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Identification and characterization of miRNAs in ripening fruit of Lycium barbarum L. using high-throughput sequencing.

Zeng S, Liu Y, Pan L, Hayward A, Wang Y - Front Plant Sci (2015)

Bottom Line: Of the novel miRNAs, 36 were specific to L. barbarum fruits compared with L. chinense.These include miR156 targeting of fructokinase and 1-deoxy-D-xylulose-5-phosphate synthase and miR164 targeting of beta-fructofuranosidase.In sum, valuable information revealed by small RNA sequencing in this study will provide a solid foundation for uncovering the miRNA-mediated mechanism of fruit ripening and quality in this nutritional food.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China ; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China.

ABSTRACT
MicroRNAs (miRNAs) are master regulators of gene activity documented to play central roles in fruit ripening in model plant species, yet little is known of their roles in Lycium barbarum L. fruits. In this study, miRNA levels in L. barbarum fruit samples at four developmental stages, were assayed using Illumina HiSeqTM2000. This revealed the presence of 50 novel miRNAs and 38 known miRNAs in L. barbarum fruits. Of the novel miRNAs, 36 were specific to L. barbarum fruits compared with L. chinense. A number of stage-specific miRNAs were identified and GO terms were assigned to 194 unigenes targeted by miRNAs. The majority of GO terms of unigenes targeted by differentially expressed miRNAs are "intracellular organelle," "binding," "metabolic process," "pigmentation," and "biological regulation." Enriched KEGG analysis indicated that nucleotide excision repair and ubiquitin mediated proteolysis were over-represented during the initial stage of ripening, with ABC transporters and sulfur metabolism pathways active during the middle stages and ABC transporters and spliceosome enriched in the final stages of ripening. Several miRNAs and their targets serving as potential regulators in L. barbarum fruit ripening were identified using quantitative reverse transcription polymerase chain reaction. The miRNA-target interactions were predicted for L. barbarum ripening regulators including miR156/157 with LbCNR and LbWRKY8, and miR171 with LbGRAS. Additionally, regulatory interactions potentially controlling fruit quality and nutritional value via sugar and secondary metabolite accumulation were identified. These include miR156 targeting of fructokinase and 1-deoxy-D-xylulose-5-phosphate synthase and miR164 targeting of beta-fructofuranosidase. In sum, valuable information revealed by small RNA sequencing in this study will provide a solid foundation for uncovering the miRNA-mediated mechanism of fruit ripening and quality in this nutritional food.

No MeSH data available.


Enriched GO term of genes targeted by differentially expressed miRNAs in Lycium barbarum ripening fruits. The differentially expressed miRNAs were defined as following the criteria of q < 0.01 and /log2(foldchange)/ > 1 based on the number of miRNA reads in small RNA libraries. Enriched GO was plotted using WEGO (http://wego.genomics.org.cn/cgi-bin/wego/index.pl).
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Figure 5: Enriched GO term of genes targeted by differentially expressed miRNAs in Lycium barbarum ripening fruits. The differentially expressed miRNAs were defined as following the criteria of q < 0.01 and /log2(foldchange)/ > 1 based on the number of miRNA reads in small RNA libraries. Enriched GO was plotted using WEGO (http://wego.genomics.org.cn/cgi-bin/wego/index.pl).

Mentions: To gain a global overview of the regulatory functions of miRNAs, the GO terms of all targets were analyzed. Among the 441 target genes, 194 target genes had GO terms. As shown in Figure S9, the major “cellular components” predicted for these GO-defined target genes were “cell part,” “organelle,” “intracellular,” “intracellular organelle,” “intracellular part,” and “membrane-bounded organelle.” The main molecular functions of target genes were classified as “binding,” “catalytic,” “transcription regulator,” and “transporter,” while the key biological processes were “cellular process,” “metabolic process,” “biological regulation,” and “pigmentation.” In order to better understand the regulatory role of miRNA expressed during L. barbarum fruit ripening, the enriched GO terms of target genes of differentially expressed miRNAs were analyzed in S1 vs. S2 (S1 vs. S2), S2 vs. S3, or S3 vs. S4 (Figure 5). As shown in Figure 5, the distribution of enriched GO terms of targets of differentially regulated miRNAs was similar for all adjacent stages, with the major cellular components of “cell part,” “intracellular,” “intracellular organelle,” “organelle,” “intracellular part,” and “membrane-bounded organelle.” The main molecular function classification was “binding” and the chief biological processes were “cellular process,” “metabolic process,” “pigmentation” as well as “biological regulation.” Noticeable exceptions were “intracellular organelle part,” “macromolecular complex,” and “transcription regulator” significantly decreased in S3 vs. S4 when compared to S1 vs. S2 or S2 vs. S3.


