Next Article in Journal
Molecular Variability of the Fusarium solani Species Complex Associated with Fusarium Wilt of Melon in Iran
Next Article in Special Issue
Genome Re-Annotation and Transcriptome Analyses of Sanghuangporus sanghuang
Previous Article in Journal
Hyphopodium-Specific Signaling Is Required for Plant Infection by Verticillium dahliae
Previous Article in Special Issue
Structural Analysis of the A Mating Type Locus and Development of the Mating Type Marker of Agaricus bisporus var. bisporus
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
JoF
Volume 9
Issue 4
10.3390/jof9040485
jof-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

The First Whole Genome Sequencing of Agaricus bitorquis and Its Metabolite Profiling

by
Chunhua Zhao
1,
Xi-long Feng
2,
Zhen-xin Wang
2 and
Jianzhao Qi
2,*
1
Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
2
Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
*
Author to whom correspondence should be addressed.
J. Fungi 2023, 9(4), 485; https://doi.org/10.3390/jof9040485
Submission received: 25 March 2023 / Revised: 16 April 2023 / Accepted: 17 April 2023 / Published: 18 April 2023
(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)
Browse Figures
Review Reports Versions Notes

Abstract

:
Agaricus bitorquis, an emerging wild mushroom with remarkable biological activities and a distinctive oversized mushroom shape, has gained increasing attention in recent years. Despite its status as an important resource of wild edible fungi, knowledge about this mushroom is still limited. In this study, we used the Illumina NovaSeq and Nanopore PromethION platforms to sequence, de novo assemble, and annotate the whole genome and mitochondrial genome (mitogenome) of the A. bitorquis strain BH01 isolated from Bosten Lake, Xinjiang Province, China. Using the genome-based biological information, we identified candidate genes associated with mating type and carbohydrate-active enzymes in A. bitorquis. Cluster analysis based on P450 of basidiomycetes revealed the types of P450 members of A. bitorquis. Comparative genomic, mitogenomic, and phylogenetic analyses were also performed, revealing interspecific differences and evolutionary features of A. bitorquis and A. bisporus. In addition, the molecular network of metabolites was investigated, highlighting differences in the chemical composition and content of the fruiting bodies of A. bitorquis and A. bisporus. The genome sequencing provides a comprehensive understanding and knowledge of A. bitorquis and the genus Agaricus mushrooms. This work provides valuable insights into the potential for artificial cultivation and molecular breeding of A. bitorquis, which will facilitate the development of A. bitorquis in the field of edible mushrooms and functional food manufacture.

1. Introduction

Mushrooms are a diverse group of organisms belonging to the kingdom Fungi and are known for their unique physical characteristics, especially their fruiting bodies, which are visible above ground or on the surface of their host substrate. While many species are consumed as food, others are known for their medicinal or psychoactive properties. Mushrooms have been integral part of human culture and traditional medicine for thousands of years and continue to be studied for their diverse properties. One of the primary ways humans utilize mushrooms is through the domestication and artificial cultivation of wild mushrooms. Among these, Agaricus bisporus, known as the button mushroom, stands out as one of the most successful examples of human utilization of mushrooms, having originated in Paris in the 18th century [1,2] and becoming a globally cultivated edible mushroom known as the ‘world mushroom’.
In recent years, another member of the Agaricus genus, Agaricus bitorquis, has attracted attention due to its antibacterial [3,4], antioxidant [3,4,5], immunomodulatory [6], and anticancer [7,8] activities, as well as its selenium enrichment properties [9]. While A. bitorquis is a rare wild edible mushroom distributed in various regions of Europe and the Americas [4,10], it is also found in Xinjiang, Qinghai, Inner Mongolia, and Hebei Province in China [5,11], where it is often referred to as the “Dafei mushroom” due to its large size. The wild fruiting bodies of A. bitorquis grow beneath the soil at a depth of about 15 cm and are generally distributed in sheets, rarely exposed to the ground. The Bosten Lake area of Xinjiang is a habitat where the local people highly value A. bitorquis and it was initially discovered by sheep. Despite the edible attributes and potential medicinal value of A. bitorquis, no large-scale cultivation has been reported; however, artificial cultivation has been implemented with promising results [12,13].
Recently, third-generation sequencing technologies have emerged, allowing for more accurate and comprehensive genome sequencing of medicinal and edible mushrooms. These technologies have facilitated research on various aspects of these fungi, including their life cycles, mating types, nutritional patterns, and biosynthesis of bioactive metabolites. As a result, the genomes of several valuable medicinal fungi, such as Inonotus obliquus [14], Hericium erinaceus [15], Laetiporus sulphureus [16], Antrodia camphorate [17], and Inonotus hispidus [18], have been successfully deciphered, which further aid in their medicinal utilization and industrial development. Moreover, the genome sequencing of some precious wild edible fungi, including Oudemansiella raphanipes [19], Naematelia aurantialba [20], and Pleurotus giganteus [21] have the potential to advance artificial cultivation and strain selection of these species.
The genus Agaricus contains a wide range of species with medical and culinary value, including A. bitorquis and A. bisporus. Despite their shared taxonomic classification, the two species exhibit differences in shape preference and morphology (Figure 1). Furthermore, while A. bisporus has been extensively studied [22,23], relatively little is known about A. bitorquis, despite its potential as a valuable source of bioactive compounds. To address this gap in knowledge, the whole genome of a wild strain of A. bitorquis was sequenced and analyzed. This effort represents the first comprehensive investigation of A. bitorquis at the chromosomal level, revealing novel insights into its mating system and carbohydrate metabolic capacity. By comparing the genomes, mitochondrial genomes, and metabolic profiles of A. bitorquis and A. bisporus, this study provides valuable new information on the genetics and physiology of these important macrofungi. Overall, this work enhances our understanding of the genome of medicinal and edible fungi and represents a significant step forward in the study of the genus Agaricus.

2. Materials and Methods

2.1. Fungal Strain and Strain Culture

The fruiting bodies in their natural habitat (Figure 1A,B) were gathered from wetlands bordering Bosten Lake in the Bayingol Mongolian Autonomous Prefecture, located in Xinjiang Province, China. The sample was identified by examination of zygote morphological characteristics and ITS sequence alignment (Figure S1) of the mycelium, and this analysis revealed the sample to be A. bitorquis, subsequently classified as A. bitorquis BH01. Tissue isolation was carried out using fresh wild fruiting bodies of the strain BH01. To obtain culturable mycelium, surface-sterilized small pieces of fruiting bodies were cultivated on potato dextrose agar (PDA) plates for 3–4 days. The identified mycelium was then deposited in the Shaanxi Key Laboratory of Natural Products and Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University. This process was necessary to ensure that the mycelium could be used for further research.

2.2. Genome Sequencing, De Novo Assembly, and Annotation

2.2.1. Extraction of Genome DNA

Cultivation of A. bitorquis BH01 mycelium was carried out in a controlled environment using potato dextrose broth (PDB) medium at 25 °C with agitation at 200 rpm for one week. The aim was to obtain an adequate amount of fresh and viable mycelia. To ensure the purity and freshness of the mycelium, it was then subjected to a series of washing steps, including centrifugation followed by rinsing with sterile water and centrifugation again to remove excess water. Genomic DNA was extracted from the mycelium using the sodium dodecyl sulphate technique, which involved grinding the mycelium with liquid nitrogen and testing the integrity of the DNA using agarose gel electrophoresis. The specific isolation and purification method is described in a previous document [24].

2.2.2. Sequencing and De Novo Assembly

The first step in the sequencing of the A. bitorquis BH01 genome involved end repair, addition of A-tails and sequencing of junctions, followed by purification and PCR amplification of the genomic DNA. Prior to library generation, high quality bulk DNA was collected and assessed for purity, concentration, and integrity. To ensure the quality of the libraries, quantification and quality checks were performed using Qubit 2.0. Sequencing was performed on both the Oxford Nanopore PromethION sequencing platform and the Illumina NovaSeq platform using 20 kb and 350 bp insert sizes, respectively. The NECAT (https://github.com/xiaochuanle/NECAT (accessed on 21 April 2021)) tool was used to correct genomic errors and splicing was performed to obtain initial splicing results from the third-generation sequencing data. Two rounds of error correction were then performed using Racon v1.4.7 (https://github.com/isovic/racon (accessed on 21 April 2021)), followed by two rounds of Pilon. Finally, the assembly result was determined after error correction and heterozygosity elimination.

