Genome Encode Analyses Reveal the Basis of Convergent Evolution of Fleshy Fruit

Fleshy fruit evolved independently multiple times during flowering plant (angiosperm) history yet many utilize the hormone ethylene to regulate ripening. The fruitENCODE project highlights three evolutionary origins of ripening regulatory circuits. Eudicots that experienced recent whole-genome duplications (WGDs) evolved their regulatory systems using duplicated floral identity genes, while others without WGD utilised carpel senescence genes. The monocot banana uses both duplicated floral-identity and leaf senescence genes, forming two interconnected regulatory circuits. Epigenetic marks restricting the expression of key ripening regulators could be tracked to their direct ancestral orthologs. Our findings suggest that evolution of climacteric fruit was constrained by limited optimal signalling molecules and genetic and epigenetic materials, and WGD provided new resources for plants to circumvent this limit. Understanding these mechanisms could improve quality, yield and minimize postharvest losses.