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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.

Show MeSH
Expression pattern confirmed by qRT-PCR and comparison with sequencing data. Relative expression pattern of six different conserved miRNAs among various libraries are confirmed by qRT-PCR results by 2-∆∆Ct method. For visualization, log10 method is applied to compute the TPM data of sequencing results. The paragraph A to F represent the expression profiles of miR166a, miR4376-5p, miR156k, miR396b-3p, miR164c* and miR159b-3p in sequence. Y-axis represents the expression level and X-axis represents different libraries. Blue lines represent the q-PCR data and red lines represent the sequencing data. The line charts indicate the similar expression patterns with miRNA sequencing.
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Fig3: Expression pattern confirmed by qRT-PCR and comparison with sequencing data. Relative expression pattern of six different conserved miRNAs among various libraries are confirmed by qRT-PCR results by 2-∆∆Ct method. For visualization, log10 method is applied to compute the TPM data of sequencing results. The paragraph A to F represent the expression profiles of miR166a, miR4376-5p, miR156k, miR396b-3p, miR164c* and miR159b-3p in sequence. Y-axis represents the expression level and X-axis represents different libraries. Blue lines represent the q-PCR data and red lines represent the sequencing data. The line charts indicate the similar expression patterns with miRNA sequencing.

Mentions: In our research, qPCR was adopted to validate the sequencing results of six miRNAs (miR166a, miR4376-5p, miR156k, miR396b-3p, miR164c*, miR159b-3p), and was able to show that these miRNA are really expressed, and the changes during the fruit development are real. The line charts indicate similar expression patterns as shown in Figure 3, although the values of miRNA expression detected by two methods varied to some extent. So, the qPCR results confirmed the reliability and expression patterns of microRNA involved in pear fruit development through high throughput sequencing.Figure 3


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)

Expression pattern confirmed by qRT-PCR and comparison with sequencing data. Relative expression pattern of six different conserved miRNAs among various libraries are confirmed by qRT-PCR results by 2-∆∆Ct method. For visualization, log10 method is applied to compute the TPM data of sequencing results. The paragraph A to F represent the expression profiles of miR166a, miR4376-5p, miR156k, miR396b-3p, miR164c* and miR159b-3p in sequence. Y-axis represents the expression level and X-axis represents different libraries. Blue lines represent the q-PCR data and red lines represent the sequencing data. The line charts indicate the similar expression patterns with miRNA sequencing.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Expression pattern confirmed by qRT-PCR and comparison with sequencing data. Relative expression pattern of six different conserved miRNAs among various libraries are confirmed by qRT-PCR results by 2-∆∆Ct method. For visualization, log10 method is applied to compute the TPM data of sequencing results. The paragraph A to F represent the expression profiles of miR166a, miR4376-5p, miR156k, miR396b-3p, miR164c* and miR159b-3p in sequence. Y-axis represents the expression level and X-axis represents different libraries. Blue lines represent the q-PCR data and red lines represent the sequencing data. The line charts indicate the similar expression patterns with miRNA sequencing.
Mentions: In our research, qPCR was adopted to validate the sequencing results of six miRNAs (miR166a, miR4376-5p, miR156k, miR396b-3p, miR164c*, miR159b-3p), and was able to show that these miRNA are really expressed, and the changes during the fruit development are real. The line charts indicate similar expression patterns as shown in Figure 3, although the values of miRNA expression detected by two methods varied to some extent. So, the qPCR results confirmed the reliability and expression patterns of microRNA involved in pear fruit development through high throughput sequencing.Figure 3

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