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MicroRNA (miRNA) are important regulators of gene expression. Plant miRNA have been reported both to target and to be regulated by transcription factors, however, genomic distribution of miRNA, transcription factor targets for miRNA, transcription factor binding sites (TFBS) of miRNA promoters and their regulatory networks have not been systematically mapped in banana. In this study, genome-wide annotation of miRNA in the most recently published banana genome sequence was used to predict miRNA promoter regions and to map TFBS of miRNA genes. A total of 183 mature miRNAs, comprising 144 orthologous miRNA and 39 Musa-specific miRNA were predicted. Following this, banana root degradome data was used to confirm miRNA targets and the transcription factor targets were placed into a predicted network together with their targeting miRNA using cytoscape. Gene ontology of the 20 transcription factors among the predicted miRNA targets, showed predominance for auxin-activated signalling and developmental processes. Profiling of TFBS motifs across miRNA promoter regions showed that binding site motifs for TCP, AP2/ERF, GATA, NF-YB, DOF, B3, bZIP, trihelix, ZF-HD, bHLH and Dehydrin transcription factor families are abundant in the Musa acuminata genome. Finally, we propose a regulatory network for the miRNA families miR156, miR164, miR166, miR171, miR319, miR396, miR528, mac-miR-new14 and mac-miR-new20 and their respective transcription factor targets. [ABSTRACT FROM AUTHOR]

In African oil palm, the formation of fruit relies on the successful progression of a 2- to 3-year phase of development of inflorescences, in particular the female inflorescence. In this study, we investigated microRNA expression in female inflorescences at two stages of floral development corresponding to the emergence of floral meristems and to the formation of floral organs. High-throughput sequencing data from messenger RNA (mRNA), small RNA, and RNA degradome libraries were used to predict and quantify orthologous and oil palm-specific microRNAs (miRNAs) and their targets. The expression of selected miRNA candidates was validated by quantitative RT-PCR. From female inflorescences, we assembled a reference transcriptome, which allowed us to identify the miRNA precursor sequences and the putative mRNA targets in oil palm. As validated by degradome analysis, we confirmed the cleavage patterns of mRNA targets for oil palm miRNAs. We report here differential gene expression patterns of 18 orthologous miRNA families and their targets in oil palm female inflorescences. Of these, we identified two distinct subsets of orthologous miRNAs that showed inverse expression patterns in female inflorescence of oil palm. We also predicted 15 putative oil palm-specific miRNAs, of which three were validated using quantitative RT-PCR. In oil palm, distinct subsets of miRNAs were differentially expressed at the stage when the floral meristems emerge and at the stage when the floral organs form. These miRNAs are likely to act in concert with their mRNA targets to regulate the early phase of floral organ establishment. [ABSTRACT FROM AUTHOR]