Identification and characterization of miRNAs in ripening fruit of Lycium barbarum L. using high-throughput sequencing.

Zeng S, Liu Y, Pan L, Hayward A, Wang Y - Front Plant Sci (2015)

Enriched GO term of genes targeted by differentially expressed miRNAs in Lycium barbarum ripening fruits. The differentially expressed miRNAs were defined as following the criteria of q < 0.01 and /log2(foldchange)/ > 1 based on the number of miRNA reads in small RNA libraries. Enriched GO was plotted using WEGO (http://wego.genomics.org.cn/cgi-bin/wego/index.pl).
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4585183&req=5

Figure 5: Enriched GO term of genes targeted by differentially expressed miRNAs in Lycium barbarum ripening fruits. The differentially expressed miRNAs were defined as following the criteria of q < 0.01 and /log2(foldchange)/ > 1 based on the number of miRNA reads in small RNA libraries. Enriched GO was plotted using WEGO (http://wego.genomics.org.cn/cgi-bin/wego/index.pl).
Mentions: To gain a global overview of the regulatory functions of miRNAs, the GO terms of all targets were analyzed. Among the 441 target genes, 194 target genes had GO terms. As shown in Figure S9, the major “cellular components” predicted for these GO-defined target genes were “cell part,” “organelle,” “intracellular,” “intracellular organelle,” “intracellular part,” and “membrane-bounded organelle.” The main molecular functions of target genes were classified as “binding,” “catalytic,” “transcription regulator,” and “transporter,” while the key biological processes were “cellular process,” “metabolic process,” “biological regulation,” and “pigmentation.” In order to better understand the regulatory role of miRNA expressed during L. barbarum fruit ripening, the enriched GO terms of target genes of differentially expressed miRNAs were analyzed in S1 vs. S2 (S1 vs. S2), S2 vs. S3, or S3 vs. S4 (Figure 5). As shown in Figure 5, the distribution of enriched GO terms of targets of differentially regulated miRNAs was similar for all adjacent stages, with the major cellular components of “cell part,” “intracellular,” “intracellular organelle,” “organelle,” “intracellular part,” and “membrane-bounded organelle.” The main molecular function classification was “binding” and the chief biological processes were “cellular process,” “metabolic process,” “pigmentation” as well as “biological regulation.” Noticeable exceptions were “intracellular organelle part,” “macromolecular complex,” and “transcription regulator” significantly decreased in S3 vs. S4 when compared to S1 vs. S2 or S2 vs. S3.

Bottom Line: Of the novel miRNAs, 36 were specific to L. barbarum fruits compared with L. chinense.These include miR156 targeting of fructokinase and 1-deoxy-D-xylulose-5-phosphate synthase and miR164 targeting of beta-fructofuranosidase.In sum, valuable information revealed by small RNA sequencing in this study will provide a solid foundation for uncovering the miRNA-mediated mechanism of fruit ripening and quality in this nutritional food.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China ; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences Guangzhou, China.

ABSTRACT
MicroRNAs (miRNAs) are master regulators of gene activity documented to play central roles in fruit ripening in model plant species, yet little is known of their roles in Lycium barbarum L. fruits. In this study, miRNA levels in L. barbarum fruit samples at four developmental stages, were assayed using Illumina HiSeqTM2000. This revealed the presence of 50 novel miRNAs and 38 known miRNAs in L. barbarum fruits. Of the novel miRNAs, 36 were specific to L. barbarum fruits compared with L. chinense. A number of stage-specific miRNAs were identified and GO terms were assigned to 194 unigenes targeted by miRNAs. The majority of GO terms of unigenes targeted by differentially expressed miRNAs are "intracellular organelle," "binding," "metabolic process," "pigmentation," and "biological regulation." Enriched KEGG analysis indicated that nucleotide excision repair and ubiquitin mediated proteolysis were over-represented during the initial stage of ripening, with ABC transporters and sulfur metabolism pathways active during the middle stages and ABC transporters and spliceosome enriched in the final stages of ripening. Several miRNAs and their targets serving as potential regulators in L. barbarum fruit ripening were identified using quantitative reverse transcription polymerase chain reaction. The miRNA-target interactions were predicted for L. barbarum ripening regulators including miR156/157 with LbCNR and LbWRKY8, and miR171 with LbGRAS. Additionally, regulatory interactions potentially controlling fruit quality and nutritional value via sugar and secondary metabolite accumulation were identified. These include miR156 targeting of fructokinase and 1-deoxy-D-xylulose-5-phosphate synthase and miR164 targeting of beta-fructofuranosidase. In sum, valuable information revealed by small RNA sequencing in this study will provide a solid foundation for uncovering the miRNA-mediated mechanism of fruit ripening and quality in this nutritional food.

No MeSH data available.