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. Overall design: 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.