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Identification and characterization of microRNAs from Chinese pollination constant non-astringent persimmon using high-throughput sequencing.

Luo Y, Zhang X, Luo Z, Zhang Q, Liu J - BMC Plant Biol. (2015)

Bottom Line: microRNAs (miRNAs) have been shown to play key roles in regulating gene expression at post-transcriptional level, but miRNAs associated with natural deastringency of Chinese pollination-constant nonastringent persimmon (CPCNA) have never been identified.In addition, dka-miR396g and miR2911a may regulate their target genes associated with glucosylation and insolubilization of tannin precursors.All of these miRNAs might play key roles in the regulation of (de)astringency in persimmon fruits under normal development conditions.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China. luoyujie200701@163.com.

ABSTRACT

Background: microRNAs (miRNAs) have been shown to play key roles in regulating gene expression at post-transcriptional level, but miRNAs associated with natural deastringency of Chinese pollination-constant nonastringent persimmon (CPCNA) have never been identified.

Results: In this study, two small RNA libraries established using 'Eshi No. 1' persimmon (Diospyros kaki Thunb.; CPCNA) fruits collected at 15 and 20 weeks after flowering (WAF) were sequenced through Solexa platform in order to identify miRNAs involved in deastringency of persimmon. A total of 6,258,487 and 7,634,169 reads were generated for the libraries at 15 and 20 WAF, respectively. Based on sequence similarity and hairpin structure prediction, 236 known miRNAs belonging to 65 miRNA families and 33 novel miRNAs were identified using persimmon transcriptome data. Sixty one of the characterized miRNAs exhibited pronounced difference in the expression levels between 15 and 20 WAF, 17 up-regulated and 44 down-regulated. Expression profiles of 12 conserved and 10 novel miRNAs were validated by stem loop qRT-PCR. A total of 198 target genes were predicted for the differentially expressed miRNAs, including several genes that have been reported to be implicated in proanthocyanidins (PAs, or called tannin) accumulation. In addition, two transcription factors, a GRF and a bHLH, were experimentally confirmed as the targets of dka-miR396 and dka-miR395, respectively.

Conclusions: Taken together, the present data unraveled several important miRNAs in persimmon. Among them, miR395p-3p and miR858b may regulate bHLH and MYB, respectively, which are influenced by SPL under the control of miR156j-5p and in turn regulate the structural genes involved in PA biosynthesis. In addition, dka-miR396g and miR2911a may regulate their target genes associated with glucosylation and insolubilization of tannin precursors. All of these miRNAs might play key roles in the regulation of (de)astringency in persimmon fruits under normal development conditions.

No MeSH data available.


Gene Ontology classifications of the target genes based on cellular component, molecular function, and biological process.
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Fig5: Gene Ontology classifications of the target genes based on cellular component, molecular function, and biological process.

Mentions: To better understand regulatory roles of the identified miRNAs, we performed GO analyses on target genes of the differentially expressed known miRNAs (Additional file 4: Table S3). Among the 428 target genes, 246 were categorized into biological processes, 166 into cellular components and 16 into molecular functions (Figure 5). The major biological processes were ‘cellular process’ and ‘metabolic process’, such as GO:0016053 and GO:0009064. The main cellular components were ‘cell’ and ‘cell junction’, such as GO:0043232 and GO:0070013. As for molecular functions, the majority of genes were clustered into ‘binding proteins’ and ‘catalytic’, such as GO:0005524 and GO:0016407. The target genes regulated by the up-regulated miRNAs encode transcription factors (GO:0003700), whereas most of the targets regulated by the down-regulated miRNA were shown to take part in leaf development (GO:0048366), shoot system development (GO:0022621, GO:0048367), response to hormone stimulus (GO:0009725, GO:0032870), and hormone-mediated signaling (GO:0009755).Figure 5


Identification and characterization of microRNAs from Chinese pollination constant non-astringent persimmon using high-throughput sequencing.

Luo Y, Zhang X, Luo Z, Zhang Q, Liu J - BMC Plant Biol. (2015)

Gene Ontology classifications of the target genes based on cellular component, molecular function, and biological process.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4308916&req=5

Fig5: Gene Ontology classifications of the target genes based on cellular component, molecular function, and biological process.
Mentions: To better understand regulatory roles of the identified miRNAs, we performed GO analyses on target genes of the differentially expressed known miRNAs (Additional file 4: Table S3). Among the 428 target genes, 246 were categorized into biological processes, 166 into cellular components and 16 into molecular functions (Figure 5). The major biological processes were ‘cellular process’ and ‘metabolic process’, such as GO:0016053 and GO:0009064. The main cellular components were ‘cell’ and ‘cell junction’, such as GO:0043232 and GO:0070013. As for molecular functions, the majority of genes were clustered into ‘binding proteins’ and ‘catalytic’, such as GO:0005524 and GO:0016407. The target genes regulated by the up-regulated miRNAs encode transcription factors (GO:0003700), whereas most of the targets regulated by the down-regulated miRNA were shown to take part in leaf development (GO:0048366), shoot system development (GO:0022621, GO:0048367), response to hormone stimulus (GO:0009725, GO:0032870), and hormone-mediated signaling (GO:0009755).Figure 5

Bottom Line: microRNAs (miRNAs) have been shown to play key roles in regulating gene expression at post-transcriptional level, but miRNAs associated with natural deastringency of Chinese pollination-constant nonastringent persimmon (CPCNA) have never been identified.In addition, dka-miR396g and miR2911a may regulate their target genes associated with glucosylation and insolubilization of tannin precursors.All of these miRNAs might play key roles in the regulation of (de)astringency in persimmon fruits under normal development conditions.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China. luoyujie200701@163.com.

ABSTRACT

Background: microRNAs (miRNAs) have been shown to play key roles in regulating gene expression at post-transcriptional level, but miRNAs associated with natural deastringency of Chinese pollination-constant nonastringent persimmon (CPCNA) have never been identified.

Results: In this study, two small RNA libraries established using 'Eshi No. 1' persimmon (Diospyros kaki Thunb.; CPCNA) fruits collected at 15 and 20 weeks after flowering (WAF) were sequenced through Solexa platform in order to identify miRNAs involved in deastringency of persimmon. A total of 6,258,487 and 7,634,169 reads were generated for the libraries at 15 and 20 WAF, respectively. Based on sequence similarity and hairpin structure prediction, 236 known miRNAs belonging to 65 miRNA families and 33 novel miRNAs were identified using persimmon transcriptome data. Sixty one of the characterized miRNAs exhibited pronounced difference in the expression levels between 15 and 20 WAF, 17 up-regulated and 44 down-regulated. Expression profiles of 12 conserved and 10 novel miRNAs were validated by stem loop qRT-PCR. A total of 198 target genes were predicted for the differentially expressed miRNAs, including several genes that have been reported to be implicated in proanthocyanidins (PAs, or called tannin) accumulation. In addition, two transcription factors, a GRF and a bHLH, were experimentally confirmed as the targets of dka-miR396 and dka-miR395, respectively.

Conclusions: Taken together, the present data unraveled several important miRNAs in persimmon. Among them, miR395p-3p and miR858b may regulate bHLH and MYB, respectively, which are influenced by SPL under the control of miR156j-5p and in turn regulate the structural genes involved in PA biosynthesis. In addition, dka-miR396g and miR2911a may regulate their target genes associated with glucosylation and insolubilization of tannin precursors. All of these miRNAs might play key roles in the regulation of (de)astringency in persimmon fruits under normal development conditions.

No MeSH data available.