Abstract The genus Zingiber represents an economically important group within Zingiberaceae, distinguished by its aromatic and bioactive rhizomes. Zingiber striolatum Diels is an endemic Chinese medicinal and edible plant highly valued for its flower buds, which are rich in natural red pigments (YRP). Here, we present the first haplotype-resolved, chromosome-scale assembly of ‘Ziyanghe,’ a purplish-red-bud cultivar widely grown in Guizhou Province. The triploid genome was resolved into three haplotypes: subA (2.80 Gb), subB1 (2.66 Gb), and subB2 (2.64 Gb), with the latter two exhibiting strong collinearity. Comparative analysis across five Zingiberaceae genomes revealed a family-specific whole-genome duplication (WGD) approximately 52.5 million years ago (Mya) and lineage-specific bursts of long terminal repeat retrotransposon (LTR-RTs) occurring between 0.5 and 0.66 Mya. These events likely contributed to substantial genome expansion in Z. striolatum. Evolutionary analysis of gene families suggested parallel subgenome adaptation to montane shade environments and rhizome-specific volatile biosynthesis. Metabolomic profiling identified cyanidin-3-O-glucoside, peonidin-3-O-glucoside, delphinidin-3-O-glucoside, and delphinidin-3-O-rutinoside as the major YRP components, with quercetin-3-O-glucoside functioning as a co-pigment. Integrated multi-omics analysis provides a preliminary molecular framework for YRP biosynthesis. This high-quality genomic resource significantly enhances phylogenomic understanding of Zingiberaceae and provides a foundation for the genetic improvement and metabolic engineering of anthocyanin biosynthesis in this species.
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