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

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.

Genome‐wide analysis of coding and non‐coding RNA reveals a conserved miR164‐NAC regulatory pathway for fruit ripening

“…For instance, miR396 controls leaf size by regulating expression of GROWTH REGULATING FACTORS (GRFs; Rodriguez et al, 2010); mutations in MIR319a lead to decreases in petal length and width (Nag et al, 2009). Omics-based studies have identified multiple fruit ripening-related miRNAs, including 28 miRNAs expressed during tomato fruit ripening (Zuo et al, 2012), 24 miRNAs differentially expressed in wildtype and late-ripening sweet orange (Wu et al, 2016), and 82 miRNAs closely associated with banana ripening (Bi et al, 2015). (Zhang et al, 2018b).…”

Comparative Analysis of Fruit Ripening-Related miRNAs and Their Targets in Blueberry Using Small RNA and Degradome Sequencing

“…Numerous fruit development-associated miRNAs have been identified in fruit-producing plants such as apple [ 19 ], grape [ 20 , 21 ], citrus [ 26 ], peach [ 23 ]. In this study, 84 known miRNAs belonging to 28 families and 16 novel miRNAs were identified in blueberry fruit.…”

“…41 miRNAs were differentially expressed between white fruit stage and blue fruit stage ( Table 2 ), suggesting that they might be involved in controlling the cellular and developmental processes during fruit maturation in blueberry. By comparing vco-miRNAs and the ones from other fruit-producing plants such as apple [ 19 ], grape [ 20 , 21 ], citrus [ 26 ], peach [ 23 ], tomato [ 31 ] and cucurbits [ 32 ], it was found that 21 miRNA families are more common across these fruit-producing plants, suggesting that they might play crucial and fundamental roles in fruit development and maturation in diverse plants. However, 7 miRNAs (such as miR2118, miR2603, miR6149, miR6478, miR7122, miR7693 and miR845) were found only in blueberry fruits.…”

“…Most recently, it was reported that miR73 was involved in regulation of strawberry fruit ripening via targeting ABI5 transcript to affect ABA (Abscisic acid) signaling pathway [ 18 ]. With the application of the high-throughput sequencing technology in miRNA-related research, numerous miRNAs involved in fruit development and maturation have been identified in many fruit-producing species such as apple [ 19 ], grape [ 20 , 21 ], peach [ 22 , 23 ], pomegranate [ 24 ], date palm [ 25 ], sweet orange [ 26 ]. Meanwhile, degradome sequencing has been developed for genome-wide identification of miRNA target genes and has been successfully applied to reveal miRNA-mRNA target pairs during fruit development [ 19 , 26 ].…”

Identification of protoplast-isolation responsive microRNAs in Citrus reticulata Blanco by high-throughput sequencing

“…Additionally, because of its advantages in high throughput, high accuracy, and less sample, the deep sequencing has been widely used in many plants, such as Arabidopsis thaliana [ 23 , 24 ], Citrus sinensis [ 25 ], Cucumis sativus [ 26 ], Medicago truncatula [ 27 ], Oryza sativa [ 28 ], and Populus trichocarpa [ 29 ]. In citrus, deep sequencing studies has been reported in Citrus grandis [ 30 ], Citrus reticulata [ 31 , 32 ], Citrus sinensis [ 25 , 33 – 35 ], and Citrus trifoliate [ 36 ].…”