Comparative genomic analysis of Sanghuangporus sanghuang with other Hymenochaetaceae species

• Published in: Brazilian journal of microbiology Vol. 55; no. 1; pp. 87 - 100
• Main Authors: Wang, Xinyue, Wei, Jiansheng, Liu, Zhenwen, Wang, Yi, Yuan, Xiaolong, Wang, Dong, Niu, Junmei, Yang, Yan, Zhou, Jing
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01.03.2024; Springer Nature B.V
• Subjects: Anticancer properties; Bacterial; Biomedical and Life Sciences; Biosynthesis; Food Microbiology; Fungal and Virus Molecular Biology - Research Paper; Fungi; Gene clusters; Genomes; Genomic analysis; Hymenochaetaceae; Life Sciences; Liquid chromatography; Mass spectrometry; Mass spectroscopy; Medical Microbiology; Metabolites; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Mycology; Non-ribosomal peptide synthase; Peptide synthase; Phenylalanine; Polyphenols; Polysaccharides; Saccharides; Sanghuangporus; Secondary metabolites; Taxonomic significance; Terpenes; Transcriptomes; Secondary metabolite; Hymenochaetaceae; Comparative genomic analysis; Sanghuangporus sanghuang
• ISSN: 1517-8382; 1678-4405; 1678-4405
• DOI: 10.1007/s42770-023-01212-x

Sanghuangporus sanghuang is a medicinal macrofungus with antioxidant and antitumor activities, and it is enriched with secondary metabolites such as polysaccharides, terpenes, polyphenols, and styrylpyrone compounds. To explore the putative core genes and gene clusters involved in sanghuang biosynthesis, we sequenced and assembled a 40.5-Mb genome of S. sanghuang (SH1 strain). Using antiSMASH, local BLAST, and NCBI comparison, 12 terpene synthases (TPSs), 1 non-ribosomal peptide synthase, and five polyketide synthases (PKSs) were identified in SH1. Combining the transcriptome analysis with liquid chromatography mass spectrometry-ion trap-time of flight analysis, we determined that ShPKS1, one phenylalanine aminolyase (ShPAL), and one P450 monooxygenase (ShC4H1) were associated with hispidin biosynthesis. Structural domain comparison indicated that ShPKS2 and ShPKS3 are involved in the biosynthesis of orsellinic acid and 2-hydroxy-6-methylbenzoic acid, respectively. Furthermore, comparative genomic analysis of SH1 with 14 other fungi from the Hymenochaetaceae family showed variation in the number of TPSs among different genomes, with Coniferiporia weirii exhibiting only 9 TPSs and Inonotus obliquus having 20. The number of TPSs also differed among the genomes of three strains of S. sanghuang , namely Kangneng (16), MS2 (9), and SH1 (12). The type and number of PKSs also varied among species and even strains, ranging from two PKSs in Pyrrhoderma noxium to five PKSs in S. sanghuang SH1. Among the three strains of S. sanghuang , both the structural domains and the number of PKSs in strains MS2 and SH1 were consistent, whereas strain Kangneng exhibited only four PKSs and lacked the PKS with the structural domain KS-AT-DH-KR-ACP. Additionally, Sanghuangporus species exhibited more similar PKSs to Inonotus , with higher gene similarity around five PKSs, while showing differences from those of other fungi in the same family, including Phellinus lamaoensis . This result supports the independent taxonomic significance of the genus Sanghuangporus to some extent.