Chromatin structure plays a critical role in the regulation of dynamic gene expression in response to different developmental and environmental cues, but as yet their involvement in fruit ripening is not well understood. Here, we profile seven histone modifications in the woodland strawberry (Fragaria vesca) genome and analyze the histone modification signatures during ripening. Collectively, segments painted by the seven marks cover ~85% of the woodland strawberry genome. We report an eight-state chromatin structure model of the woodland strawberry based on the above histone marks, which reveals a diverse chromatin environment closely associated with transcriptional apparatus. Upon this model we build a chromatin-centric annotation to the strawberry genome. Expression of many genes essential for fruit ripening, such as abscisic acid catabolism, anthocyanin accumulation and fruit softening, are associated with shifts of active genic states and polycomb-associated chromatin states. Particularly, the expression levels of ripening-related genes are well correlated with histone acetylation, indicating a regulatory role of histone acetylation in strawberry ripening. Our identification of the chromatin states underpinning genome expression during fruit ripening not only elucidates the coordination of different pathways of morphological and metabolic development but also provides a framework to understand the signals that regulate fruit ripening.

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