2.2.3. Gene Prediction and Annotation

BRAKER v2.1.4 (https://github.com/Gaius-Augustus/BRAKER (accessed on 22 April 2021)) was primarily used to predict gene sequences. GeneMark-EX was then used to train the model and AUGUSTUS (https://github.com/Gaius-Augustus/Augustus (accessed on 22 April 2021)) to predict open reading frames (ORFs). INFERNAL v1.1.2 (https://github.com/EddyRivasLab/infernal (accessed on 22 April 2021)) was used to predict and categorize non-coding RNA based on the Rfam database. In addition, RepeatModeler v1.0.4 (https://github.com/Dfam-consortium/RepeatModeler (accessed on 22 April 2021)) was used to generate a repeat library after integration of the Rebase library, while RepeatMasker v4.0.5 (https://github.com/rmhubley/RepeatMasker (accessed on 22 April 2021)) was used to annotate repetitive genomic sequences. Finally, BLAST searches of non-redundant protein sequences from the NCBI, Swiss-Prot, COG, and KEGG databases were performed to annotate the gene products.

2.3. Comparative Genomics Analysis

To analyze and visualize genome collinearity, McscanX (https://github.com/wyp1125/MCScanX (accessed on 4 March 2023)) was employed. Single-copy genes were utilized to undertake comparative genomic analysis within Agaricus species, and the results were visualized using jVenn (http://jvenn.toulouse.inra.fr/app/index.html (accessed on 2 March 2023)). To calculate the synonymous substitution rate (Ks) between two A. bisporus species and A. bitorquis BH01, wgd v1.1 (https://github.com/arzwa/wgd (accessed on 13 March 2023)) was employed. a genome-wide duplication analysis was performed. To acquire collinear block pairs among the species, wgd was utilized with coding-gene sequences, amino acid sequences, and genome annotation files. Subsequently, ParaAT v2.0 was employed to convert the homologous protein sequence pairs to CDS pairs. Homologous sequence pairings were estimated by wgd, and the results were displayed using Rstudio v4.20.

2.4. Phylogenomic Analysis

Phylogenetic analysis was performed to investigate the evolutionary relationships between Agaricus strains and 27 other representative strains of Basidiomycetes. Single-copy homologous genes were identified using OrthoFinder v2.5.4 with the parameters “-S diamond -M msa -T raxml-ng”. A total of 344 single-copy orthologous sequences from 24 strains were used to predict divergence time using the MCMC tree method (http://abacus.gene.ucl.ac.uk/software/paml.html (accessed on 12 March 2023)). The calibrated points of several groups of recent ancestor divergence times were queried in timetree.org (http://www.timetree.org/ (accessed on 11 March 2023)), including Hericium alpestre vs. Stereum hirsutum (91.8–195.5 MYA), and Ganoderma sinense vs. Laetiporus sulphureus (99–152.5 MYA).

2.5. CAZy Family and Cytochrome P450 Analyses

To annotate and classify the genes encoding carbohydrate-active enzymes (CAZymes) from the genomes of A. bitorquis BH01 and other white rot fungi, the CAZy database (http://bcb.unl.edu/dbCAN2/ (accessed on 8 March 2023)) was used with the HMMER 3.2.1 tool (filter parameter E-value < e−5; coverage > 0.35). A bubble plot of the CAZyme analysis was generated for I. hispidus using the Complex Heatmap package in Rstudio v4.20.
The Diamond 2.9.0 (e-value > e−5) was used with the Hmmer package to predict P450s and annotate the target protein sequence. Reference P450 sequences for cluster analyses were obtained from the Fungal Cytochrome P450 database (http://p450.riceblast.snu.ac.kr/index.php?a=view (accessed on 8 March 2023)). For the phylogenetic tree analysis, 115 predicted P450 proteins from A. bitorquis BH01 and several other Basidiomycetes selected from the Fungal P450 database were clustered with accurate classification. A maximum likelihood tree was constructed using IQ-tree 2.2.3 (https://github.com/iqtree/iqtree2 (accessed on 10 March 2023)) with the options “-m MFP -bb 1000 -alrt 1000 -abayes -nt AUTO”.

2.6. Sequencing, Assembly, Annotation, and Comparative Analysis of Mitogenome

The mitochondrial genome sequencing was conducted utilizing a hybrid approach of Illumina NovaSeq and Nanopore sequencing technology, generating an average genome coverage of 150-fold with a paired-end library. The de novo assembly of the reads was accomplished using SOAPdenovo 2.0425 (https://github.com/aquaskyline/SOAPdenovo2 (accessed on 25 April 2021)). The sequencing data derived from the Nanopore platform were corrected by aligning with the Illumina sequencing reads utilizing BLASR26 (https://github.com/jcombs1/blasr (accessed on 25 April 2021)), and then assembled using the Celera Assembler (https://www.cbcb.umd.edu/software/celera-assembler (accessed on 25 April 2021)). The accuracy of the sequencing reads was further improved by correcting them again based on the Illumina data, following the generation of reliable scaffolds. The final output represents the complete genome sequences with high accuracy and reliability. The mitogenomes of I. Hispidus and P. gilvus were de novo assembled from Nanopore raw reads using minimap2 v2.17-r94 (https://github.com/lh3/minimap2 (accessed on 21 February 2023)) and miniasm v0.3-r179 (https://github.com/lh3/miniasm (accessed on 21 February 2023)), and further refined using racon v1.4.20 (https://github.com/isovic/racon (accessed on 21 February 2023)) and pilon v1.23 (https://github.com/broadinstitute/pilon (accessed on 21 February 2023)), based on Illumina data. The final assemblies were assessed for quality using samtools (http://www.htslib.org/ (accessed on 21 February 2023)).
The mitogenomes were subjected to annotation using the website MFannot (https://megasun.bch.umontreal.ca/apps/mfannot/ (accessed on 25 March 2023)), utilizing the genetic code 4 to predict protein-coding genes (PCGs), tRNA genes, rRNA genes, and partial open reading frames. The annotation process involved manual proofreading, and the tRNA and rRNA genes were further validated using RNAweasel (https://github.com/BFL-lab/RNAweasel (accessed on 27 February 2023)) and tRNAScan (https://www.psc.edu/resources/software/trnascan-se/ (accessed on 27 February 2023)), respectively. The type I intron was also evaluated for its adherence to normal sequence characteristics using RNAweasel. MAFFT (https://mafft.cbrc.jp/alignment/software/ (accessed on 28 February 2023)) and blast analysis (https://blast.ncbi.nlm.nih.gov/Blast.cgi (accessed on 28 February 2023)) were employed to confirm the starting and ending positions of rns, rps3, the 14 conserved PCGs, and intron insertion sites. Additionally, ORF Finder (https://www.ncbi.nlm.nih.gov/orffinder/ (accessed on 1 March 2023)) was utilized to explore open reading frames in intergenic regions and intron regions exceeding 300 bp, while Blastn and Blastp were employed to ascertain the starting points and functions of ORFs within the intron. Finally, OGDraw v1.2 (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html (accessed on 1 March 2023)) was utilized to create graphical maps of the complete mitogenomes.

2.7. Metabolite Profiling Comparison

Twenty grams of fresh substrates of A. bitorquis and A. bisporus, respectively, were extracted with ethyl acetate, concentrated, and then used for mass spectrometric (MS) quantification. The High-Resolution MS detection was carried out using AB Sciex TripleTOF 6600 mass spectrometer in both positive-ion and negative-ion modes. Molecular network analysis of HPLC-HRMS data of crude extract was performed using GNPS (https://gnps.ucsd.edu (accessed on 17 March 2023)) with default parameters. The molecular network was visualized finally by Cytoscape 3.9.1.

2.8. Data Availability

The ITS sequence of strain A. bitorquis BH01 has been deposited in the National Center for Biotechnology Information (NCBI) GenBank under accession number OQ581725. The final genome assembly results and related data of A. bitorquis BH01 have been submitted to the NCBI under the BioProject PRJNA946023 and BioSample SAMN33801832, respectively. The mitogenome sequence and annotation of strain A. bitorquis BH01 has been deposited in the NCBI GenBank under accession number OQ571893.

