Genome sequencing of Inonotus obliquus reveals insights into candidate genes involved in secondary metabolite biosynthesis

Abstract

Background 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. Results 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. Conclusions 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.

Diverse Metabolites and Pharmacological Effects from the Basidiomycetes Inonotus hispidus

“…I. obliquus is a congener species of I. hispidus. Although the genome of I. obliquus contains at least 4 types of 20 sesquiterpene synthases [ 54 ], only 8 sesquiterpenoids of the drimane-type have been reported [ 55 ]. So far, only one sesquiterpenoid ( 61 ) has been reported for I. obliquus [ 21 ], and the type and number of sesquiterpene synthases are also unknown.…”

“…Current research has not paid enough attention to I. hispidus , despite its significant medicinal efficacy and functional food value. Although the genomes of multiple rare medicinal fungi including I. obliquus [ 54 ] have been sequenced, the genome of I. hispidus has not been sequenced. The lack of genomic information of I. hispidus severely hampered the biosynthetic pathway elucidation of its active compounds.…”

“…The lack of genomic information of I. hispidus severely hampered the biosynthetic pathway elucidation of its active compounds. As a result, it is critical to complete the genome sequencing of I. hispidus [ 54 ] using rapidly developing sequencing technology, which will lay a firm foundation for biosynthesis research and synthetic biology production of valuable compounds to meet the needs of the drug development and functional food industries.…”

Whole Genome Sequence of an Edible Mushroom Oudemansiella raphanipes (Changgengu)

“…As sequencing technology advances, genome sequencing has been extensively applied to investigate the genetic traits of mushrooms [ 12 , 13 , 14 ]. In particular, numerous genomes of mushrooms, including Pleurotus giganteus [ 15 ], Clitopilus passeckerianus [ 16 ], Stropharia rugosoannulata [ 17 ], Gomphus purpuraceus [ 18 ], Inonotus obliquus [ 19 ], Inonotus hispidus [ 20 ], and Laetiporus sulphureus [ 21 ], among others, have been most recently reported, which will provide valuable genetic resources and molecular markers for biological and genetic studies of edible mushrooms and also disease. Therefore, the availability of high-quality whole genomic sequencing for O. raphanipes is imperative to carry out, as it would facilitate the identification of functional candidate genes and genetic breeding of the cultivars.…”

Chromosome-Level Genome Sequences, Comparative Genomic Analyses, and Secondary-Metabolite Biosynthesis Evaluation of the Medicinal Edible Mushroom Laetiporus sulphureus

“…The resolution of genomic information on wood-dwelling macrofungi will help to understand their life cycle, mating types, and nutritional models. To date, the genomes of several valuable medicinal (edible) fungi, including Ganoderma lucidum ( 25 , 26 ), Inonotus obliquus ( 27 ), Hericium erinaceus ( 28 ), Naematelia aurantialba ( 29 ), Antrodia camphorata ( 30 ), and Sanghuangporus sanghuang ( 31 ), have been deciphered, thereby further facilitating their medicinal utilization and industrial development. L. sulphureus is a wood-dwelling-type medical and edible fungus that has attracted much attention, although the genomes of its five subspecies ( 10 , 32 – 34 ) have been sequenced and used to analyze the lignocellulosic biomass degradation characteristics ( 10 , 33 ).…”