A chromosome-level genome assembly of Alpinia officinarum Hance sheds new light on its evolution and flavonoid biosynthesis

Alpinia officinarum Hance, a medicinal and edible plant in the Zingiberaceae family, has applications in pharmaceuticals, food, nutraceuticals, spices, cosmetics, and fruit and vegetable preservation. However, the molecular mechanisms governing the biosynthesis of flavonoids, the primary bioactive compounds in A. officinarum, remain unclear. This study provided the first chromosome-grade genome assembly of A. officinarum, revealing it to be a triploid species with a 2.10-Gb haploid genome. Using integrated transcriptomic and metabolomic analysis, 107 flavonoid compounds selectively accumulated in the rhizome and prospective rhizome-specific flavonoid genes were identified. Gene-metabolite correlation analysis and weighted gene co-expression network analysis suggested that AobHLH94 was imperative to flavonoid biosynthesis regulation in the rhizome. Functional assays confirmed that AobHLH94 was a key regulator in the flavonoid biosynthesis pathway in A. officinarum and enhanced flavonoid accumulation in rice (Oryza sativa). We also discovered that AobHLH94 bound to the e-box elements (-CANNTG-) in the promoters of AoC4H and AoCHI genes, thereby upregulating their expression levels and enhancing flavonoid synthesis. Simultaneously, AobHLH94 indirectly modulated AoCHS. Our research explains the regulatory processes behind rhizome-specific flavonoid accumulation and provides relevant information for future A. officinarum improvement and breeding efforts.