3. Results

3.1. Genome Sequence Assembly and Annotation of A. bitorquis BH01

A total of 34,235,978 clean reads were generated, resulting in 5,135,396,700 bases with a GC content of 45.19% (Tables S1 and S2). These reads were assembled into a high-quality genome of 32.35 Mb, consisting of 22 contigs (Figure 2A, Table 1). The N50 value of the assembly was 1,791,120 bp (Table S3). The presence of two peaks with a 2-fold relationship in the K-mer curve indicated that the genome of A. bitorquis BH01 was heterozygous, with a heterozygosity of 0.665% (Figure S2, Table S4), suggesting that this fungus was a dikaryon. The completeness of the genome assembly was assessed by a coverage of 99.83% (Table S5) and a BUSCO value of 90.8% (Table S6) based on the fungi_odb10 database.
There were 10,028 protein-coding genes predicted by BRAKER, equipped with Augustus. These genes had an average length of 1883.52 bp, consisting of 67,319 exons and 67,319 introns, with average lengths of 180.16 bp and 73.58 bp, respectively (Table S7). In addition, various non-coding RNAs including 109 tRNAs, 25 rRNAs, 11 snRNAs, and 1 sRNA were predicted (Table S8). Repeat sequence analysis revealed the presence of 11,738 repeats with a total length of 7,694,206 bp, accounting for 23.79% of the whole genome. Among these repeats, four scattered repeats, namely SINE, LINE, LTR, and DNA transposons, accounted for 0.01% (6), 4.73% (1041), 12.16% (2613), and 7.72% (1379), respectively (Table S9). These findings provide insight into the genome structure of the mushroom under study.
To achieve a comprehensive functional annotation of protein-coding genes, sequence similarity analysis and motif similarity search were performed on 10,028 genes based on nine public databases (NCBI nr, Pfam, eggCOG, Uniprot, KEGG, GO, Pathway, Refseq, Interproscan) (Table S10). The annotation results from the Nr library showed that 9253 genes, representing 92.27% of all protein-coding genes, were annotated. Among these genes, 49.67% matched A. bisporus var. bisporus H97 and 41.98% matched A. bisporus var. bumeti JB137-S8 (Figure S3), indicating a close relationship between A. bitorquis and A. bisporus. However, 4.99% of the genes matched Leucaganius sp. SymC. Cos (Figure S3), reflecting the intergeneric variability within the genus Agaricus.
Functional annotation of protein-coding genes in strain BH01 revealed their functional diversity in different databases. Among the 5021 genes annotated by the GO database, the classification of cellular components was the most prominent group (Figure S4). Based on the COG database, 976 genes were identified, with 154 genes belonging to the J group, which is related to translation, ribosomal structure, and biogenesis (Figure S5). The KEGG database identified 5010 genes involved in five types of pathways, with the highest number of genes involved in metabolic pathways (Figure S6). In addition, a motif search using the Pfam database identified 7023 genes, of which the top 20 motifs with the most annotated genes are shown in Figure S7. These results highlight the functional diversity of protein-coding genes in strain BH01 from different perspectives and levels of annotation.

3.2. Identification of the Mating Genes

In the sexual development of mushroom-forming fungi, mating is a crucial step that is guided by specific mating loci. The mating type (MAT) loci are located in different genomic regions [26]. Heterozygous cooperation, which accounts for up to 90% of fungal mating types, could be classified into bipolar and tetrapolar mating types. Among these, the tetrapolar mating system is the most widespread and complex sexual reproduction control system found in Basidiomycetes to date [27,28]. Given the unknown reasons for the formation of the large fruiting bodies and the potential demand for cultivation of A. bitorquis, it is necessary to analyze and identify its mating system.
In this research, the MAT-A locus was found to be located on Chr 2 by homology search with the mitochondrial intermediate peptidase (mip) codon gene and a homeodomain transcription factor-codon gene as probes, which are from A. bisporus var. bisporus H97 [23]. The MAT-A locus of A. bitorquis contains a glycosyltransferase family 8 protein codon gene (glgen, g4765), two unknown conserved fungal protein-codon genes (β-fg, g4764 and g4761), three homeodomain transcription factors-codon genes (HD1, g4759, as well as HD2, g4763, and g4760), and a mip (g4758). The order of the genes present in clusters on the MAT-A locus is consistent with those of A. bisporus var. bisporus H97 (Figure 2B), whereas the MAT-B locus contains at least four unclustered ste3, including g142, g182, g7283, and g9071. Of these, g142 and g182 are located on ctg14, while g7283 and g9071 are located on chr3 and chr12, respectively (Figure 2B). The current analysis has shown that the mat-A and mat-B loci of A. bitorquis are not located in the same contig, indicating the presence of a tetrapolar mating system [27,28]. However, this finding only scratches the surface of the intricate genomic architecture of A. bitorquis mating type loci. Further investigation is essential to gain a full understanding of the mechanisms underlying sexual reproduction in A. bitorquis, which is crucial to elucidate the evolutionary trajectory of this fascinating fungal species.

3.3. Phylogenomic and Evolutionary Analysis

The present study used a phylogenomic approach based on an alignment of 344 single-copy orthologous genes from 60,935 orthogroups to elucidate the evolutionary relationships among 29 fungal species, including two Agaricus species (Figure 3). The inferred phylogenetic tree was strongly supported by bootstrap values. The mean divergence time between Agaricales and Polyporales was estimated to be 169.78 Mya with 95% highest posterior density (HPD) of 115.50–294.61 Mya, while that between these two orders and Hymenochaetes was estimated to be 204.64 Mya (95% HPD of 125.66–348.17 Mya). Furthermore, the emergence of Agaricus was estimated to have occurred at the crown age of 64.97 Mya (95% HPD of 41.30–94.06 Mya), with the divergence between A. bitorquis and A. bisporus estimated at 8.21 Mya (95% HPD of 4.28–12.34 Mya) (Figure 3).
Interestingly, gene family contraction events were found to be more frequent than gene family expansion events in the evolutionary history of the 29 fungal species studied (Figure 3). In particular, Agaricus and Cortinarius (or Psilocybe) showed the most significant contraction events, affecting a total of 313 gene families. In the genus Agaricus, 242 and 167 gene families were contracted in A. bitorquis and A. bisporus, respectively, whereas 438 and 125 gene families were expanded in these two species, respectively. These results suggest that the genus Agaricus has undergone considerable changes during its evolutionary history (Figure 3).

3.4. CAZymes Analysis

Edible fungi are widely cultivated on cellulose- and lignin-rich substrates such as wood chips and straw. The ability of edible fungi to degrade and utilize these substrates is closely related to their expression of CAZymes [29,30]. Given the potential for large-scale cultivation of A. bitorquis due to its nutritional value, we investigated its CAZyme repertoire. Our analysis identified 114 genes encoding 123 CAZymes, consisting of 66 glycoside hydrolases (GHs), 22 auxiliary activities (Aas), 14 glycoesterases (Ces), 9 carbohydrate-binding modules (CBMs), 8 polysaccharide lyases (PLs), and 4 glycosyltransferases (GTs). Notably, nine CAZyme-encoding genes (g227, g412, g3471, g3563, g3645, g3914, g7640, g8449, and g9072) were found to possess two functional structural domains (Table S11, and Dataset_1). When the CAZyme profiles of A. bisporus BH01 were compared with those of A. bisporus var. burnettii H119 (Figure 4A, Table S11), no significant differences were observed. In addition, we compared the CAZyme repertoires of A. bisporus BH01 and 17 other edible fungi and found that the number and types of CAZymes were not species-specific (Figure 4B, Table S11). The strains Lactarius deliciosus EDB83 and Paxillus involutus ATCC 200,175 showed the greatest similarity to A. bisporus BH01 in terms of their CAZyme profiles, whereas A. bisporus var. burnettii H119 did not (Figure 4B).

3.5. Cytochrome P450 Family Analysis

Cytochrome P450s (CYPs) are a ubiquitous class of enzymes found in living organisms and play essential roles in various biological processes. In fungi, the CYP51A1 subfamily is typically responsible for the critical enzyme C14α-demethylation, which is involved in the synthesis of ergosterol [31]. Consequently, CYPs have emerged as a promising target for the inhibition of pathogenic fungi. To gain insight into the functional gene composition of A. bitorquis, the number and type of its P450s were analyzed and investigated. Using Pfam prediction based on domain features, we screened a total of 100 P450-encoding genes (115 P450 proteins) in the genome of A. bitorquis BH01. Using cluster analysis, we identified clear classifications based on the evolutionary association of these 115 protein sequences with representative basidiomycete P450 sequences from the Fungal Cytochrome P450 Database (Figure S8). These clustering results provided a clear indication of the categorization of the P450s of A. bitorquis BH01. In addition, the cluster analysis revealed the presence of 11 CYP subfamilies and ten uncertain groups (Figure 5). Among the identified CYP families, CYP5144 had the highest number of members with 38, followed by CYP512 with 13, and the remaining families had less than 10 members. In particular, 29 P450s were scattered in ten uncertain groups, accounting for 25.22% (Figure 5). These unidentified P450s suggest the presence of potential new P450 types that require further analysis and characterization.

