Genome-wide identification and characterization of long noncoding RNAs involved in apple fruit development and ripening

Abstract

Long noncoding RNAs (lncRNAs) have been reported to play a regulatory role during fresh fruit ripening. However, the functions of lncRNAs during apple fruit ripening have received relatively little attention. Here, we performed strand-specific RNA-seq and lncRNA identification at four developmental stages of ‘Pinova’ apple (Malus domestica) fruits. A total of 12,570 differentially expressed mRNAs and 3571 differentially expressed lncRNAs were identified among the four fruit developmental stages. Co-localization and co-expression principles were used to explore lncRNA–mRNA target relationships. Interestingly, most lncRNA targeted mRNAs appeared to participate in various fruit ripening pathways involving the cell wall, photosystems, biosynthesis and metabolic processes. To further explore the potential correlations between lncRNAs and mRNAs, a group of 8239 mRNAs and 3566 lncRNAs were used for cluster and co-expression network analysis, and 15 clusters were obtained. Four different clusters were selected for functional analysis and the construction of co-expression networks. mRNAs differentially expressed in the early ripening stages were mainly involved with photosynthesis, whereas those differentially expressed at later stages were associated with metabolic pathways, consistent with the dynamic accumulation of metabolites in ripening fruits. Based on these analyses, we identified a series of genes that play vital roles in fruit ripening and are regulated by lncRNAs; these included IAA32, SAUR36, and PA2. qRT-PCR analysis also validated these regulatory relationships. Previous studies have shown that lncRNAs can repress miRNA–mRNA targeting by acting as endogenous target mimics (eTMs). We therefore investigated the involvement of lncRNAs in miRNA targeting of mRNA, and eTMs of lncRNAs involved in the targeting of GAMYB (transcriptional factor in anthocyanin synthesis) by miR159 were identified. These results provide insight for future studies of lncRNA regulation during apple fruit ripening.