Genome-scale mRNA and miRNA transcriptomic insights into the regulatory mechanism of cucumber corolla opening

'Corollas and spines' is an important trait for fresh market cucumber. In a unique cucumber line, '6457', the super ovary is much larger and corolla opening is delayed by 4-5 days, thus the resulting fruit has a flower that remains on the tip, which has a high commodity value. In this study, to better understand the molecular basis of corolla opening, mRNA and miRNA transcriptome analyses were performed during corolla development of the super and normal ovaries. A total of 234 differentially expressed miRNAs (DEMs) and 291 differentially expressed target genes (DE-target genes) were identified from four developmental stages, and the greatest number of DEMs was found at the yellow bud stage. Thirty of the DE-target genes were regulated by more than five DEMs, among which, CsHD-Zip was regulated by 28 DEMs, followed by DD2X (18). In addition, the expression patterns of miRNA_104, miRNA_157, miRNA_349, miRNA_242, and miRNA_98 were similar during corolla development, and they shared the same target gene, CsCuRX. Moreover, several critical candidate DEMs and DE-target genes were characterized and profiled by a qRT-PCR experiment. Three of the miRNAs, miRNA_157-CsCuRX, miRNA_411-CsGH3.6, and miRNA_161/297/257-CsHD-Zip, might be responsible for corolla opening in the cucumber super ovary. This integrated study on the transcriptional and post-transcriptional profiles can provide insights into the molecular regulatory mechanism underlying corolla opening in the cucumber.