflect miRNA abundance and Dicer-1 RNAi assay is a reliable method to validate novel miRNAs. Small RNAs were sequenced whole body of the last instar nymph and adult ovaries of the cockroach Blattella germanica.

2011-01-01 | E-GEOD-22892 | biostudies-arrayexpress

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