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

Amauroderma rugosum 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 Amauroderma rugosum (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 A. rugosum and Ganoderma sinense 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 Amauroderma 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，可用于抗炎、利尿、改善胃部不适以及癌症预防。本研究报道了保藏编号为ACCC 51706的皱盖假芝的基因组资源，以助力解析其生物学特性并探索其活性成分的合成通路。研究人员提取了该菌株的基因组DNA，采用Illumina HiSeq X Ten与PacBio Sequel I测序平台进行测序。最终组装获得的基因组大小为40.66 Mb，支架序列N50长度达36.6 Mb，共编码10181个推定预测基因，其中6931个基因完成了功能注释。系统发育基因组学分析结果显示，皱盖假芝与紫芝（Ganoderma sinense）未聚类为同一分支，紫芝与多孔菌科（Polyporaceae）物种聚为一类。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。本研究是首个针对假芝属（Amauroderma）物种的基因组级别的组装与注释研究。新型次生代谢产物生物合成基因簇的鉴定，将推动未来的药理学研究与新型活性化合物的研发工作。