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, yet the extent to which shared chromatin-level mechanisms underlie this convergence remains poorly understood, partly due to technical challenges posed by metabolite-rich fruit tissues. Here, we develop iCUT&Tag, an improved chromatin profiling method requiring as few as 500 nuclei, and apply it to generate histone modification profiles across 12 fruit species spanning 9 botanical families, demonstrating its broad application in metabolite-rich fruit tissues. Comparative profiling of climacteric (tomato, apple) and non-climacteric (citrus, strawberry) fruit identifies H3K9 acetylation (H3K9ac) as a recurrently enriched chromatin feature associated with ripening-linked gene activation, regardless of the dominant hormonal system. In tomato, SlHDA1 loss is accompanied by premature H3K9ac accumulation at ripening-associated loci, whereas in strawberry, FaHDA19 silencing is associated with increased H3K9ac at transcriptionally activated ripening-related loci. Mechanistically, comparative genetic analyses suggest a bipartite regulatory architecture: H3K9ac-mediated permissive chromatin state appears conserved across lineages, yet productive transcription additionally 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.