Comparative Analysis of miRNAs and Their Target Transcripts between a Spontaneous Late-Ripening Sweet Orange Mutant and Its Wild-Type Using Small RNA and Degradome Sequencing.

Juxun Wu,Guizhi Feng,Saisai Zheng,Hualin Yi

doi:10.3389/fpls.2016.01416

Abstract

Fruit ripening in citrus is not well-understood at the molecular level. Knowledge of the regulatory mechanism of citrus fruit ripening at the post-transcriptional level in particular is lacking. Here, we comparatively analyzed the miRNAs and their target genes in a spontaneous late-ripening mutant, “Fengwan” sweet orange (MT) (Citrus sinensis L. Osbeck), and its wild-type counterpart (“Fengjie 72-1,” WT). Using high-throughput sequencing of small RNAs and RNA degradome tags, we identified 107 known and 21 novel miRNAs, as well as 225 target genes. A total of 24 miRNAs (16 known miRNAs and 8 novel miRNAs) were shown to be differentially expressed between MT and WT. The expression pattern of several key miRNAs and their target genes during citrus fruit development and ripening stages was examined. Csi-miR156k, csi-miR159, and csi-miR166d suppressed specific transcription factors (GAMYBs, SPLs, and ATHBs) that are supposed to be important regulators involved in citrus fruit development and ripening. In the present study, miRNA-mediated silencing of target genes was found under complicated and sensitive regulation in citrus fruit. The identification of miRNAs and their target genes provide new clues for future investigation of mechanisms that regulate citrus fruit ripening.

Highlights

Citrus is one of the most widely grown fruit tree crops in the world, with a high economic value
To identify the miRNAs involved in the citrus fruit ripening process, the pulps of MT and WT harvested at 170 days after flowering (DAF) were used to construct four sRNA libraries with two biological replicates for each sample, which were sequenced using Illumina HiSeqTM2000
We identified 107 known miRNAs belonging to 53 families and 21 novel miRNAs from the fruit of navel orange (Tables S1, S2)

Summary

Introduction

Citrus is one of the most widely grown fruit tree crops in the world, with a high economic value. The maturity time of citrus fruits varies among different varieties. The ripening stage is accompanied by the synthesis of numerous proteins and the transcription of many genes. Carotenoids, sugars, and other soluble compounds accumulate; organic acid contents and chlorophyll are reduced; the cell wall is extensively modified; and the concentration of a number of volatiles increases (Katz et al, 2011; Yu et al, 2012). The elucidation of citrus fruit ripening regulatory pathways and networks is important for the improvement of citrus varieties.

Methods

Results

Conclusion