3.6. Comparative Genomic Analysis within Agaricus Species

The size difference between the fruiting bodies of A. bitorquis and A. bisporus makes us curious to know how their genomes differ. Comparative genome analysis shows that the genome size of A. bitorquis BH01 is a slightly larger than that of A. bisporus var. bisporus H97 and burnettii H119, but encodes fewer proteins (Table 1). Moreover, the genome assembly quality of A. bitorquis BH01 is superior to those of A. bisporus mushrooms, as indicated by the numbers of scaffolds and contigs, as well as Scaffold L50 (Table 1). Collinearity analysis shows that most genomic regions of A. bitorquis BH01 are syntenic to those of A. bisporus, with chr1-chr9 of BH01 showing high synteny to specific regions of the A. bisporus genomes (Figure 2A).
Comparative analysis of orthologous groups between the three Agaricus variants identified a total of 6798 groups, with A. bitorquis containing more unique orthologous groups (125) than A. bisporus var. bisporus H97 (89), but fewer than burnettii H119 (157). The two A. bisporus share more orthologous groups (1143) than that of each of them share with A. bitorquis BH01 (236 and 616), respectively (Figure 2C). This normal difference suggested that the intraspecific differences of the two most common A. bisporus species variants were smaller than the interspecific differences between them and A. bitorquis. To gain further insight into these differences, a genome-wide duplication analysis based on synonymous mutation rates (Ks) was performed. The trends of the Ks curves of the two species of A. bisporus to A. bitorquis were consistent, but the trend of Ks curves within A. bisporus were not consistent with it (Figure 2D). This finding reflects the intraspecific uniformity within A. bisporus, and interspecific difference between A. bitorquis and A. bisporus species.

3.7. The Mitogenome of A. bitorquis and Comparative Mitogenomic Analysis within Agaricus Species

The mitochondrion, a critical organelle involved in energy production, ageing, and various physiological processes, has received considerable attention for its utility in deciphering fungal phylogeny, evolution, species identification, taxonomic research, variety protection, and fungal breeding [32,33]. In this regard, the mitochondrial genome of A. bitorquis was well-assembled and annotated, alongside its chromosomal genome. The circular DNA molecule of the complete mitogenome spans 153,897 bp with 29.01% GC content and harbors 14 conserved protein-coding genes (PCGs) associated with oxidative phosphorylation, an additional PCG (rps3), 27 tRNA genes, 2 rRNA genes (rns and rnl), and 58 un_ORFs of unknown function or structure (Figure 6A, Table 2).
Further comparative analyses of the mitogenomes of A. bitorquis and A. bisporus revealed differences and similarities. Despite their different sizes, both genomes have very similar GC contents and intron numbers. The longer mitogenome of A. bitorquis carries more un_ORFs but fewer tRNAs, whereas A. bisporus shows the opposite pattern (Table 2). In addition, synteny analysis based on nucleic acid sequences revealed several large regions of highly similar sequences between A. bitorquis and A. bisporus (Figure 6B). Considering the conservation of PCGs and the potential influence of GC content on the reading frame [34], a comparison of the GC content of 15 PCGs in the two species showed little difference between the two Agaricus species (Figure 6C, Table S12).
Table
Table 2. Mitogenomic comparison between A. bitorquis and A. bisporus.
Table 2. Mitogenomic comparison between A. bitorquis and A. bisporus.
EntryA. bitorquis BH01A. bisporus var. bisporus H97
Total length (bp)153,897135,055
GC content (%)29.01%29.07%
AT-skew0.0190.011
GC-skew0.03040.0088
No. of tRNA2735
No. of un_ORFs5829
No. of introns4746
Length of the cox1 gene (bp)30,17829,908
ReferencesThis study[35]

3.8. Metabolic Profiling Comparison between A. bitorquis and A. bisporus

Agaricus bisporus, the best-known member of the Agaricus genus, is not only a globally consumed mushroom with high nutritional value, but also because of its significant medicinal value and prospects for complementary and alternative medicine [36,37]. As an emerging member of the genus Agaricus, A. bitorquis shows great potential in biological activities such as immunomodulation [4], and anticancer [5,6]. Therefore, to examine the differences between the two in terms of bioactive small molecules, a GNPS-based metabolite profile comparison was performed. The visualized molecular network showed that the chemical compositions and contents of the two species are significantly different (Figure S9).
Furthermore, totals of 23 compounds were identified by comparison of their MS and MS2 characteristics with the previous literature, including γ-L-Glutaminyl-3,4-benzoquinone (1), blazeispirols B-E (2–5), (22E,24R)-3β,5α,6β,9α,14α,25-hexhydroxyergosta-7,22-diene (6), blazeispirols X and Y (7–8), blazeispirol A (9), demethylincisterol A3 (10), 11,12-dihydroxy-15-drimeneoic acid (11), benzoyl-ergostane (12), blazeispirols I and F (13–14), ergosterol (15), brefeldin A (16), 3β,11,12-trihydroxydrimene (17), 5-methyl-tryptophan (18), melatonin (19), agaritine (20), N-(γ-L-glutamyl)-4-hydroxyaniline (21), β-N-(γ-glutamyl)-4-formylphenyl-hydrazine (22) (Figure 7 and Figure S10, Table 3). Among the 18 shared compounds, blazeispirols and lanostane triterpenoids were the most abundant, and most of them (2–9) were in the same network (Figure 7A). Blazeispirols (2–5, 7–9, and 13–14), a class of des-A-ergostane-type compounds, clustered with lanostane derivatives in the same network, suggesting their natural correlation. In addition, A. bitorquis and A. bisporus have their own unique metabolites, 18 and 19, and two identified indole derivatives appear in the unique network of A. bisporus (Figure 7B), whereas, 20–22, three identified y-glutamyl-substituted arylhydrazine derivatives appear in the unique network of A. bitorquis (Figure 7C). Metabolic profiling revealed similarities and differences in the metabolites of A. bitorquis and A. bisporus, reflecting the diversity and complexity of metabolites within the genus Agaricus.

4. Discussion

The genus Agaricus is a well-known taxon in the order Agaricaceae, but their genomes have not been extensively investigated. This study presents the first report of the genome of a wild member of the genus Agaricus, A. bitorquis, at the chromosome level. Recent advances in technology have enabled the assembly and annotation of A. bitorquis to be of superior quality to that previously reported for A. bisporus. Using single-copy genes to infer an evolutionary tree, the divergence of A. bitorquis and A. bisporus is estimated to have occurred approximately 8.21 Mya (Figure 3). However, the expansion and contraction of gene families experienced by both species since their divergence has resulted in obvious differences in their genome sizes (Table 1). Comparative genome analysis based on orthologous groups reveals interspecific convergence between A. bitorquis and A. bisporus and intraspecific variation in A. bisporus (Figure 2C). In contrast, Ks-based evolutionary pressure selection analysis explains the interspecific variability between A. bitorquis and A. bisporus, and the intraspecific uniformity observed within A. bisporus (Figure 2D). These results provide valuable insights into the complexity of the genome of the genus Agaricus.
The exaggerated fruiting body size of A. bitorquis compared to A. bisporus is another point of interest (Figure 1). In particular, comparative genomics revealed the presence of 125 orthologous genes unique to A. bitorquis, which may hold the key to unravelling this morphological difference. Functional annotation and clustering analysis of the 278 proteins encoded by these 125 orthologs has identified four A. bitorquis-specific transcription factor-encoding genes (g3057, 5076, 6604, and 8494) and several other promising candidate genes (Figure S11, Table S13). However, it remains to be determined whether these orthologs are indeed associated with fruiting body development in A. bitorquis, which will require further validation by transcriptome comparisons and other means. To extend this research, we sought to investigate it using genes involved in the development of A. bisporus-derived fruiting bodies. Specifically, we used genes that have been implicated in fruiting body development, such as those related to ATP synthase subunits atpD and septin protein gene sepA [49], urease and tyrosinase encoding genes [50], polyphenoloxidase genes [51], and specifically expressed genes discovered through transcriptomics [52], as probes for genome mining in A. bisporus. Our comparison of the homologous genes between A. bitorquis and A. bisporus revealed important similarities (Table S14), which serve as a reference for uncovering the underlying mechanisms responsible for the oversized fruiting bodies in A. bitorquis.
Despite the general trend of morphological stability within the same genus mushrooms, some exceptions exist, as is the case for A. bitorquis. This species exhibits significant variation in size, which is not commonly observed in other members of the genus Agaricus. Although bioactive compounds in fungi are highly diverse, they often exhibit species-specific distribution patterns. For instance, Ganoderic acids are tetracyclic triterpenoids that are characteristic metabolites of the genus Ganoderma [53], and styrylpyrones are a group of polyphenols compounds commonly found in the genus Phellinus and Inonotus species [54,55]. Interestingly, the des-A-ergostane-type compounds, blazeispirols, were initially discovered in Agaricus blazei [39]. Here, the metabolite profile comparison revealed the presence of blazeispirol compounds in both A. bitorquis and A. bisporus. This finding suggests that the blazeispirol compounds may be characteristic of the whole Agaricus genus. Moreover, the availability of the A. bitorquis genome provides a necessary condition to investigate the biosynthesis of these compounds further.

