Genome sequencing highlights the fungal sclerotium formation of medicinal fungi Polyporus umbellatus

Abstract

Objectives

Polyporus umbellatus is a well-known medicinal fungus in Asia. Due to its long growth cycle, wild resources of P. umbellatus are rapidly declining. Research on P. umbellatus growth is scarce, thereby impeding the investigation into the mechanism of sclerotium formation. In this study, the whole genome sequence of P. umbellatus was assembled and annotated.

Data description

The generated genome was 79.74 Mb with an N50 of 969.73 Kbp, a GC content of 50.63%, encoding 10,864 protein-coding genes. Additionally, 82 ribosomal RNAs, 488 transfer RNAs, 25 small nuclear RNAs (snRNAs) and 741 micro RNA (miRNAs) were identified. This genomic resource will unveil molecular mechanisms of sclerotium formation and provides insight into the underlying molecular processes in medicinal fungi.

Objective

Polyporus umbellatus is a well-known edible and medicinal mushroom. The life cycle of P. umbellatus includes three stages of mycelium, sclerotium, and fruiting bodies with the dominant stage of sclerotium development. P. umbellatus sclerotia have been utilized in traditional Chinese medicine for over a millennium [1, 2]. In recent years, the polysaccharide extracted from P. umbellatus sclerotia has been demonstrated anti-cancer, immunomodulatory, antioxidant, anti-inflammatory and renoprotective activity [3, 4]. However, wild sclerotia of P. umbellatus have been largely depleted due to insufficient protection, over-harvesting and severe habitat loss. At present, the artificial sclerotium cultivation primarily relies on the asexual breeding of P. umbellatus sclerotium and its symbiotic fungi, Armillaria species. The growth cycle of P. umbellatus sclerotia typically spans 3 to 4 years before mature sclerotia can be harvested. Our previous studies have shown that P. umbellatus sclerotium formation is induced by abiotic stress, such as low temperature, hypoxia and osmotic stress [5,6,7], as well as the invasion of symbiotic Armillaria species and associated bacteria [8, 9].

Genome sequencing of fungi offers an opportunity to decipher the mechanisms underpinning the gene regulation in sclerotium development. The advent of genome sequencing and comparative analysis has largely contributed to identifying factors involved in sclerotium formation in related species, such as Wolfiporia cocos [10]. Many studies have explored the secondary metabolites and formation conditions of P. umbellatus sclerotium [11], yet a genomic perspective is lacking. Here, we report the complete genome sequence of P. umbellatus to facilitate the exploration the molecular mechanism underlying its slow growth, development and sclerotium formation.

Data description

The detail description of the methodology is represented in Table 1 Data file1. The ultimate clean Illumina and Pacbio reads used for genome assembly were 5.73 Gbp and 7.29 Gbp, respectively. The final genome assembly of P. umbellatus comprises 318 scaffolds with an estimated size of 79.74 Mb, a GC content of 50.63%, and an N50 of 969.73 Kbp (Table 1 Data file2). The repeats of P. umbellatus genome account for 58.62% (46.75 Mp) of the whole genome, among which long terminal repeats (LTR) were the most, accounting for 43.43%. For non-coding RNA (ncRNA), there were 488 tRNAs, 25 snRNAs and 741 miRNAs in P. umbellatus genome. The ribosomal RNA genes of P. umbellatus were composed of twenty-two 2121 bp 28 S subunit, fifty-one 15,804 bp 18 S subunit, and nine 900 bp 5.8 S subunits.

A total of 10,864 CDSs were predicted for the P. umbellatus genome with an average length of 1,339 bp. The cumulative length of encoded genes was 19.38 Mb, which accounted for 24.3% of the whole genome. The average exon numbers per gene was 5.79. Our genome assembly contains 96.2% (920/956) complete BUSCO genes, being 811 complete and single-copy BUSCOs, 109 complete and duplicated BUSCOs, 7 fragmented genes, and 29 missing genes, that indicating our high quality in terms of completeness [12].

Table 1 Overview of data files/data sets

Total 94.4% (10,258/10,864) of the protein-coding genes matched to public databases in similarity searches. Among them, 6,062 genes could be annotated by all these databases, and 5,340 predicted proteins have corresponding GO term annotations while the number for KEGG pathway is 6,955 (Table 1 Data file3). P. umbellatus has 6,780 genes that were assigned to the NOG categories (Table 1 Data file3), the majority of which belong to the “Posttranslational modification, protein turnover, chaperones” (692, 10.21%), “Carbohydrate transport and metabolism (512, 7.55%)” and “Intracellular trafficking, secretion, and vesicular transport (502, 7.40%)”.

A total of 330 candidate CAZymes were identified in the genome of P. umbellatus, which included 152 glycoside hydrolases (GHs), 86 auxiliary activities enzymes (AAs), 41 carbohydrate-binding modules (CBMs), 33 glycosyl transferases (GTs), 11 carbohydrate esterases (CEs), and 7 polysaccharide lyases (PLs) (Table 1 Data file3). Among the 152 GHs, there were just 24 enzymes for the digestion of plant cell wall polysaccharides (6 cellulose, 6 hemicelluloses and 12 pectin).

According to antiSMASH investigations, P. umbellatus possesses at least 21 gene clusters involved in biosynthesis, including ten terpene gene clusters, four NRPS-like gene clusters, five T1PKS gene clusters, one fungal-RiPP-like gene cluster, and one other gene cluster (Table 1 Data file3).

In conclusion, the complete sequencing, assembly, and annotation of P. umbellatus have provided valuable new insights into the genomic structure, genetics, evolution, and phylogeny related to sclerotium development. The data are pivotal for the domestication, cultivation, production, and evaluation of the medicinal properties of this traditional medicine.

Limitations

The primary limitation is that the P. umbellatus assembly reported in this study is not completeness, lacking chromosome-level informaiton. This restriction limits the subsequent biological insights we can derive from the data. To address this limitation, future research should incorporate Nanopore sequencing technology, which has the potential to significantly enhance the completeness and accuracy of the genome assembly by generating longer reads that can span complex genomic regions.