Key Laboratory for Enzyme and Enzyme-Like Material Engineering of Heilongjiang, College of Life Science, Northeast Forestry University, Harbin, 150040, Heilongjiang, China.
Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
BMC Genomics. 2022 Apr 20;23(1):314. doi: 10.1186/s12864-022-08511-x.
Inonotus obliquus is an important edible and medicinal mushroom that was shown to have many pharmacological activities in preclinical trials, including anti-inflammatory, antitumor, immunomodulatory, and antioxidant effects. However, the biosynthesis of these pharmacological components has rarely been reported. The lack of genomic information has hindered further molecular characterization of this mushroom.
In this study, we report the genome of I. obliquus using a combined high-throughput Illumina NovaSeq with Oxford Nanopore PromethION sequencing platform. The de novo assembled 38.18 Mb I. obliquus genome was determined to harbor 12,525 predicted protein-coding genes, with 81.83% of them having detectable sequence similarities to others available in public databases. Phylogenetic analysis revealed the close evolutionary relationship of I. obliquus with Fomitiporia mediterranea and Sanghuangporus baumii in the Hymenochaetales clade. According to the distribution of reproduction-related genes, we predict that this mushroom possesses a tetrapolar heterothallic reproductive system. The I. obliquus genome was found to encode a repertoire of enzymes involved in carbohydrate metabolism, along with 135 cytochrome P450 proteins. The genome annotation revealed genes encoding key enzymes responsible for secondary metabolite biosynthesis, such as polysaccharides, polyketides, and terpenoids. Among them, we found four polyketide synthases and 20 sesquiterpenoid synthases belonging to four more types of cyclization mechanism, as well as 13 putative biosynthesis gene clusters involved in terpenoid synthesis in I. obliquus.
To the best of our knowledge, this is the first reported genome of I. obliquus; we discussed its genome characteristics and functional annotations in detail and predicted secondary metabolic biosynthesis-related genes, which provides genomic information for future studies on its associated molecular mechanism.
桦褐孔菌是一种重要的食用和药用蘑菇，在临床前试验中显示出许多药理活性，包括抗炎、抗肿瘤、免疫调节和抗氧化作用。然而，这些药理成分的生物合成很少有报道。缺乏基因组信息阻碍了对这种蘑菇的进一步分子特征描述。
本研究使用 Illumina NovaSeq 与 Oxford Nanopore PromethION 测序平台相结合的高通量测序技术，报道了桦褐孔菌的基因组。从头组装的 38.18 Mb 桦褐孔菌基因组包含 12525 个预测的蛋白编码基因，其中 81.83%的基因与公共数据库中其他基因具有可检测的序列相似性。系统发育分析表明，桦褐孔菌与 Hymenochaetales 目中的 Fomitiporia mediterranea 和 Sanghuangporus baumii 具有密切的进化关系。根据与繁殖相关的基因分布，我们预测该蘑菇具有四极异宗配合的繁殖系统。桦褐孔菌基因组编码了一系列参与碳水化合物代谢的酶，同时还编码了 135 种细胞色素 P450 蛋白。基因注释揭示了编码多糖、聚酮化合物和萜类化合物等次生代谢物生物合成关键酶的基因，其中我们发现了桦褐孔菌中属于四种不同环化机制的四个聚酮合酶和 20 个倍半萜合酶，以及 13 个可能参与萜类化合物合成的生物合成基因簇。
据我们所知，这是桦褐孔菌的首个基因组报告；我们详细讨论了其基因组特征和功能注释，并预测了次生代谢物生物合成相关基因，为进一步研究其相关分子机制提供了基因组信息。