5. Conclusions

A. bitorquis is a giant wild mushroom with various biological activities. In this study, we present for the first time the whole genome and mitogenome of A. bitorquis. The chromosome-level assembly and functional annotation of the genome offer crucial clues for investigating the mating loci and CAZymes of this wild mushroom, which will aid in its artificial cultivation. Cluster analysis reflects the diversity of P450s in A. bitorquis. Comparative genomic and mitogenomic analyses reveal distinct genetic compositions among the Agaricus genus, while phylogenetic and evolutionary analyses of the genus Agaricus reveal contraction and expansion of their gene families, and species divergence times. Additionally, molecular network-based metabolite analysis revealed differences in chemical composition and content in the fruiting bodies of A. bitorquis and A. bisporus, and suggests that blazeispirols are the characteristic compounds of the genus Agaricus. This study not only fills the gap in the genetic information of A. bitorquis, but also provides significant insights into the genome of mushrooms in the Agaricus genus. These results will pave the way for the development of functional foods using A. bitorquis.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/jof9040485/s1, Supplementary Materials: Table S1: Statistics of Oxford Nanopore PromethION sequencing data volume of A. bitorquis BH01 genome. Table S2: Statistics of Illumina NovaSeq sequencing data volume information of A. bitorquis BH01 genome. Table S3: Assembly results statistics of A. bitorquis BH01 genome. Table S4: Genome size estimates for A. bitorquis BH01 genome. Table S5: Statistics of Illumina NovaSeq sequencing data mapping of A. bitorquis BH01 genome. Table S6: Statistics of BUSCO evaluation of A. bitorquis BH01 genome. Table S7: Annotation Statistics of coding gene from the A. bitorquis BH01 genome. Table S8: Statistics of non-coding RNA annotation results in A. bitorquis BH01 genome. Table S9: Statistics of A. bitorquis BH01 repetitive sequence annotation results. Table S10: Statistics of A. bitorquis BH01 protein-coding gene annotation. Table S11: The composition of CAZymes of Agaricus and edible mushrooms. Table S12: GC contents of the mitogenomes of A. bisporus var. bisporus H97 and A. bitorquis BH01. Table S13: Analysis of orthologous genes unique to A. bitorquis BH01. Table S14: Homologous genes of A. bisporus fruiting body development related genes in A. bitorquis BH01. Figure S1: ITS alignment of the strain BH01. Figure S2: K-mer-Depth and K-mer Species-Frequency Distribution Plot. Figure S3: Species distribution map of Nr database alignment to sequences. Figure S4: Statistical map of functional annotation classification based on GO database Figure S5: Statistical Chart of COG Functional Annotated Classification. Figure S6: KEGG Pathway Functional Classification Chart. Figure S7: Domain annotation based on the Pfam database. Figure S8: P450s Cluster analysis of A. bitorquis BH01 and other Basidiomycetes. Figure S9: Molecular network analysis of metabolites from the fruiting bodies of A. bitorquis and A. bisporus. Figure S10: The LC-ESI-HRMS and LC-ESI-HRMS/MS spectrums of isolates from the fruiting bodies of A. bitorquis and A. bisporus. Figure S11: Clustering analysis of orthologous genes unique to A. bitorquis BH01. References. Dataset_S1: gene distribution of 18 edible fungi based on the six major modules of CAZymes. Dataset_S2: the protein sequences of the predicted genes for A. bitorquis BH01. Reference [56] is cited in the Supplementary Materials.

Author Contributions

Conceptualization and funding acquisition, C.Z. and J.Q.; methodology, software, validation, and investigation, C.Z., X.-l.F. and J.Q.; data curation and writing—original draft preparation, C.Z., Z.-x.W. and J.Q.; writing—review and editing, C.Z. and J.Q.; visualization, Z.-x.W. and J.Q. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the Key R&D Projects in Shaanxi Province of China (No. 2023-YBSF-164), the National Natural Science Foundation of China (31800031), Natural Science Basic Research Plan in Shaanxi Province of China (2019JQ-046).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The network file based on positive-ion mode MS data can be found and accessed at https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=6e5a34d20bc14673a01f9e61627f73a5 (accessed on 17 March 2023).

