Effects of the deletion of tomato m6A demethylase SlALKBH2 on transcriptome-wide gene expression profiles during the initiation of fruit ripeing.

RNA-seq analysis was conducted to elucidate the transcriptome-wide gene expression differences between the wild-type and the slalkbh2 mutants (slalkbh2-25 and slalkbh2-28). In comparison to the wild-type, we identified 602 downregulated genes and 833 upregulated genes in the slalkbh2-25 mutant, as well as 556 downregulated genes and 470 upregulated genes in the slalkbh2-28 mutant (with a cutoff criterion of FPKM fold change = 1.5 and P value < 0.05). Consequently, 281 downregulated genes and 126 upregulated genes were consistently identified in both slalkbh2 mutants, which were considered differentially expressed genes. 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 RNA-seq analysis, in triplicate, using the Illumina Hiseq X system.