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Comparative genomic analysis of Sanghuangporus sanghuang with other Hymenochaetaceae species

  • Bacterial, Fungal and Virus Molecular Biology - Research Paper
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Abstract

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.

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Data Availability

This study project is available under NCBI BioProject accession number PRJNA960849 and BioSample accession number SAMN34331867. The complete genome assembly of Sanghuangporus sanghuang SH1 is available under GenBank accession number JASFXP000000000.

Abbreviations

C. sulphurascens:

Coniferiporia sulphurascens

C. weirii:

Coniferiporia weirii

F. mediterranea:

Fomitiporia mediterranea

G. junonius:

Gymnopilus junonius

I. hispidus:

Inonotus hispidus

I. obliquus:

Inonotus obliquus

Pd. pouzarii:

Phellinidium pouzarii

Pn. lamaoensis:

Phellinus lamaoensis

Pl. nigrolimitatus:

Phellopilus nigrolimitatus

Po. pini:

Porodaedalea pini

Py. noxium:

Pyrrhoderma noxium

S. baumii:

Sanghuangporus baumii

S. sanghuang:

Sanghuangporus sanghuang

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Acknowledgements

We acknowledge TopEdit LLC for the linguistic editing and proofreading during the preparation of this manuscript.

Funding

This work was supported by a grant from the National Natural Science Foundation of China (31860177), General Project of Basic Research Program in Yunnan Province (202101AT070218), the Reserve Talents for Young and Middle-aged Academic and Technical Leaders of the Yunnan Province (202205AC160044).

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Authors and Affiliations

  1. School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, 1168 Western Chunrong Road, Yuhua Street, Chenggong New City, Kunming, 650500, China

    **nyue Wang, Junmei Niu & **g Zhou

  2. Laboratory of Forest Plant Cultivation and Utilization, The Key Laboratory of Rare and Endangered Forest Plants of State Forestry Administration, Yunnan Academy of Forestry and Grassland, Kunming, 650201, China

    **nyue Wang, Jiansheng Wei, Zhenwen Liu, Yi Wang, **aolong Yuan & Dong Wang

  3. Haba Snow Mountain Provincial Nature Reserve Management and Protection Bureau, Diqing, 674402, China

    Jiansheng Wei

  4. College of Forestry, Southwest Forestry University, Kunming, 650224, Yunnan, China

    Dong Wang

  5. Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China

    Yan Yang

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Contributions

Conceptualization, JZ and YW; methodology, YW, XYW, and ZWL; software, YW, XLY, and DW; formal analysis, ZWL; investigation, JMN and XLY; resources, YY; writing—original draft preparation, XYW; writing—review and editing, XYW, YW, and JZ.

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Wang, X., Wei, J., Liu, Z. et al. Comparative genomic analysis of Sanghuangporus sanghuang with other Hymenochaetaceae species. Braz J Microbiol 55, 87–100 (2024). https://doi.org/10.1007/s42770-023-01212-x

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