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Summary: Understanding the molecular regulation of plant cold response is the basis for cold resistance germplasm improvement. Here, we revealed that the apple histone deacetylase MdHDA6 can perform histone deacetylation on cold‐negative regulator genes and repress their expression, leading to the positive regulation of cold tolerance in apples. Moreover, MdHDA6 directly interacts with the transcription factor MdTCP15. Phenotypic analysis of MdTCP15 transgenic apple lines and wild types reveals that MdTCP15 negatively regulates cold tolerance in apples. Furthermore, we found that MdHDA6 can facilitate histone deacetylation of MdTCP15 and repress the expression of MdTCP15, which positively contributes to cold tolerance in apples. Additionally, the transcription factor MdTCP15 can directly bind to the promoter of the cold‐negative regulator gene MdABI1 and activate its expression, and it can also directly bind to the promoter of the cold‐positive regulator gene MdCOR47 and repress its expression. However, the co‐expression of MdHDA6 and MdTCP15 can inhibit MdTCP15‐induced activation of MdABI1 and repression of MdCOR47, suggesting that MdHDA6 suppresses the transcriptional regulation of MdTCP15 on its downstream genes. Our results demonstrate that histone deacetylase MdHDA6 plays an antagonistic role in the regulation of MdTCP15‐induced transcriptional activation or repression to positively regulate cold tolerance in apples, revealing a new regulatory mechanism of plant cold response. [ABSTRACT FROM AUTHOR]

• Herein, we identify lncRNAs involved in four stages from early to fully-ripening stage of apple (Malus domestica) fruit. • 12,570 differentially expressed mRNAs and 3571 differentially expressed lncRNAs were identified. • The targeted relationship of lncRNA-mRNA was analyzed by using co-location, co-expression, and cluster networks. • Three lncRNAs (TCONS_00131720, TCONS_00025525, TCONS_00032426) were identified to target the mRNAs of IAA32, SAUR36, and PA2 which were involved in apple fruit development process. • The related lncRNAs (TCONS_00060619, TCONS_00178112, TCONS_00065854) were analyzed by combining with miRNAs data and GAMYB-miR159a regulation was identified which might related to apple coloring. 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. [ABSTRACT FROM AUTHOR]