iCUT&Tag-based pan-fruit epigenomic profiling identifies recurrent H3K9 acetylation enrichment during fleshy fruit...

Fleshy fruit ripening involves broadly convergent physiological changes across phylogenetically distinct species, but the extent to which shared chromatin-level mechanisms underlie this convergence is poorly understood, in part because of technical challenges posed by metabolite-rich fruit tissues. Here, we developed iCUT&Tag, an improved chromatin profiling method that requires as few as 500 nuclei, and used it to generate histone-modification profiles of 12 fruit species from nine botanical families, demonstrating its broad application to metabolite-rich fruit tissues. Comparative profiling of climacteric (tomato and apple) and non-climacteric (citrus and strawberry) fruit identified H3K9 acetylation (H3K9ac) as a recurrently enriched chromatin feature associated with the activation of ripening-linked genes, regardless of the dominant hormonal system. In tomato, SlHDA1 loss was accompanied by premature H3K9ac accumulation at ripening-associated loci, whereas in strawberry, FaHDA19 silencing was associated with increased H3K9ac at transcriptionally activated ripening-related loci. Comparative genetic analyses suggested a bipartite regulatory architecture: H3K9ac-mediated permissive chromatin state appears to be conserved across lineages, but productive transcription also requires species-specific transcription factor activity-SlNOR in tomato and FaMYB10 in strawberry-to drive phenotypically convergent ripening. Our study provides a validated technological framework for plant epigenomics and identifies a recurrent associated chromatin-level feature that may underlie the convergent evolution of fleshy fruit ripening.