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Cappelli, A. Fungi Europaei. Agaricus L Ex Fr. Ss Karsten (Psaliota Fr.); Edizioni Candusso: Origgio, Italy, 1984; pp. 123–125. [Google Scholar]
  2. Flegg, P.; Spencer, D.M.; Wood, D.A. The Biology and Technology of the Cultivated Mushroom; Wiley: Hoboken, NJ, USA, 1985; pp. 295–336. [Google Scholar]
  3. Ozturk, M.; Duru, M.E.; Kivrak, S.; Mercan-Dogan, N.; Turkoglu, A.; Ozler, M.A. In vitro antioxidant, anticholinesterase and antimicrobial activity studies on three Agaricus species with fatty acid compositions and iron contents: A comparative study on the three most edible mushrooms. Food Chem. Toxicol. 2011, 49, 1353–1360. [Google Scholar] [CrossRef] [PubMed]
  4. Glamočlija, J.; Stojković, D.; Nikolić, M.; Ćirić, A.; Reis, F.S.; Barros, L.; Ferreira, I.C.F.R.; Soković, M. A comparative study on edible Agaricus mushrooms as functional foods. Food Funct. 2015, 6, 1900–1910. [Google Scholar] [CrossRef] [PubMed]
  5. Kuang, H.; Jiao, Y.; Wang, W.; Wang, F.; Chen, Q. Characterization and antioxidant activities of intracellular polysaccharides from Agaricus bitorquis (QuéL.) Sacc. Chaidam ZJU-CDMA-12. Int. J. Biol. Macromol. 2020, 156, 1112–1125. [Google Scholar] [CrossRef] [PubMed]
  6. Lin, X.; Li, W.; Yuen, H.; Yuen, M.; Peng, Q. Immunomodulatory effect of intracellular polysaccharide from mycelia of Agaricus bitorquis (QuéL.) Sacc. Chaidam by TLR4-mediated MyD88 dependent signaling pathway. Int. J. Biol. Macromol. 2021, 183, 79–89. [Google Scholar] [CrossRef]
  7. Nandan, C.K.; Patra, P.; Bhanja, S.K.; Adhikari, B.; Sarkar, R.; Mandal, S.; Islam, S.S. Structural characterization of a water-soluble β-(1→6)-linked D-glucan isolated from the hot water extract of an edible mushroom, Agaricus bitorquis. Carbohydr. Res. 2008, 343, 3120–3122. [Google Scholar] [CrossRef]
  8. Beattie, K.D.; Ulrich, R.; Grice, I.D.; Uddin, S.J.; Blake, T.B.; Wood, K.A.; Steele, J.; Iu, F.; May, T.W.; Tiralongo, E. Ethanolic and aqueous extracts derived from Australian fungi inhibit cancer cell growth in vitro. Mycologia 2011, 103, 458–465. [Google Scholar] [CrossRef]
  9. Falandysz, J. Selenium in Edible Mushrooms. J. Environ. Sci. Health Pt. C-Environ. Carcinog. Ecotoxicol. Rev. 2008, 26, 256–299. [Google Scholar] [CrossRef]
  10. Distribution of Agaricus bitorquis (Quél.) Sacc. Available online: https://www.gbif.org/species/5243374 (accessed on 17 March 2023).
  11. Mingguang, L.; Weili, C.; Fengjun, G. Research progress of the biological characteristics of Agaricus bitorquis and its development. Edible and Medicinal Mushrooms 2022, 30, 32–35. [Google Scholar]
  12. Navarro, M.J.; López-Serrano, F.R.; Escudero-Colomar, L.A.; Gea, F.J. Cultivation of Agaricus bitorquis mushroom as an strategy for the Integrated Pest Management of the myceliophagous mite Microdispus lambi. Pest Manag. Sci. 2020, 76, 2953–2958. [Google Scholar] [CrossRef]
  13. Colauto, N.B.; Fermor, T.R.; Eira, A.F.; Linde, G.A. Pseudomonas putida stimulates primordia on Agaricus bitorquis. Curr. Microbiol. 2016, 72, 482–488. [Google Scholar] [CrossRef]
  14. Duan, Y.; Han, H.; Qi, J.; Gao, J.-M.; Xu, Z.; Wang, P.; Zhang, J.; Liu, C. Genome sequencing of Inonotus obliquus reveals insights into candidate genes involved in secondary metabolite biosynthesis. BMC Genom. 2022, 23, 314. [Google Scholar] [CrossRef]
  15. Gong, W.; Wang, Y.; Xie, C.; Zhou, Y.; Zhu, Z.; Peng, Y. Whole genome sequence of an edible and medicinal mushroom, Hericium erinaceus (Basidiomycota, Fungi). Genomics 2020, 112, 2393–2399. [Google Scholar] [CrossRef]
  16. Dong, W.G.; Wang, Z.X.; Feng, X.L.; Zhang, R.Q.; Shen, D.Y.; Du, S.; Gao, J.M.; Qi, J. Chromosome-Level Genome Sequences, Comparative Genomic Analyses, and Secondary-Metabolite Biosynthesis Evaluation of the Medicinal Edible Mushroom Laetiporus sulphureus. Microbiol. Spectr. 2022, 10, e0243922. [Google Scholar] [CrossRef]
  17. Lu, M.Y.; Fan, W.L.; Wang, W.F.; Chen, T.; Tang, Y.C.; Chu, F.H.; Chang, T.T.; Wang, S.Y.; Li, M.Y.; Chen, Y.H.; et al. Genomic and transcriptomic analyses of the medicinal fungus Antrodia cinnamomea for its metabolite biosynthesis and sexual development. Proc. Natl. Acad. Sci. USA 2014, 111, E4743–E4752. [Google Scholar] [CrossRef]
  18. Zhang, R.-Q.; Feng, X.-L.; Wang, Z.-X.; Xie, T.-C.; Duan, Y.; Liu, C.; Gao, J.-M.; Qi, J. Genomic and Metabolomic Analyses of the Medicinal Fungus Inonotus hispidus for Its Metabolite’s Biosynthesis and Medicinal Application. J. Fungi 2022, 8, 1245. [Google Scholar] [CrossRef]
  19. Zhu, L.; Gao, X.; Zhang, M.; Hu, C.; Yang, W.; Guo, L.; Yang, S.; Yu, H.; Yu, H. Whole Genome Sequence of an Edible Mushroom Oudemansiella raphanipes (Changgengu). J. Fungi 2023, 9, 266. [Google Scholar] [CrossRef]
  20. Sun, T.; Zhang, Y.; Jiang, H.; Yang, K.; Wang, S.; Wang, R.; Li, S.; Lei, P.; Xu, H.; Qiu, Y.; et al. Whole Genome Sequencing and Annotation of Naematelia aurantialba (Basidiomycota, Edible-Medicinal Fungi). J. Fungi 2022, 8, 6. [Google Scholar] [CrossRef]
  21. Yu, H.; Zhang, M.; Sun, Y.; Li, Q.; Liu, J.; Song, C.; Shang, X.; Tan, Q.; Zhang, L.; Yu, H. Whole-genome sequence of a high-temperature edible mushroom Pleurotus giganteus (zhudugu). Front. Microbiol. 2022, 13, 941889. [Google Scholar] [CrossRef]
  22. Sun, L.; Fu, Y.; Yang, Y.; Wang, X.; Cui, W.; Li, D.; Yuan, X.; Zhang, Z.; Fu, Y.; Li, Y. Genomic Analyses Reveal Evidence of Independent Evolution, Demographic History, and Extreme Environment Adaptation of Tibetan Plateau Agaricus bisporus. Front. Microbiol. 2019, 10, 1786. [Google Scholar] [CrossRef]
  23. Morin, E.; Kohler, A.; Baker, A.R.; Foulongne-Oriol, M.; Lombard, V.; Nagye, L.G.; Ohm, R.A.; Patyshakuliyeva, A.; Brun, A.; Aerts, A.L.; et al. Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc. Natl. Acad. Sci. USA 2012, 109, 17501–17506. [Google Scholar] [CrossRef]
  24. Hei, Y.; Zhang, H.; Tan, N.; Zhou, Y.; Wei, X.; Hu, C.; Liu, Y.; Wang, L.; Qi, J.; Gao, J.M. Antimicrobial activity and biosynthetic potential of cultivable actinomycetes associated with Lichen symbiosis from Qinghai-Tibet Plateau. Microbiol. Res. 2021, 244, 126652. [Google Scholar] [CrossRef] [PubMed]
  25. Sonnenberg, A.S.M.; Sedaghat-Telgerd, N.; Lavrijssen, B.; Ohm, R.A.; Hendrickx, P.M.; Scholtmeijer, K.; Baars, J.J.P.; van Peer, A. Telomere-to-telomere assembled and centromere annotated genomes of the two main subspecies of the button mushroom Agaricus bisporus reveal especially polymorphic chromosome ends. Sci. Rep. 2020, 10, 14653. [Google Scholar] [CrossRef] [PubMed]
  26. Brown, A.J.; Casselton, L.A. Mating in mushrooms: Increasing the chances but prolonging the affair. Trends Genet. 2001, 17, 393–400. [Google Scholar] [CrossRef] [PubMed]
  27. Bistis, G.N. Genetics of Sexuality in Higher Fungi. Mycologia 1967, 59, 384. [Google Scholar] [CrossRef]
  28. Kües, U. From two to many: Multiple mating types in Basidiomycetes. Fungal Biol. Rev. 2015, 29, 126–166. [Google Scholar] [CrossRef]
  29. Sista Kameshwar, A.K.; Qin, W. Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi. Mycology 2018, 9, 93–105. [Google Scholar] [CrossRef]
  30. Rytioja, J.; Hildén, K.; Yuzon, J.; Hatakka, A.; De Vries, R.P.; Mäkelä, M.R. Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes. Microbiol. Mol. Biol. Rev. 2014, 78, 614–649. [Google Scholar] [CrossRef]
