Phellinus gilvus (Schwein.) Pat, a species of ‘Sanghuang’, has been well-documented for various medicinal uses, but the genome information and active constituents are largely unknown. Here, we sequenced the whole-genome of P. gilvus, identified phenylpropanoids as its key anti-cancer components, and deduced their biosynthesis pathways. A 41.11-Mb genome sequence was assembled and the heatmap created with high-throughput chromosome conformation capture techniques data suggested all bins could be clearly divided into 11 pseudochromosomes. Cellular experiments showed that P. gilvus fruiting body was more effective to inhibit hepatocellular carcinoma cells than mycelia. High resolution electrospray ionization mass spectroscopy (HR-ESI-MS) analysis revealed P. gilvus fruiting body was rich in phenylpropanoids, and several unique phenylpropanoids in Phellinus spp. exhibited potent anti-carcinogenesis activity. Based on genomic, HR-ESI-MS information and differentially expressed genes in transcriptome analysis, we deduced the biosynthesis pathway of four major phenylpropanoids in P. gilvus. Transcriptome analysis revealed the deduced genes expressions were synergistically changed with the production of phenylpropanoids. The optimal candidate genes of phenylpropanoids’ synthesis pathway were screened by molecular docking analysis. Overall, our results provided a high-quality genomic data of P. gilvus and inferred biosynthesis pathways of four phenylpropanoids with potent anti-carcinogenesis activities. These will be a valuable resource for further genetic improvement and effective use of the P. gilvus.

桑黄（Phellinus gilvus（Schwein。）Pat）是一种“桑黄”物种，已被广泛用于各种医学用途，但基因组信息和活性成分在很大程度上尚不清楚。在这里，我们对P. gilvus的全基因组进行了测序，确定了苯丙烷类化合物为其关键的抗癌成分，并推导了它们的生物合成途径。组装了一个41.11-Mb基因组序列，并使用高通量染色体构象捕获技术创建了热图，数据表明所有bin均可清楚地分为11个假染色体。细胞实验表明，P。gilvus子实体比菌丝体更有效地抑制肝癌细胞。高分辨率电喷雾电离质谱（HR-ESI-MS）分析显示P. gilvus子实体富含苯丙类化合物，而桑黄属中有几种独特的苯丙类化合物。表现出强大的抗癌活性。基于基因组，HR-ESI-MS信息和转录组分析中差异表达的基因，我们推导了P. gilvus中的四种主要苯基丙烷的生物合成途径。转录组分析表明，推导的基因表达与苯丙烷类化合物的产生协同变化。通过分子对接分析筛选了苯丙烷类化合物合成途径的最佳候选基因。总体而言，我们的结果提供了P. gilvus的高质量基因组数据。并推断出具有有效抗癌活性的四种苯基丙烷的生物合成途径。这些将是进一步遗传改良和有效利用吉氏疟原虫的宝贵资源。