Genome sequencing and annotation and phylogenomic analysis of the medicinal mushroom <i>Amauroderma rugosum</i>, a traditional medicinal species in the family Ganodermataceae

<i>Amauroderma rugosum</i> is one of the traditional Chinese medicinal mushrooms and is used to reduce inflammation, treat diuretic and upset stomach, and prevent cancer. Here, we present a genomic resource of <i>Amauroderma rugosum</i> (ACCC 51706) for further understanding its biology and exploration of the synthesis pathway of bioactive compounds. Genomic DNA was extracted and then subjected to Illumina HiSeq X Ten and PacBio Sequel I sequencing. The final genome is 40.66 Mb in size, with an N₅₀ scaffold size of 36.6 Mb, and encodes 10 181 putative predicted genes. Among them, 6931 genes were functionally annotated. Phylogenomic analysis suggested that <i>A. rugosum</i> and <i>Ganoderma sinense</i> were not clustered together into a group and the latter was grouped with the Polyporaceae. Further, we also identified 377 carbohydrate-active enzymes (CAZymes) and 15 secondary metabolite biosynthetic gene clusters. This is the first genome-scale assembly and annotation for an <i>Amauroderma</i> species. The identification of novel secondary metabolite biosynthetic gene clusters would promote pharmacological research and development of novel bioactive compounds in the future.皱盖假芝（Amauroderma rugosum）是中国传统药用真菌之一，可用于抗炎、利尿、缓解胃脘不适，并预防癌症。本研究报道了皱盖假芝（Amauroderma rugosum）菌株ACCC 51706的基因组资源，以期进一步解析其生物学特性，并探索其生物活性化合物的合成通路。研究人员提取了该菌株的基因组DNA，随后采用Illumina HiSeq X Ten与PacBio Sequel I平台进行测序。最终组装的基因组大小为40.66 Mb，支架序列N50长度为36.6 Mb，共编码10181个推定基因。其中，6931个基因完成了功能注释。系统基因组学分析结果显示，皱盖假芝与紫芝（Ganoderma sinense）并未聚为同一分支，紫芝与多孔菌科（Polyporaceae）真菌聚为一类。此外，本研究还鉴定出377个碳水化合物活性酶（carbohydrate-active enzymes, CAZymes）以及15个次生代谢产物生物合成基因簇。这是假芝属（Amauroderma）物种首个完成全基因组组装与功能注释的基因组资源。本次鉴定得到的新型次生代谢产物生物合成基因簇，将为未来的药理学研究及新型生物活性化合物的研发提供重要支撑。