  31. Vanden Bossche, H.; Marichal, P.; Gorrens, J.; Coene, M.C. Biochemical basis for the activity and selectivity of oral antifungal drugs. Br. J. Clin. Pract. 1990, 71, 41–46. [Google Scholar]
  32. Li, Q.; Yang, L.; Xiang, D.; Wan, Y.; Wu, Q.; Huang, W.; Zhao, G. The complete mitochondrial genomes of two model ectomycorrhizal fungi (Laccaria): Features, intron dynamics and phylogenetic implications. Int. J. Biol. Macromol. 2020, 145, 974–984. [Google Scholar] [CrossRef]
  33. Wang, X.; Wang, Y.; Yao, W.; Shen, J.; Chen, M.; Gao, M.; Ren, J.; Li, Q.; Liu, N. The 256 kb mitochondrial genome of Clavaria fumosa is the largest among phylum Basidiomycota and is rich in introns and intronic ORFs. IMA Fungus 2020, 11, 26. [Google Scholar] [CrossRef]
  34. Singer, G.A.C.; Hickey, D.A. Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol. Biol. Evol. 2000, 17, 1581–1588. [Google Scholar] [CrossRef]
  35. Férandon, C.; Xu, J.; Barroso, G. The 135 kbp mitochondrial genome of Agaricus bisporus is the largest known eukaryotic reservoir of group I introns and plasmid-related sequences. Fungal Genet. Biol. 2013, 55, 85–91. [Google Scholar] [CrossRef]
  36. Da Silva de Souza, A.C.; Correa, V.G.; Goncalves, G.A.; Soares, A.A.; Bracht, A.; Peralta, R.M. Agaricus blazei Bioactive Compounds and their Effects on Human Health: Benefits and Controversies. Curr. Pharm. Des. 2017, 23, 2807–2834. [Google Scholar] [CrossRef]
  37. Tomatsu, M.; Shimakage, A.; Shinbo, M.; Yamada, S.; Takahashi, S. Novel angiotensin I-converting enzyme inhibitory peptides derived from soya milk. Food Chem. 2013, 136, 612–616. [Google Scholar] [CrossRef]
  38. Weaver, R.F.; Rajagopalan, K.V.; Handler, P.; Rosenthal, D.; Jeffs, P.W. Isolation from the Mushroom Agaricus bisporus and Chemical Synthesis of γ-l-Glutaminyl-4-hydroxybenzene. J. Biol. Chem. 1971, 246, 2010–2014. [Google Scholar] [CrossRef]
  39. Hirotani, M.; Sai, K.; Hirotani, S.; Yoshikawa, T. Blazeispirols B, C, E and F, des-A-ergostane-type compounds, from the cultured mycelia of the fungus Agaricus Blazei. Phytochem. 2001, 59, 571–577. [Google Scholar] [CrossRef]
  40. Rao, J.S.; Kumar, K.R. Bioactive molecules and their antioxidant activity of Agaricus bisporus. JCBPS 2013, 3, 1222–1228. [Google Scholar]
  41. Ueguchi, Y.; Matsunami, K.; Otsuka, H.; Kondo, K. Constituents of cultivated Agaricus blazei. J. Nat. Med. 2011, 65, 307–312. [Google Scholar] [CrossRef]
  42. Zhao, J.Y.; Ding, J.H.; Li, Z.H.; Dong, Z.J.; Feng, T.; Zhang, H.B.; Liu, J.K. Two new sesquiterpenes from cultures of the basidiomycete Agaricus arvensis. J. Asian Nat. Prod. Res. 2013, 15, 305–309. [Google Scholar] [CrossRef]
  43. Hirotani, M.; Sai, K.; Nagai, R.; Hirotani, S.; Takayanagi, H.; Yoshikawa, T. Blazeispirane and protoblazeispirane derivatives from the cultured mycelia of the fungus Agaricus blazei. Phytochemistry 2002, 61, 589–595. [Google Scholar] [CrossRef]
  44. Takaku, T.; Kimura, Y.; Okuda, H. Isolation of an Antitumor Compound from Agaricus blazei Murill and Its Mechanism of Action. J. Nutr. 2001, 131, 1409–1413. [Google Scholar] [CrossRef] [PubMed]
  45. Dong, S.; Furutani, Y.; Kimura, S.; Zhu, Y.; Kawabata, K.; Furutani, M.; Nishikawa, T.; Tanaka, T.; Masaki, T.; Matsuoka, R.; et al. Brefeldin A is an estrogenic, Erk1/2-activating component in the extract of Agaricus blazei mycelia. J. Agric. Food Chem. 2013, 61, 128–136. [Google Scholar] [CrossRef] [PubMed]
  46. Muszyńska, B.; Sułkowska-Ziaja, K.; Ekiert, H. Indole compounds in fruiting bodies of some edible Basidiomycota species. Food Chem. 2011, 125, 1306–1308. [Google Scholar] [CrossRef]
  47. Tsuji, H.; Ogawa, T.; Bando, N.; Sasaoka, K. Incorporation of chorismic acid and 4-aminobenzoic acid into the 4-hydroxyaniline moiety of N-(gamma-L-glutamyl)-4-hydroxyaniline in Agaricus bisporus. Biochim. Et Biophys. Acta BBA-Gen. Subj. 1985, 840, 287–290. [Google Scholar] [CrossRef]
  48. Chulia, A.J.; Bernillon, J.; Favre-Bonvin, J.; Kaouadji, M.; Arpin, N. Isolation of β-N-(γ-glutamyl)-4-formylphenylhydrazine (agaritinal) from Agaricus campestris. Phytochemistry 1988, 27, 929–930. [Google Scholar] [CrossRef]
  49. De Groot, P.W.J.; Schaap, P.J.; Van Griensven, L.J.L.D.; Visser, J. Isolation of developmentally regulated genes from the edible mushroom Agaricus bisporus. Microbiology 1997, 143, 1993–2001. [Google Scholar] [CrossRef]
  50. Wagemaker, M.J.M.; Eastwood, D.C.; van der Drift, C.; Jetten, M.S.M.; Burton, K.; Van Griensven, L.J.L.D.; Op den Camp, H.J.M. Expression of the urease gene of Agaricus bisporus: A tool for studying fruit body formation and post-harvest development. Appl. Microbiol. Biotechnol. 2006, 71, 486–492. [Google Scholar] [CrossRef]
  51. Li, N.-Y.; Cai, W.-M.; Jin, Q.-L.; Qin, Q.-P.; Ran, F.-L. Molecular Cloning and Expression of Polyphenoloxidase Genes from the Mushroom, Agaricus bisporus. Agric. Sci. China 2011, 10, 185–194. [Google Scholar] [CrossRef]
  52. Yuan, S.; Qiuhui, H.; Anxiang, S.; Fei, P.; Gaoxing, M.; Ning, M.; Wenjian, Y. Transcriptomic Analysis of the Mechanism Underlying the Effect of Methyl Jasmonate on the Size of Agaricus bisporus. Shipin Kexue/Food Sci. 2021, 42, 130–137. [Google Scholar]
  53. Bishop, K.S.; Kao, C.H.; Xu, Y.; Glucina, M.P.; Paterson, R.R.; Ferguson, L.R. From 2000 years of Ganoderma lucidum to recent developments in nutraceuticals. Phytochemistry 2015, 114, 56–65. [Google Scholar] [CrossRef]
  54. Wang, Z.X.; Feng, X.L.; Liu, C.; Gao, J.M.; Qi, J. Diverse Metabolites and Pharmacological Effects from the Basidiomycetes Inonotus hispidus. Antibiotics 2022, 11, 1097. [Google Scholar] [CrossRef]
  55. Lee, I.K.; Yun, B.S. Styrylpyrone-class compounds from medicinal fungi Phellinus and Inonotus spp., and their medicinal importance. J. Antibiot. 2011, 64, 349–359. [Google Scholar] [CrossRef]
  56. Minh, B.Q.; Schmidt, H.A.; Chernomor, O.; Schrempf, D.; Woodhams, M.D.; von Haeseler, A.; Lanfear, R. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. 2020, 37, 1530–1534. [Google Scholar] [CrossRef]
Jof 09 00485 g001 550
Figure 1. Morphologic comparison in size of the genus Agaricus mushrooms. (A,B) The fruiting bodies of wild A. bitorquis BH01. (C,D) The fruiting bodies of cultivated A. bisporus var. bisporus H97.
Figure 1. Morphologic comparison in size of the genus Agaricus mushrooms. (A,B) The fruiting bodies of wild A. bitorquis BH01. (C,D) The fruiting bodies of cultivated A. bisporus var. bisporus H97.
Jof 09 00485 g001
Jof 09 00485 g002 550
Figure 2. Genomic characterization, mating-type loci, and comparative genomic analysis. (A) Genomic collinearity analysis between A. bitorquis and A. bisporus species. From the outside to the inside are I. Chromosome and Contigs; II–IV. GC-density, GC-skew, AT-skew (window size 10 kb), V. Gene-density (window size 100 kb), VI. Whole-genome collinearity analysis based on protein-coding genes between A. bitorquis and A. bisporus species. (B) Structural diagram of the genes on the matA locus and matB locus of A. bitorquis, the numbers on the similarity diagrams indicate the identity between corresponding genes. (C) Venn schematic of comparative genomes between A. bitorquis and A. bisporus species. (D) Ks comparison between A. bitorquis and A. bisporus species.
