Identification and characterization of miRNAs in ripening fruit of lycium barbarum L. Using high-throughput sequencing

Zeng, Shaohua, Liu, Yongliang, Pan, Lizhu, Hayward, Alice and Wang, Ying (2015) Identification and characterization of miRNAs in ripening fruit of lycium barbarum L. Using high-throughput sequencing. Frontiers in Plant Science, 6 September: . doi:10.3389/fpls.2015.00778

Author Zeng, Shaohua
Liu, Yongliang
Pan, Lizhu
Hayward, Alice
Wang, Ying
Title Identification and characterization of miRNAs in ripening fruit of lycium barbarum L. Using high-throughput sequencing
Journal name Frontiers in Plant Science   Check publisher's open access policy
ISSN 1664-462X
Publication date 2015-09-25
Year available 2015
Sub-type Article (original research)
DOI 10.3389/fpls.2015.00778
Open Access Status DOI
Volume 6
Issue September
Total pages 15
Place of publication Lausanne, Switzerland
Publisher Frontiers Research Foundation
Collection year 2016
Language eng
Formatted 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.
Keyword Fruit ripening
High-throughput sequencing
Lycium barbarum L
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Alliance for Agriculture and Food Innovation
Official 2016 Collection
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