Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches

Auxin has long been known as a critical phytohormone that regulates fruit development in plants. However, due to the lack of an enlarged ovary wall in the model plants Arabidopsis and rice, the molecular regulatory mechanisms of fruit division and enlargement remain unclear. In this study, we performed small RNA sequencing and degradome sequencing analyses to systematically explore post-transcriptional regulation in the mesocarp at the hard core stage following treatment of the peach (Prunus persica L.) fruit with the synthetic auxin α-naphthylacetic acid (NAA). Our analyses identified 24 evolutionarily conserved miRNA genes as well as 16 predicted genes. Experimental verification showed that the expression levels of miR398 and miR408b were significantly upregulated after NAA treatment, whereas those of miR156, miR160, miR166, miR167, miR390, miR393, miR482, miR535 and miR2118 were significantly downregulated. Degradome sequencing coupled with miRNA target prediction analyses detected 119 significant cleavage sites on several mRNA targets, including SQUAMOSA promoter binding protein-like (SPL), ARF, (NAM, ATAF1/2 and CUC2) NAC, Arabidopsis thaliana homeobox protein (ATHB), the homeodomain-leucine zipper transcription factor revoluta(REV), (teosinte-like1, cycloidea and proliferating cell factor1) TCP and auxin signaling F-box protein (AFB) family genes. Our systematic profiling of miRNAs and the degradome in peach fruit suggests the existence of a post-transcriptional regulation network of miRNAs that target auxin pathway genes in fruit development.