Identification of miRNAs involved in fruit ripening in Cavendish bananas by deep sequencing

Abstract

BackgroundMicroRNAs (miRNAs) are a family of non-coding small RNAs that play an important regulatory role in various biological processes. Previous studies have reported that miRNAs are closely related to the ripening process in model plants. However, the miRNAs that are closely involved in the banana fruit ripening process remain unknown.MethodsHere, we investigated the miRNA populations from banana fruits in response to ethylene or 1-MCP treatment using a deep sequencing approach and bioinformatics analysis combined with quantitative RT-PCR validation.ResultsA total of 125 known miRNAs and 26 novel miRNAs were identified from three libraries. MiRNA profiling of bananas in response to ethylene treatment compared with 1-MCP treatment showed differential expression of 82 miRNAs. Furthermore, the differentially expressed miRNAs were predicted to target a total of 815 target genes. Interestingly, some targets were annotated as transcription factors and other functional proteins closely involved in the development and the ripening process in other plant species. Analysis by qRT-PCR validated the contrasting expression patterns between several miRNAs and their target genes.ConclusionsThe miRNAome of the banana fruit in response to ethylene or 1-MCP treatment were identified by high-throughput sequencing. A total of 82 differentially expressed miRNAs were found to be closely associated with the ripening process. The miRNA target genes encode transcription factors and other functional proteins, including SPL, APETALA2, EIN3, E3 ubiquitin ligase, β-galactosidase, and β-glucosidase. These findings provide valuable information for further functional research of the miRNAs involved in banana fruit ripening.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1995-1) contains supplementary material, which is available to authorized users.

Cold stress responsive microRNAs and their targets in Musa balbisiana

“…In this study, the length of these 32 potential novel miRNA precursors ranged from 44 to 273 nt, which was close to the length of miRNA precursors in Cavendish banana fruits [22] . Except for mba-miR19 and mba-miR22, the minimum free energy (MFE) folding value of these miRNA precursors ranged from -92.5.1 kJ$mol -1 to -841.0 kJ$mol -1 , with an average of 282.2 kJ$mol -1 , which was consistent with the previously published low MFE characteristics of miRNA [33] and much higher than the published sequencing data for miRNA precursors from banana fruit (194.6 kJ$mol -1 ) [22] . In addition, Meyers et al reported the existence of complementary sequences increases the authenticity of predicted novel miRNAs [27] .…”

“…Although miRNAs in bananas were identified in previous studies [15,[19][20][21][22][23] , compared with the number of identified miRNAs in other plants such as rice and maize, the number of known miRNAs in banana is still very low. Moreover, there is no report on cold-responsive miRNAs from M. balbisiana, a wild banana species.…”

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).…”

Dietary plant miRNAs as an augmented therapy: cross-kingdom gene regulation

“…Most of the miRNAs have regulatory roles at endogenous level. The development of fruits and their ripening is also reported to be regulated by endogenous miRNAs in tomato [6] and banana [7].…”