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Background  Epigenetic mark such as DNA methylation plays pivotal roles in regulating ripening of both climacteric and non-climacteric fruits. However, it remains unclear whether mRNA m 6 A methylation, which has been shown to regulate ripening of the tomato, a typical climacteric fruit, is functionally conserved for ripening control among different types of fruits.    Results  Here we show that m 6 A methylation displays a dramatic change at ripening onset of strawberry, a classical non-climacteric fruit. The m 6 A modification in coding sequence (CDS) regions appears to be ripening-specific and tends to stabilize the mRNAs, whereas m 6 A around the stop codons and within the 3′ untranslated regions is generally negatively correlated with the abundance of associated mRNAs. We identified thousands of transcripts with m 6 A hypermethylation in the CDS regions, including those of  NCED5 ,  ABAR , and  AREB1  in the abscisic acid (ABA) biosynthesis and signaling pathway. We demonstrate that the methyltransferases MTA and MTB are indispensable for normal ripening of strawberry fruit, and MTA-mediated m 6 A modification promotes mRNA stability of  NCED5  and  AREB1 , while facilitating translation of  ABAR .    Conclusion  Our findings uncover that m 6 A methylation regulates ripening of the non-climacteric strawberry fruit by targeting the ABA pathway, which is distinct from that in the climacteric tomato fruit.    Supplementary Information  The online version contains supplementary material available at 10.1186/s13059-021-02385-0.

N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner