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Molecular Genetics and Genomics of Mushroom-Forming Fungi

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A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Fungal Genomics, Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 23281

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Prof. Dr. Hoi Shan Kwan

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School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
Interests: mushroom genomics; fungal evolution; molecular genetics of mushrooms; population genomics of mushrooms; fungal pathogens of trees
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

I am pleased to invite you to contribute to this Journal of Fungi Special Issue, “Molecular Genetics and Genomics of Mushroom-Forming Fungi”. This is a terrific opportunity for those with a passion for the study of mushrooms to publish their recent achievements in a Special Issue of this excellent emerging journal. Mushroom-forming fungi serve as excellent models for the study of fungal development, differentiation, genetic regulation, morphogenesis, and evolution. We have all been fascinated by the complex structure of microscopic mycelium. Conspicuous mushrooms and their related sclerotia enable relatively easy investigation of many biological processes in the fungal life cycle. However, although mushrooms have been used as food and medicine for thousands of years, their basic biology and genetics have not been well understood. It was not until the early 1990s, when advancements in molecular genetic technology enabled the study of living organisms with less-known basic genetics and genetic tools, that molecular genetic studies of mushrooms began. These advances in genomic technology (a result of the human genome project) allowed researchers to conduct more in-depth and wholistic analyses of mushrooms’ gene regulation, genetic structure, development, and evolution. Now, with the improved power and accessibility of advanced molecular genetic and genomic tools, researchers can develop a better understanding of mushroom biology. The scope of existing studies has expanded from single-gene to whole-genome studies, and from model mushrooms to those with nutritional and medicinal values. The advancement of basic and applied mushroom science has indeed been immense.

I encourage you to join me in showcasing recent achievements in the molecular genetics and genomics of mushroom-forming fungi in this focused Special Issue of the Journal of Fungi. This issue will serve as a benchmark for the high level of science conducted in this interesting and exciting field of Mushroom Biology.

Prof. Dr. Hoi Shan Kwan
Guest Editor

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Keywords

mushrooms
genomics
population genomics
DNA sequencing
RNA sequencing
transcriptomics
epigenomics
phylogeny
evolution
multicellularity
mating types
genetic architecture
fruiting body development
CRISPR

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Published Papers (11 papers)

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Research

16 pages, 3210 KiB

Open AccessArticle

A Comprehensive Assessment of Ultraviolet-Radiation-Induced Mutations in Flammulina filiformis Using Whole-Genome Resequencing

by Qianhui Huang, Xing Han, Zongjun Tong, Youjin Deng, Luyu Xie, Shengrong Liu, Baogui Xie and Weirui Zhang

J. Fungi 2024, 10(3), 228; https://doi.org/10.3390/jof10030228 - 20 Mar 2024

Viewed by 1673

Abstract

Nucleotide substitutions have played an important role in molecular evolution, and understanding their dynamics would contribute to genetic studies. Related research with defined DNA sequences lasted for decades until whole-genome sequencing arose. UV radiation (UVR) can generate base changes and other genetic variations in a short period of time, so it would be more meaningful to explore mutations caused by UVR from a genomic perspective. The monokaryon enoki strain WT583 was selected as the experimental material in this study because it can spontaneously produce large amounts of oidia on PDA plates, and the monokaryons originating from oidia have the same genotype as their mother monokaryon. After exposure to UV radiation, 100 randomly selected mutants, with WT583 as the reference genome, were sent for genome sequencing. BWA, samtools, and GATK software were employed for SNP calling, and the R package CMplot was used to visualize the distribution of the SNPs on the contigs of the reference genome. Furthermore, a k-mer-based method was used to detect DNA fragment deletion. Moreover, the non-synonymous genes were functionally annotated. A total of 3707 single-base substitutions and 228 tandem mutations were analyzed. The immediate adjacent bases showed different effects on the mutation frequencies of adenine and cytosine. For adenine, the overall effects of the immediate 5′-side and 3′-side bases were T > A > C > G and A > T > G > C, respectively; for cytosine, the overall effects of the immediate 5′-side and 3′-side bases were T > C > A > G and C > T > A > G, respectively. Regarding tandem mutations, the mutation frequencies of double-transition, double-transversion, 3′-side transition, and 5′-side transition were 131, 8, 72, and 17, respectively. Transitions at the 3′-side with a high mutation frequency shared a common feature, where they held transversions at the 5′-side of A→T or T→A without covalent bond changes, suggesting that the sequence context of tandem motifs might be related to their mutation frequency. In total, 3707 mutation sites were non-randomly distributed on the contigs of the reference genome. In addition, pyrimidines at the 3′-side of adenine promoted its transversion frequency, and UVR generated DNA fragment deletions over 200 bp with a low frequency in the enoki genome. The functional annotation of the genes with non-synonymous mutation indicated that UVR could produce abundant mutations in a short period of time. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)

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19 pages, 4963 KiB

Open AccessArticle

Transcriptome Analysis Reveals Mycelial and Fruiting Responses to Lithium Chloride in Coprinopsis cinerea

by Po-Lam Chan, Hoi-Shan Kwan, Yichun Xie, Ka-Hing Wong and Jinhui Chang

J. Fungi 2024, 10(2), 140; https://doi.org/10.3390/jof10020140 - 9 Feb 2024

Viewed by 1506

Abstract

Lithium chloride (LiCl) has been used in signalling and molecular studies of animals, plants, and yeast. However, information on its roles in basidiomycetous fungi is still limited. In this study, we used RNA-Seq to study the effects of LiCl on Coprinopsis cinerea. LiCl enhanced mycelial growth and inhibited fruiting body formation in C. cinerea. RNA-Seq of the LiCl-treated C. cinerea resulted in a total of 14,128 genes. There were 1199 differentially expressed genes (DEGs) between the LiCl-treated samples and control samples in the mycelium stage (the first time point), and 1391 DEGs were detected when the control samples were forming hyphal knots while the treated samples were still in the mycelium (the second time point). Pathway enrichment analysis of the DEGs revealed a significant association between enhanced mycelium growth in the LiCl-treated C. cinerea and metabolic pathways. In addition, the DEGs involved in cellular process pathways, including “cell cycle-yeast” and “meiosis-yeast”, were identified in suppressed C. cinerea fruiting body formation by LiCl under favourable environmental conditions. As LiCl can predominantly inhibit the activity of glycogen synthase kinase3 (GSK3), our findings suggest that LiCl affects the expression of genes involved in fruiting body initiation and cellular processes by inhibiting GSK3 activity which is essential for fruiting body formation. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)

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23 pages, 3817 KiB

Open AccessArticle

Molecular and Functional Analyses of Characterized Sesquiterpene Synthases in Mushroom-Forming Fungi

by Shengli Wang, Ruiqi Chen, Lin Yuan, Chenyang Zhang, Dongmei Liang and Jianjun Qiao

J. Fungi 2023, 9(10), 1017; https://doi.org/10.3390/jof9101017 - 14 Oct 2023

Cited by 2 | Viewed by 1958

Abstract

Sesquiterpenes are a type of abundant natural product with widespread applications in several industries. They are biosynthesized by sesquiterpene synthases (STSs). As valuable and abundant biological resources, mushroom-forming fungi are rich in new sesquiterpenes and STSs, which remain largely unexploited. In the present study, we collected information on 172 STSs from mushroom-forming fungi with experimentally characterized products from the literature and sorted them to develop a dataset. Furthermore, we analyzed and discussed the phylogenetic tree, catalytic products, and conserved motifs of STSs. Phylogenetic analysis revealed that the STSs were clustered into four clades. Furthermore, their cyclization reaction mechanism was divided into four corresponding categories. This database was used to predict 12 putative STS genes from the edible fungi Flammulina velutipes. Finally, three FvSTSs were selected to experimentally characterize their functions. FvSTS03 predominantly produced Δ-cadinol and FvSTS08 synthesized β-barbatene as the main product; these findings were consistent with those of the functional prediction analysis. A product titer of 78.8 mg/L β-barbatene was achieved in Saccharomyces cerevisiae via metabolic engineering. Our study findings will help screen or design STSs from fungi with specific product profiles as functional elements for applications in synthetic biology. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)

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21 pages, 3790 KiB

Open AccessArticle

The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of Coprinopsis cinerea

by Yichun Xie, Po-Lam Chan, Hoi-Shan Kwan and Jinhui Chang

J. Fungi 2023, 9(9), 915; https://doi.org/10.3390/jof9090915 - 9 Sep 2023

Cited by 3 | Viewed by 1814

Abstract

Coprinopsis cinerea is one of the model species used in fungal developmental studies. This mushroom-forming Basidiomycetes fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in C. cinerea development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in C. cinerea during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in C. cinerea. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that C. cinerea applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)

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10 pages, 1206 KiB

Open AccessArticle

Dicarboxylic Amino Acid Permease 7219 Regulates Fruiting Body Type of Auricularia heimuer

by Jia Lu, Lixin Lu, Fangjie Yao, Ming Fang, Xiaoxu Ma, Jingjing Meng and Kaisheng Shao

J. Fungi 2023, 9(9), 876; https://doi.org/10.3390/jof9090876 - 25 Aug 2023

Viewed by 1474

Abstract

Auricularia heimuer is a widely cultivated jelly mushroom. The fruiting bodies are categorized into cluster and chrysanthemum types. With changing consumer demands and the need to reduce bio-waste, the demand for clustered fruiting bodies is increasing. Therefore, gene mining for fruiting body types is a matter of urgency. We determined that the A. heimuer locus for fruiting body type was located at one end of the genetic linkage map. The locus was localized between the markers D23860 and D389 by increasing the density of the genetic linkage map. BlastN alignment showed that the marker SCL-18 was also located between D23860 and D389, and a total of 25 coding genes were annotated within this interval. Through parental transcriptome analysis and qRT-PCR verification, the locus g7219 was identified as the gene controlling the fruiting body type. A single-nucleotide substitution in the TATA box of g7219 was detected between the parents. By PCR amplification of the promoter region of g7219, the TATA-box sequences of the cluster- and chrysanthemum-type strains were found to be CATAAAA and TATAAAA, respectively. This study provides a foundation for the breeding of fruiting body types and strain improvement of A. heimuer. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)

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12 pages, 2594 KiB

Open AccessArticle

Overexpression of the Capebp2 Gene Encoding the PEBP-like Protein Promotes the Cap Redifferentiation in Cyclocybe aegerita

by Bopu Cheng, Nan Tao, Yuanhao Ma, Hongmei Chai, Ping Liu, Weimin Chen and Yongchang Zhao

J. Fungi 2023, 9(6), 657; https://doi.org/10.3390/jof9060657 - 12 Jun 2023

Cited by 2 | Viewed by 1508

Abstract

Phosphatidylethanolamine-binding protein (PEBP) is widely involved in various physiological behaviors, such as the transition from vegetative growth to reproductive growth in plants, tumorigenesis in the human, etc. However, few functional studies have examined pebp genes affecting the development of fungi. In this study, Capebp2 was cloned from Cyclocybe aegerita AC0007 strains based on the genome sequence and gene prediction, and the sequence alignment of CaPEBP2 with other PEBP proteins from other biological sources including plant, animal, fungi, and bacteria indicated that PEBP had low sequence similarity in fungi, whereas all protein sequences had some conserved motifs such as DPDAP and HRY. Expression analysis showed the transcription level of Capebp2 increased approximately 20-fold in fruiting bodies compared with mycelia. To uncover the function of Capebp2 in C. aegetita development, Capebp2 was cloned into a pATH vector driven by the actin promoter for obtaining overexpression transformant lines. Fruiting experiments showed the transformed strains overexpressing Capebp2 exhibited redifferentiation of the cap on their surface, including intact fruiting bodies or partial lamella during fruiting development stage, and the longitudinal section indicated that all regenerated bodies or lamella sprouted from the flesh and shared the epidermis with the mother fruiting bodies. In summary, the sequence characterization of Capebp2, expression level during different development stages, and function on fruiting body development were documented in this study, and these findings provided a reference to study the role of pebp in the development process of basidiomycetes. Importantly, gene mining of pebp, function characterization, and the regulating pathways involved need to be uncovered in further studies. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)

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16 pages, 10791 KiB

Open AccessArticle

Genome Re-Annotation and Transcriptome Analyses of Sanghuangporus sanghuang

by Zi-Qi Shen, Ji-Hang Jiang, Chang-Tian Li, Yu Li and Li-Wei Zhou

J. Fungi 2023, 9(5), 505; https://doi.org/10.3390/jof9050505 - 23 Apr 2023

Cited by 5 | Viewed by 2600

Abstract

Sanghuangporus sanghuang, the generic type of Sanghuangporus belonging to Hymenochaetaceae, is a precious medicinal wood-inhabiting macrofungus with high commercial potential. To facilitate the medicinal utilization of this fungal resource, transcriptome sequences are newly generated from S. sanghuang strain MS2. In association with the previously generated genome sequences from the same strain by our lab and all available fungal homologous protein sequences in the UniProtKB/Swiss-Prot Protein Sequence Database, a new methodology was employed for genome assembly and annotation. A total of 13,531 protein-coding genes were identified from the new version of the genome of S. sanghuang strain MS2 with a complete BUSCOs of 92.8%, which indicates a remarkable improvement in the accuracy and completeness of the genome assembly. In general, more genes involved in medicinal functions were annotated compared with the original version of the genome annotation, and most of these genes were also found in the transcriptome data of the currently sampled growth period. Given the above, the current genomic and transcriptomic data provides valuable insights into the evolution and metabolites analysis of S. sanghuang. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)

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18 pages, 4046 KiB

Open AccessArticle

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

by Chunhua Zhao, Xi-long Feng, Zhen-xin Wang and Jianzhao Qi

J. Fungi 2023, 9(4), 485; https://doi.org/10.3390/jof9040485 - 18 Apr 2023

Cited by 8 | Viewed by 2517

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. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)

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10 pages, 1915 KiB

Open AccessArticle

Structural Analysis of the A Mating Type Locus and Development of the Mating Type Marker of Agaricus bisporus var. bisporus

by Yeon-Jae Choi, Sujin Jung, Hyerang Eom, Thimen Hoang, Hui-Gang Han, Sinil Kim and Hyeon-Su Ro

J. Fungi 2023, 9(3), 284; https://doi.org/10.3390/jof9030284 - 21 Feb 2023

Cited by 1 | Viewed by 1720

Abstract

Karyotyping in Agaricus bisporus is crucial for both the isolation of homokaryotic strains and the confirmation of dikaryon establishment. For the verification of the karyotype, the A mating type loci of two homokaryotic strains, H39 and H97, were analyzed through comparative sequence analysis. The two loci showed major differences in two sequence regions designated as Region 1 and Region 2. H97 had a putative DNA transposon in Region 1 that had target site duplications (TSDs), terminal inverted repeats (TIRs), and a loop sequence, in contrast to H39, which only had the insertional target sequence. Homologous sequences of the transposon were discovered in the two different chromosomes of H97 and in one of H39, all of which have different TSDs but share high sequence homology in TIR. Region 2 shared three consensus sequences between H97 and H39. However, it was only from H97 that a large insertional sequence of unknown origin was discovered between the first and second consensus sequences. The difference in length in Region 1, employed for the verification of the A mating type, resulted in the successful verification of mating types in the heterokaryotic and homokaryotic strains. This length difference enables the discrimination between homo- and heterokaryotic spores by PCR. The present study suggests that the A mating type locus in A. bisporus H97 has evolved through transposon insertion, allowing the discrimination of the mating type, and thus the nuclear type, between A. bisporus H97 and H39. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)

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15 pages, 2946 KiB

Open AccessArticle

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

by Liping Zhu, Xia Gao, Meihua Zhang, Chunhui Hu, Wujie Yang, Lizhong Guo, Song Yang, Hailong Yu and Hao Yu

