Yellowhorn (Xanthoceras sorbifolium), especially its varieties, is the red petal yellowhorn (X. sorbifolium var. purpurea), an important tree species with great ornamental value, and its flower petals change color throughout the flowering period. In this study, we mainly focused on the mechanism of the petal color change with transcriptomics and metabolomics data. A phased chromosome-scale assembly of the red petal yellowhorn genome was generated using the PacBio high-fidelity reads, Illumina short reads, and Phase genomics Proximo Hi-C data. The final de novo assembly yielded 533.67 Mb with a contig N50 of 5.42 Mb, and 27 501 protein-coding genes were predicted. Notably, an alternate haplotig assembly was also obtained. Furthermore, a variation database for the alleles within the genome was constructed. Subsequently, the expression pattern of flower pigmentation-related genes and allelic expression imbalance events were investigated. Apart from 6 genes involved in the anthocyanin biosynthesis pathway regulated by the activation of 15 MYB-bHLH-WD40s, the increased expression of senescence-related gene 1 (SRG1) and 2-oxoglutarate-dependent dioxygenase (DIOX5) might also result in decreasing content of lutein and increasing abundance of (E/Z)-phytoene, cyanidin-3-O-rutinoside, and cyanidin-3-O-sambubioside. These changes in genes and metabolites were most likely related to the petal color change in red petal yellowhorn. This phased chromosome-scale genome assembly provides more accurate genomic information for future molecular breeding and facilitates allele function studies of the red petal yellowhorn.

黄角树（Xanthoceras sorbifolium），特别是其品种，是红瓣黄角树（X. sorbifolium v​​ar. purpurea），是一种极具观赏价值的重要树种，其花瓣在整个花期都会变色。在本研究中，我们主要利用转录组学和代谢组学数据来研究花瓣颜色变化的机制。使用 PacBio 高保真读数、Illumina 短读数和 Phase Genomics Proximo Hi-C 数据生成红花瓣黄角犀基因组的定相染色体规模组装。最终的从头组装产生了 533.67 Mb，重叠群 N50 为 5.42 Mb，并预测了 27 501 个蛋白质编码基因。值得注意的是，还获得了替代单倍体组装。此外，还构建了基因组内等位基因的变异数据库。随后，研究了花色素沉着相关基因的表达模式和等位基因表达失衡事件。除了通过 15 个 MYB -bHLH-WD40的激活调节参与花青素生物合成途径的 6 个基因外，衰老相关基因 1 ( SRG1 ) 和 2-酮戊二酸依赖性双加氧酶 ( DIOX5 )表达的增加也可能导致叶黄素含量和 (E/Z)-八氢番茄红素、花青素-3- O-芸香苷和花青素-3- O-桑布双糖苷丰度增加。这些基因和代谢物的变化很可能与红花瓣黄角犀的花瓣颜色变化有关。这种分阶段的染色体规模基因组组装为未来的分子育种提供了更准确的基因组信息，并促进了红瓣黄角犀的等位基因功能研究。