Transcriptome and methylome analysis reveals effects of ripening on and off the vine on flavor quality of tomato fruit

•Off-vine ripened tomatoes have inferior flavor than fruit ripe on vine.•Low sugar/acid ratio and changes in volatiles causes flavor loss of tomatoes.•Transcripts related to flavor, ethylene and auxin metabolism show major difference.•Off-vine ripened tomatoes have reduced DNA methylation level than fruit ripe on vine.