Effects of the deletion of tomato m6A demethylase SlALKBH2 on m6A RNA methylomes during the initiation of fruit ripeing.

We conducted m6A-seq on the fruits of both wild-type and slalkbh2 mutants (slalkbh2-25 and slalkbh2-28) at the mature green (MG) stage, which represents the onset of fruit ripening, to identify putative SlALKBH2 targets. Approximately 10,000 high-confidence m6A peaks were identified in the fruit samples of wild-type, slalkbh2-25, and slalkbh2-28, predominantly situated near the stop codons and in the 3’ UTR regions of gene transcripts. Analysis of differential m6A methylomes revealed 117 and 79 hypermethylated m6A peaks in slalkbh2-25 and slalkbh2-28, respectively, along with only 8 and 15 hypomethylated m6A peaks compared to the wild-type. This suggests a notable increase in total m6A methylation under SlALKBH2 deficiency during ripening initiation. These hypermethylated m6A peaks located in numerous gene transcripts that potentially serve as targets of SlALKBH2. Tomato fruits were harvested from the wild-type, slalkbh2-25, and slalkbh2-28 mutants at the MG (39 dpa) stage and then subjected to m6A-seq analysis, in triplicate, using the Illumina Hiseq X system.