Abstract
Cunninghamia lanceolata, a coniferous timber species solely endemic to China, possesses a natural variant known as Red-heart Chinese fir. This variant is renowned for the distinctive color of its heartwood, where the chestnut-brown xylem significantly enhances the economic value of Cunninghamia lanceolata. To uncover the mechanism of heartwood formation for Red-heart Chinese fir, we conducted a combined analysis of the metabolome and transcriptome during the radial alteration of mature Red-heart Chinese fir xylem. It was determined that the transition zone serves as a critical site for the transformation of primary metabolites to secondary metabolites without the xylem of mature red cedar. Additionally, we demonstrated that increasing tree age enriches the metabolites of the heartwood of red cedar to the downstream products of the biosynthetic pathway of flavonoids. Pelargonidin and Tricetin are the key substances for the colour development of the heartwood of mature Red-heart Chinese, and WRKY, MYB, LOB, GRAS, and AP2 are transcription factors that potentially play pivotal roles in regulating flavonoid biosynthesis. This study provides novel insights into the molecular regulatory mechanisms underlying heartwood formation in forest trees.