Figure 2. Genomic characterization, mating-type loci, and comparative genomic analysis. (A) Genomic collinearity analysis between A. bitorquis and A. bisporus species. From the outside to the inside are I. Chromosome and Contigs; II–IV. GC-density, GC-skew, AT-skew (window size 10 kb), V. Gene-density (window size 100 kb), VI. Whole-genome collinearity analysis based on protein-coding genes between A. bitorquis and A. bisporus species. (B) Structural diagram of the genes on the matA locus and matB locus of A. bitorquis, the numbers on the similarity diagrams indicate the identity between corresponding genes. (C) Venn schematic of comparative genomes between A. bitorquis and A. bisporus species. (D) Ks comparison between A. bitorquis and A. bisporus species.
Jof 09 00485 g002
Jof 09 00485 g003 550
Figure 3. The evolutionary relationship and expanded and contracted gene families among Agaricus species and 27 representative Basidiomycetes. The maximum likelihood method credibility tree was inferred from 27 single-copy orthologous genes. All nodes received full bootstrap support. The divergence time is labeled as the mean crown age for each node, while the 95% highest posterior density is also given within the Agaricus clade. The black numbers at the branches indicate the corresponding divergence times in millions of years (MYA). The proportion of expansion and contraction in the genome of each species was displayed before its species name.
Figure 3. The evolutionary relationship and expanded and contracted gene families among Agaricus species and 27 representative Basidiomycetes. The maximum likelihood method credibility tree was inferred from 27 single-copy orthologous genes. All nodes received full bootstrap support. The divergence time is labeled as the mean crown age for each node, while the 95% highest posterior density is also given within the Agaricus clade. The black numbers at the branches indicate the corresponding divergence times in millions of years (MYA). The proportion of expansion and contraction in the genome of each species was displayed before its species name.
Jof 09 00485 g003
Jof 09 00485 g004 550
Figure 4. CAZymes analysis of Agaricus and related edible mushrooms. (A) Composition comparison of CAZymes between A. bitorquis BH01 and A. bisporus var. burnettii H119. (B) Composition comparison of CAZymes between Agaricus species and related edible mushrooms.
Figure 4. CAZymes analysis of Agaricus and related edible mushrooms. (A) Composition comparison of CAZymes between A. bitorquis BH01 and A. bisporus var. burnettii H119. (B) Composition comparison of CAZymes between Agaricus species and related edible mushrooms.
Jof 09 00485 g004
Jof 09 00485 g005 550
Figure 5. Maximum likelihood tree of 115 cytochrome P450s from A. bitorquis BH01. Each cytochrome P450 family is shown in a separate color, and the branch reliability value of over than 50 is marked on the corresponding branch node.
Figure 5. Maximum likelihood tree of 115 cytochrome P450s from A. bitorquis BH01. Each cytochrome P450 family is shown in a separate color, and the branch reliability value of over than 50 is marked on the corresponding branch node.
Jof 09 00485 g005
Jof 09 00485 g006 550
Figure 6. Mitogenome of A. bitorquis BH01 and its comparative analyses. (A) Circular map of A. bitorquis BH01 mitogenome. (B) Genomic collinearity analysis. (C) GC content comparison of 15 PCGs between A. bitorquis BH01 and A. bisporus var. bisporus H97.
Figure 6. Mitogenome of A. bitorquis BH01 and its comparative analyses. (A) Circular map of A. bitorquis BH01 mitogenome. (B) Genomic collinearity analysis. (C) GC content comparison of 15 PCGs between A. bitorquis BH01 and A. bisporus var. bisporus H97.
Jof 09 00485 g006
Jof 09 00485 g007 550
Figure 7. GNPS-based molecular network identification of metabolites from the fruiting bodies of A. bitorquis and A. bisporus. (A) The network of shared molecules. (B) The molecular networks unique to A. bisporus. (C) The molecular network unique to A. bitorquis.
Figure 7. GNPS-based molecular network identification of metabolites from the fruiting bodies of A. bitorquis and A. bisporus. (A) The network of shared molecules. (B) The molecular networks unique to A. bisporus. (C) The molecular network unique to A. bitorquis.
Jof 09 00485 g007
Table
Table 1. Genomic comparison within Agaricus species.
Table 1. Genomic comparison within Agaricus species.
EntryA. bitorquis BH01A. bisporus var.
bisporus H97		A. bisporus var. burnettii H119
Sequencing technologylumina NovaSeq 6000
Nanopore PromethION		Sanger dideoxy PacBio RSII
Sequencing depth145×8.29×70×
No. of contigs227016
Total length (bp)32,345,19330,417,84430,702,502
Largest length (bp)3,210,7513,550,2053,639,502
Scaffold N50 (bp)2,052,2132,550,6811,931,181
Scaffold L501056
GC content (%)46.0546.546.6
No. of protein-coding genes10,02810,43810,421
GenBank accession No.PRJNA946023GCA_000300575.1GCA_014872705.1
ReferencesThis study[23][25]
Table
Table 3. The identified metabolites from A. bitorquis and/or A. bisporus.
Table 3. The identified metabolites from A. bitorquis and/or A. bisporus.
NoPutative
Metabolite		Molecular
Formula		Adductm/zSourceReference
A. bisporusA. bitorquis
1γ-L-Glutaminyl-3,4-benzoquinoneC11H12N2O4[M + Na]+259.12√NAWeaver, et al. [38]
2blazeispirol BC25H34O4[M + H]+399.259√√Masao, et al. [39]
3blazeispirol CC25H36O4[M-H2O + H]+383.203√√Masao, et al. [39]
4blazeispirol DC24H32O4[M-H2O + H]+367.234√√Masao, et al. [39]
5blazeispirol EC25H34O5[M-H2O + H]+397.228√√Masao, et al. [39]
6(22E,24R)-3β,5α,6β,9α,14α,25-hexhydroxyergosta-7,22-dieneC28H46O6[M + H2O + H]+497.343√√Rao, et al. [40]
7blazeispirol XC28H38O4[M + Na]+461.225√√Masao, et al. [39]
8blazeispirol YC28H36O6[M + Na]+491.293√√Masao, et al. [39]
9blazeispirol AC25H34O4[M + H]+399.208√√Masao, et al. [39]
10demethyl-incisterol A3C21H32O3[M + Na]+355.28√√Yumi, et al. [41]
1111,12-dihydroxy-15-drimeneoic acidC15H24O4[M + H]+269.251√NAZhao, et al. [42]
12benzoyl ergostaneC35H50O4[M + H]+535.359NA√Yumi, et al. [41]
13blazeispirol IC25H34O5[M + H]+415.26√√Masao, et al. [43]
14blazeispirol FC24H35O4[M + H]+387.248√√Masao, et al. [43]
15ergosterolC28H44O[M-H2O + H]+379.352√√Takeshi, et al. [44]
16brefeldin AC16H24O4[M + H]+281.183√√Dong, et al. [45]
173β,11,12-trihydroxydrimeneC15H26O3[M + H]+255.228√√Zhao, et al. [42]
185-CH3-Tryptophan
5-methyltryptamine		C12H14N2O2[M + H]+219.107√NAMuszyńska, et al. [46]
19melatoninC13H16N2O2[M + H]+233.135√NAMuszyńska, et al. [46]
20agaritineC12H17N3O4[M + H]+268.133NA√Levenberg
21N-(γ-L-glutamyl)-4-hydroxyanilineC11H14N2O4[M + H]+239.091NA√Tsuji, et al. [47]
22β-N-(γ-glutamyl)-4-formylphenyl-hydrazineC12H15N3O4[M + H]+266.117NA√Albert J., et al. [48]
NA indicates not available.
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Zhao, C.; Feng, X.-l.; Wang, Z.-x.; Qi, J. The First Whole Genome Sequencing of Agaricus bitorquis and Its Metabolite Profiling. J. Fungi 2023, 9, 485. https://doi.org/10.3390/jof9040485

AMA Style

Zhao C, Feng X-l, Wang Z-x, Qi J. The First Whole Genome Sequencing of Agaricus bitorquis and Its Metabolite Profiling. Journal of Fungi. 2023; 9(4):485. https://doi.org/10.3390/jof9040485

Chicago/Turabian Style

Zhao, Chunhua, Xi-long Feng, Zhen-xin Wang, and Jianzhao Qi. 2023. "The First Whole Genome Sequencing of Agaricus bitorquis and Its Metabolite Profiling" Journal of Fungi 9, no. 4: 485. https://doi.org/10.3390/jof9040485

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop