Ontology highlight
ABSTRACT:
PROVIDER: PRJNA647155 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12265740_1.fastq.gz | Fastqsanger.gz | |||
| SRR12265740_2.fastq.gz | Fastqsanger.gz | |||
| SRR12265741_1.fastq.gz | Fastqsanger.gz | |||
| SRR12265741_2.fastq.gz | Fastqsanger.gz | |||
| SRR12265742_1.fastq.gz | Fastqsanger.gz |
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Project description:MicroRNAs (miRNAs) are a class of non-coding RNA molecules which have significant gene regulation roles in organisms. The advent of new high throughput sequencing technologies has enabled the revelation of novel miRNAs. Although there are two recent reports on high throughput sequencing analysis of small RNA libraries from different organs of two grapevine wine varieties, there were significant divergence in the number and kinds of miRNAs sequenced in these studies. More sequencing of small RNA libraries is still important for the discovery of novel miRNAs in grapevine. Here, we initially constructed a small RNA library of flower and fruit tissues of a table grapevine cultivar ‘Summer Black’ and performed sequencing and analysis of sRNAs using the Illumina Solexa platform, expecting to discover more miRNAs related to the development of grapevine flowers and berries and the formation of dessert quality in grapevine berries. Totally, 130 conserved grapevine miRNA (Vv-miRNA) belonging to 28 Vv-miRNA families were validated, and 92 novel potential grapevine-specific ones representing 80 unique ones were first discovered. Forty-two (48.84%) of the novel miRNAs possessed differential semi-quantitative PCR expression profiles in various grapevine tissues that could further confirm their existence in the grapevine, among which twenty were expressed only in grapevine berries, indicating some fruit-specificity. 130 target genes for 46 novel miRNAs could be predicted. The locations of these potential target genes on grapevine chromosomes and their complementary levels with the corresponding miRNAs were also analyzed.
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Project description:microRNAs(miRNAs) play critical regulatory roles mainly through cleaving targeted mRNAs or repressing gene translation during plant developments. Grapevine is amongst the most economically important fruit crops with whole genome available, and the study on grapevine miRNAs (Vv-miRNAs) have also been emphasized. However, the regulation mode of Vv-miRNAs on their target mRNAs during grapevine development has not been studied well, especially on a transcriptome-wide level. Here, six small RNA (sRNA) and mRNA libraries from various grapevine tissues were constructed for Illumina and Degradome sequencing. Subsequently, the spatiotemporal variation in the Vv-miRNAs’ regulation on their target genes was systematically analyzed. Totally, 242 known and 132 novel Vv-miRNAs were identified, and 193 target mRNAs including 103 for known and 90 for novel miRNAs were validated in one or more of tissues examined. The interesting finding was that over 50% of novel miRNAs were expressed exclusively in flowers or berries where they had tissue-specific cleavage roles on their target genes, especially, the breadth of their cleavage sites in flower tissues. Moreover, six novel miRNAs in berries were found to response to exogenous gibberellin (GA) and/or ethylene by real time RT-PCR (qRT-PCR) analysis, confirming their regulatory functions during berry development. Other finding was that about 93.6% of the known miRNAs possessed the high conservation in various tissues where their expression levels exhibited some dynamic variations during grapevine development. Significantly, it was found the phenomena that some Vv-miRNA families exist one key member that act as the main regulator of their target genes during grapevine development.
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