J. Fungi 2023, 9(2), 266; https://doi.org/10.3390/jof9020266 - 16 Feb 2023

Cited by 9 | Viewed by 3286

Abstract

Oudemansiella raphanipes, considered as a well-known culinary edible mushroom with a high content of natural bioactive substances, is widely cultivated in China with the commercial name Changgengu. However, due to the lack of genomic data, molecular and genetic study on O. raphanipes is rare. To obtain a comprehensive overview of genetic characteristics and enhance the value of O. raphanipes, two mating-compatible monokaryons isolated from the dikaryon were applied for de novo genome sequencing and assembly using Nanopore and /or Illumina sequencing platforms. One of the monokaryons, O. raphanipes CGG-A-s1, was annotated with 21,308 protein-coding genes, of which 56 were predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I PKS, NRPS, and siderophore. Phylogenetic and comparative analysis of multiple fungi genomes revealed a close evolutionary relationship between O. raphanipes and Mucidula mucid based on single-copy orthologous protein genes. Significant collinearity was detected between O. raphanipes and Flammulina velutipes on the synteny of inter-species genomes. 664 CAZyme genes in CGG-A-s1 were identified with GHs and AAs families significantly elevated when compared with the other 25 sequenced fungi, indicating a strong wood degradation ability. Furthermore, the mating type locus analysis revealed that CGG-A-s1 and CGG-A-s2 were conserved in the gene organization of the mating A locus but various in that of the mating B locus. The genome resource of O. raphanipes will provide new insights into its development of genetic studies and commercial production of high-quality varieties. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)

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16 pages, 5196 KiB

Open AccessArticle

Comparative Proteomic Analyses within Three Developmental Stages of the Mushroom White Hypsizygus marmoreus

by Lili Xu, Rongmei Lin, Xiaohang Li, Chenxiao Zhang, Xiuqing Yang, Lizhong Guo, Hao Yu, Xia Gao and Chunhui Hu

J. Fungi 2023, 9(2), 225; https://doi.org/10.3390/jof9020225 - 8 Feb 2023

Cited by 4 | Viewed by 2056

Abstract

(1) Background: The Hypsizygus marmoreus is a popular edible mushroom in East Asian markets. In a previous study, we reported the proteomic analyses of different developmental stages of H. marmoreus, from primordium to mature fruiting body. However, the growth and protein expression changes from scratching to primordium are unclear. (2) Methods: A label-free LC-MS/MS quantitative proteomic analysis technique was adopted to obtain the protein expression profiles of three groups of samples collected in different growth stages from scratching to the tenth day after scratching. The Pearson’s correlation coefficient analysis and principal component analysis were performed to reveal the correlation among samples. The differentially expressed proteins (DEPs) were organized. Gene Ontology (GO) analysis was performed to divide the DEPs into different metabolic processes and pathways. (3) Results: From the 3rd day to the 10th day after scratching, mycelium recovered gradually and formed primordia. Compared with the Rec stage, 218 highly expressed proteins were identified in the Knot stage. Compared with the Pri stage, 217 highly expressed proteins were identified in the Rec stage. Compared with the Pri stage, 53 highly expressed proteins were identified in the Knot stage. A variety of the same highly expressed proteins were identified in these three developmental stages, including: glutathione S-transferase, acetyltransferase, importin, dehydrogenase, heat-shock proteins, ribosomal proteins, methyltransferase, etc. The key pathways in the development of H. marmoreus are metabolic process, catabolic process, oxidoreductase activity and hydrolase activity. DEPs in the Knot or Pri stages compared with the Rec stage were significantly decreased in the metabolic-, catabolic- and carbohydrate-related process; and the oxidoreductase, peptidase, and hydrolase activity, which can serve as targets for selectable molecular breeding in H. marmoreus. A total of 2000 proteins were classified into eight different modules by WGCNA, wherein 490 proteins were classified into the turquoise module. (4) Conclusions: Generally, from the 3rd day to the 10th day after scratching, mycelium recovered gradually and formed primordia. Importin, dehydrogenase, heat-shock proteins, ribosomal proteins, transferases were all highly expressed in these three developmental stages. DEPs in the Rec stage compared with the Knot or Pri stages were significantly enriched in the metabolic-, catabolic- and carbohydrate-related process; and in oxidoreductase, peptidase and hydrolase activities. This research contributes to the understanding of the mechanisms of the development changes before primordium of H. marmoreus. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Mushroom-Forming Fungi)

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