Epigenomic reprograming underlies internodal developmental heterogeneity in rapidly elongating bamboo shoots

Shoots of Ma bamboo (Dendrocalamus latiflorus) are widely valued for their high yield, extended harvest period, and nutritional richness. Despite their economic and ecological importance, the epigenetic mechanisms governing shoot development remain largely unexplored. Here, we integrated cytological, transcriptomic, proteomic, and multi-epigenomic analyses to characterize the developmental gradient from the basal mature region to the apical proliferative zone. Cytological observation revealed a transition from structurally reinforced cells at the basal internode to actively dividing cells at the apical internode. Genome-wide bisulfite sequencing showed a progressive increase in CG methylation and a decrease in CHG methylation within gene bodies, accompanied by promoter-enriched CHH methylation that was positively correlated with transcriptional activation. Chromatin profiling demonstrated elevated H3K36me3 active marks and enhanced chromatin accessibility at the apical internode. In contrast, N6-methyladenosine (m6A) levels declined from the basal internode to the apical internode, coinciding with the activation of growth-related genes. Using nanopore-based sequencing, we further found that poly(A) tail lengths (PALs) were positively associated with m6A accumulation and gene body CG methylation but negatively correlated with H3K27me3 and H3K36me3 levels. Together, this study establishes an integrated epigenetic framework in which DNA methylation, histone modifications, m6A, and PAL dynamics collectively fine-tune transcription and translation during bamboo shoot elongation. Our study provides a multi-epigenomic model for D. latiflorus development and broadens our understanding of epigenetic coordination in a monocot, thereby offering valuable insights for future genetic improvement.