Dataset Information

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

ABSTRACT: 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.

ORGANISM(S): Prunus persica

PROVIDER: GSE83110 | GEO | 2017/02/11

SECONDARY ACCESSION(S): PRJNA324775

REPOSITORIES: GEO

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Project description:MicroRNAs (miRNAs) play a important part in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice and other plants. However, the number of miRNAs discovered in grape is relatively low and little is known about miRNAs responded gibberellin during fruit germination. In this study, a small RNA library from gibberellin grape fruits was sequenced by the high throughput sequencing technology. A total of 16,033,273 reads were obtained. 812,099 total reads representing 1726 unique sRNAs matched to known grape miRNAs. Further analysis confirmed a total of 149 conserved grapevine miRNA (Vv-miRNA) belonging to 27 Vv-miRNA families were validated, and 74 novel potential grapevine-specific miRNAs and 23 corresponding novel miRNAs* were discovered. Twenty-seven (36.5%) of the novel miRNAs exhibited differential QRT-PCR expression profiles in different development gibberellin-treated grapevine berries that could further confirm their existence in grapevine. QRT-PCR analysis on transcript abundance of 27 conserved miRNA family and the new candidate miRNAs revealed that most of them were differentially regulated by the gibberellin, with most conserved miRNA family and 26 miRNAs being specifically induced by gibberellin exposure. All novel sequences had not been earlier described in other plant species. In addition, 117 target genes for 29 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in gibberellin-treated grape berries. This study led to the confirmation of 101 known miRNAs and the discovery of 74 novel miRNAs in grapevine. Identification of miRNAs resulted in significant enrichment of the gibberellin of grapevine miRNAs and provided insights into miRNA regulation of genes expressed in grape berries. GSM604831 is the control for the gibberellin-treated sample.

Dataset Information

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

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