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Identification of miRNAs involved in pear fruit development and quality.

Wu J, Wang D, Liu Y, Wang L, Qiao X, Zhang S - BMC Genomics (2014)

Bottom Line: Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages.Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling.Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. wujun@njau.edu.cn.

ABSTRACT

Background: MicroRNAs (miRNAs) are a class of small, endogenous RNAs that take part in regulating genes through mediating gene expressions at the post-transcriptional level in plants. Previous studies have reported miRNA identification in various plants ranging from model plants to perennial fruit trees. However, the role of miRNAs in pear (Pyrus bretschneideri) fruit development is not clear. Here, we investigated the miRNA profiles of pear fruits from different time stages during development with Illumina HiSeq 2000 platform and bioinformatics analysis. Quantitative real-time PCR was used to validate the expression levels of miRNAs.

Results: Both conserved and species-specific miRNAs in pear have been identified in this study. Total reads, ranging from 19,030,925 to 25,576,773, were obtained from six small RNA libraries constructed for different stages of fruit development after flowering. Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages. KEGG pathway analysis on 2,216 target genes of 188 known miRNAs and 1,127 target genes of 184 novel miRNAs showed that miRNAs are widely involved in the regulation of fruit development. Among these, a total of eleven miRNAs putatively participate in the pathway of lignin biosynthesis, nine miRNAs were identified to take part in sugar and acid metabolism, and MiR160 was identified to regulate auxin response factor.

Conclusion: Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling. Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species.

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The distribution of target gene numbers for each conserved miRNA among developmental stages. X-axis represents the interval for the target gene number of each conserved miRNA. Y-axis represents the number of miRNA in each interval.
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Fig6: The distribution of target gene numbers for each conserved miRNA among developmental stages. X-axis represents the interval for the target gene number of each conserved miRNA. Y-axis represents the number of miRNA in each interval.

Mentions: MicroRNA regulates gene expression through inhibiting translation or degrading mRNA at a certain site[46]. Currently, bioinformatics methods have been used to decipher target genes in several studies[47, 48]. To better understand the roles pear miRNAs play in fruit development, PickPlantTar was used to predict potential miRNA target genes by using the most abundant mature miRNA as queries. By a stringent criteria described in the methodology, 2,216 targets for 188 known miRNAs and 1,127 targets for 184 novel miRNAs with differential expression patterns were predicted (Additional file6). The number of putative target genes for each conserved miRNA varied from 1 to 226. As showed in FigureĀ 6, more than 50 miRNAs targeted 4 to 10 genes. Thirty-three miRNAs had only one target gene, which may suggest a unique regulatory function played by these miRNAs. Meanwhile, we found that 4 miRNAs had more than 100 predicted target genes. For instance, miR396b targeted 226 genes, the highest among the known miRNAs, followed by miR5564 and miR4993 with 149 and 137 target gene numbers, respectively, which might indicate the wide regulation functions of these miRNAs. In addition, as suggested by Bonnet et al.[49], highly repetitive motifs corresponding to the miRNA sequence may contribute to the ubiquity of target genes, which means the possibility of the potential false prediction. Further experiments are needed to confirm the accurate function for these miRNAs.Figure 6


Identification of miRNAs involved in pear fruit development and quality.

Wu J, Wang D, Liu Y, Wang L, Qiao X, Zhang S - BMC Genomics (2014)

The distribution of target gene numbers for each conserved miRNA among developmental stages. X-axis represents the interval for the target gene number of each conserved miRNA. Y-axis represents the number of miRNA in each interval.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4233070&req=5

Fig6: The distribution of target gene numbers for each conserved miRNA among developmental stages. X-axis represents the interval for the target gene number of each conserved miRNA. Y-axis represents the number of miRNA in each interval.
Mentions: MicroRNA regulates gene expression through inhibiting translation or degrading mRNA at a certain site[46]. Currently, bioinformatics methods have been used to decipher target genes in several studies[47, 48]. To better understand the roles pear miRNAs play in fruit development, PickPlantTar was used to predict potential miRNA target genes by using the most abundant mature miRNA as queries. By a stringent criteria described in the methodology, 2,216 targets for 188 known miRNAs and 1,127 targets for 184 novel miRNAs with differential expression patterns were predicted (Additional file6). The number of putative target genes for each conserved miRNA varied from 1 to 226. As showed in FigureĀ 6, more than 50 miRNAs targeted 4 to 10 genes. Thirty-three miRNAs had only one target gene, which may suggest a unique regulatory function played by these miRNAs. Meanwhile, we found that 4 miRNAs had more than 100 predicted target genes. For instance, miR396b targeted 226 genes, the highest among the known miRNAs, followed by miR5564 and miR4993 with 149 and 137 target gene numbers, respectively, which might indicate the wide regulation functions of these miRNAs. In addition, as suggested by Bonnet et al.[49], highly repetitive motifs corresponding to the miRNA sequence may contribute to the ubiquity of target genes, which means the possibility of the potential false prediction. Further experiments are needed to confirm the accurate function for these miRNAs.Figure 6

Bottom Line: Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages.Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling.Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China. wujun@njau.edu.cn.

ABSTRACT

Background: MicroRNAs (miRNAs) are a class of small, endogenous RNAs that take part in regulating genes through mediating gene expressions at the post-transcriptional level in plants. Previous studies have reported miRNA identification in various plants ranging from model plants to perennial fruit trees. However, the role of miRNAs in pear (Pyrus bretschneideri) fruit development is not clear. Here, we investigated the miRNA profiles of pear fruits from different time stages during development with Illumina HiSeq 2000 platform and bioinformatics analysis. Quantitative real-time PCR was used to validate the expression levels of miRNAs.

Results: Both conserved and species-specific miRNAs in pear have been identified in this study. Total reads, ranging from 19,030,925 to 25,576,773, were obtained from six small RNA libraries constructed for different stages of fruit development after flowering. Comparative profiling showed that an average of 90 miRNAs was expressed with significant differences between various developmental stages. KEGG pathway analysis on 2,216 target genes of 188 known miRNAs and 1,127 target genes of 184 novel miRNAs showed that miRNAs are widely involved in the regulation of fruit development. Among these, a total of eleven miRNAs putatively participate in the pathway of lignin biosynthesis, nine miRNAs were identified to take part in sugar and acid metabolism, and MiR160 was identified to regulate auxin response factor.

Conclusion: Comparative analysis of miRNAomes during pear fruit development is presented, and miRNAs were proved to be widely involved in the regulation of fruit development and formation of fruit quality, for example through lignin synthesis, sugar and acid metabolism, and hormone signaling. Combined with computational analysis and experimental confirmation, the research contributes valuable information for further functional research of microRNA in fruit development for pear and other species.

Show MeSH