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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.


Venn distribution of differentially expressed miRNAs in ripening fruit samples. (A) showed the number of differentially expressed miRNA in ripening fruits. (B) showed the exact miRNA(s) differentially expressed in ripening fruits. (C) indicated that the 60 miRNAs differentially expressed in all ripening fruit samples. The differentially expressed Lycium barbarum 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.
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Figure 3: Venn distribution of differentially expressed miRNAs in ripening fruit samples. (A) showed the number of differentially expressed miRNA in ripening fruits. (B) showed the exact miRNA(s) differentially expressed in ripening fruits. (C) indicated that the 60 miRNAs differentially expressed in all ripening fruit samples. The differentially expressed Lycium barbarum 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.

Mentions: As shown in Figure 3, miR166e-3p and miR2111a-5p were stage-specifically expressed in S2 and miR1863a was specific to S4. Six S3-specific miRNAs were identified, comprising miR169f.1/t, miR6025a/d, miR156g, and miR25. Eight miRNAs were common to S1, S2 and S3 but not S4; these were miR23, miR29, miR39, miR49, miR171a, miR6022, miR164e, and LbamiR403. In addition, three miRNAs (miR6164a, miR21, and miR24) were only expressed in S2 and S3, while miR5538 was specific to the late stages S3 and S4. The remaining 60 miRNAs were differentially expressed in all stages (Figure 3C). As shown in Figure S6, miRNAs were expressed abundantly in S1 and S2 and decreased in S3 and S4 during fruit ripening. Among the known miRNAs, miR166a, miR2911, miR166g-3p, miR482c, miR162a, miR164a, miR167a, miR166m, miR168a, and miR5301 were consistently more highly expressed during fruit ripening than miR5538, miR6025d, miR157a, miR1863a, miR6022, miR156g, miR156j, miR166e-3p, miR6025a, miR6164a, miR2111a-5p, miR169t, miR169h, and miR169f.1 (Figure 4A). The latter miRNAs were the stage-specific miRNAs discussed above, and were expressed at a low level.


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)

Venn distribution of differentially expressed miRNAs in ripening fruit samples. (A) showed the number of differentially expressed miRNA in ripening fruits. (B) showed the exact miRNA(s) differentially expressed in ripening fruits. (C) indicated that the 60 miRNAs differentially expressed in all ripening fruit samples. The differentially expressed Lycium barbarum 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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585183&req=5

Figure 3: Venn distribution of differentially expressed miRNAs in ripening fruit samples. (A) showed the number of differentially expressed miRNA in ripening fruits. (B) showed the exact miRNA(s) differentially expressed in ripening fruits. (C) indicated that the 60 miRNAs differentially expressed in all ripening fruit samples. The differentially expressed Lycium barbarum 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.
Mentions: As shown in Figure 3, miR166e-3p and miR2111a-5p were stage-specifically expressed in S2 and miR1863a was specific to S4. Six S3-specific miRNAs were identified, comprising miR169f.1/t, miR6025a/d, miR156g, and miR25. Eight miRNAs were common to S1, S2 and S3 but not S4; these were miR23, miR29, miR39, miR49, miR171a, miR6022, miR164e, and LbamiR403. In addition, three miRNAs (miR6164a, miR21, and miR24) were only expressed in S2 and S3, while miR5538 was specific to the late stages S3 and S4. The remaining 60 miRNAs were differentially expressed in all stages (Figure 3C). As shown in Figure S6, miRNAs were expressed abundantly in S1 and S2 and decreased in S3 and S4 during fruit ripening. Among the known miRNAs, miR166a, miR2911, miR166g-3p, miR482c, miR162a, miR164a, miR167a, miR166m, miR168a, and miR5301 were consistently more highly expressed during fruit ripening than miR5538, miR6025d, miR157a, miR1863a, miR6022, miR156g, miR156j, miR166e-3p, miR6025a, miR6164a, miR2111a-5p, miR169t, miR169h, and miR169f.1 (Figure 4A). The latter miRNAs were the stage-specific miRNAs discussed above, and were expressed at a low level.

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.