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Genetics and Breeding of Basidiomycetes for Biotechnology

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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 May 2022) | Viewed by 41247

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Prof. Dr. Lucïa Ramírez

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Genetics, Genomics and Microbiology Research Group, Institute for Multidisciplinary Research in Applied Biology (IMAB-UPNa), Public University of Navarre, 31006 Pamplona, Spain
Interests: the genetics and breeding of higher basidiomycetes

Prof. Dr. Antonio Pisabarro

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Institute for Multidisciplinary Research in Applied Biology (IMAB), Public University of Navarra (UPNA), 31006 Pamplona, Spain
Interests: fungal genome; transcriptome and proteome analysis; fungal biotechnology; fungal metabolism; infectious diseases
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Dear Colleagues,

Basidiomycetes are the second most abundant group of fungi on Earth. The group includes human and plant pathogens, as well as ecologically essential fungi such as ectomycorrhizas and lignocellulose degraders. Many basidiomycetes are especially useful as edible fungi, and some of them are agro-industrially produced for food, proteins, or secondary metabolites with pharmacological applications. Additionally, some basidiomycetes have been extensively studied as model systems of fungal development and mating control. In the last decade, the advances in genome sequencing and analysis have produced a wealth of data covering genome organization and structure, whole-genome transcription in different organisms, developmental stages and culture conditions, epigenetic modifications including methylation, transposon-mediated gene regulation, and proteomic information. This information permits the design of fungal breeding programs to enlarge the number of cultivable species, improve the production of biomass and fungal-derived products, understand and manipulate pathogenic and mycorrhizal interactions, and explore the dikaryotic lifestyle that is unique to this type of organism.

This Special Issue in the Journal of Fungi reviews these topics focusing on basidiomycete-based biotechnology applications such as the production of new strains, their industrial cultivation, the exploitation of their primary and secondary products, and their use in bioprocesses.

Prof. Dr. Lucïa Ramírez
Prof. Dr. Antonio Pisabarro
Guest Editors

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Keywords

genome analysis
transcriptome analysis
epigenome analysis
basidiomycete cultivation
mating types
lignocellulose recycling
ectomycorrhizas
fungal pathogens
secondary metabolites
dikaryotic lifestyle in basidiomycetes
genetics
mating types
secondary metabolites
interaction with other organisms, nutritional properties
genetics
cell biology
nanotechnology
enzymes
fungal interaction
functional nutrients
nanp-coatings

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Published Papers (11 papers)

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Research

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16 pages, 4373 KiB

Open AccessArticle

FFGA1 Protein Is Essential for Regulating Vegetative Growth, Cell Wall Integrity, and Protection against Stress in Flammunina filiformis

by Muyun Du, Yongbo Xie, Meng Wang, Huan Yang, Banghui Hu, Irum Mukhtar, Yuanyuan Liu, Yongxin Tao, Fang Liu and Baogui Xie

J. Fungi 2022, 8(4), 401; https://doi.org/10.3390/jof8040401 - 14 Apr 2022

Cited by 11 | Viewed by 2805

Abstract

Flammulina filiformis is a popular mushroom which has been regarded as a potential model fungus for mycelium growth, fruiting body development, and stress response studies. Based on a genome-wide search, four genes encoding heterotrimeric G protein α subunits were identified in F. filiformis. The data of conserved domain analysis showed that these genes contain only one subgroup I of Gα subunit (Gαi), similar to many other fungi. To explore the function of Gαi, FfGa1 over-expression (OE) and RNA interference (RNAi) strains were generated using the Agrobacterium tumefaciens-mediated transformation (ATMT) approach. RNAi transformant strains showed remarkably reduced growth on PDA medium and added sensitivity to cell wall-enforcing agents with maximum growth inhibition, but showed better growth in response to hypertonic stress-causing agents, while OE strains exhibited more resistance to thermal stress and mycoparasite Trichoderma as compared to the wild-type and RNAi strains. Taken together, our results indicated that FfGa1 positively regulates hyphal extension, and is crucial for the maintenance of cell wall integrity and protection against biotic and abiotic (hypertonic and thermal) stress. Full article

(This article belongs to the Special Issue Genetics and Breeding of Basidiomycetes for Biotechnology)

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20 pages, 5956 KiB

Open AccessArticle

The First Whole Genome Sequence Discovery of the Devastating Fungus Arthrinium rasikravindrae

by Abdul Qayoom Majeedano, Jie Chen, Tianhui Zhu, Shujiang Li, Zeeshan Ghulam Nabi Gishkori, Sumbul Mureed Mastoi and Gang Wang

J. Fungi 2022, 8(3), 255; https://doi.org/10.3390/jof8030255 - 2 Mar 2022

Cited by 4 | Viewed by 3713

Abstract

Devastating fungi are one of the most important biotic factors associated with numerous infectious diseases not only in plants but in animals and humans too. Arthrinium rasikravindrae a devastating fungus is responsible for severe infections in a large number of host plants all over the world. In the present study, we analyzed the whole genome sequence of devastating fungus A. rasikravindrae strain AQZ-20, using Illumina Technology from the Novogene Bio-informatics Co., Ltd. Beijing, China. To identify associated annotation results, various corresponding functional annotations databases were utilized. The genome size was 48.24 MB with an N90 (scaffolds) length of 2,184,859 bp and encoded putative genes were 11,101, respectively. In addition, we evaluated the comparative genomic analyses with 4 fungal strains of Ascomycetes. Two related species showed a strong correlation while others exhibited a weak correlation with the A. rasikravindrae AQZ-20 fungus. This study is a discovery of the genome-scale assembly, as well as annotation for A. rasikravindrae. The results obtained from the whole genome sequencing and genomic resources developed in this study will contribute significantly to genetic improvement applications against diseases caused by A. rasikravindrae. In addition, the phylogenetic tree, followed by genomic RNA, transcriptomic, proteomic, metabolic, as well as pathogenic data reported in current research will provide deep insight for further studies in the future. Full article

(This article belongs to the Special Issue Genetics and Breeding of Basidiomycetes for Biotechnology)

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12 pages, 7547 KiB

Open AccessArticle

Establishment of an Efficient Polyethylene Glycol (PEG)-Mediated Transformation System in Pleurotus eryngii var. ferulae Using Comprehensive Optimization and Multiple Endogenous Promoters

by Qi Zhang, Liting Zhao, Mengye Shen, Jingyun Liu, Youran Li, Sha Xu, Lei Chen, Guiyang Shi and Zhongyang Ding

J. Fungi 2022, 8(2), 186; https://doi.org/10.3390/jof8020186 - 14 Feb 2022

Cited by 11 | Viewed by 3866

Abstract

Pleurotus eryngii var. ferulae, a fungus of the genus Pleurotus, efficiently degrades lignin, especially during co-cultivation with other fungi. However, low transformation efficiency and heterologous gene expression restrict systematic studies of the molecular mechanisms and metabolic control of natural products in this mushroom. In this study, the homologous resistance marker carboxin (cbx) was used to establish a polyethylene glycol-mediated transformation (PMT) system in P. eryngii var. ferulae. Optimization of the transformation process greatly improved the number of positive transformants. In particular, we optimized: (i) protoplast preparation and regeneration; (ii) screening methods; and (iii) transformation-promoting factors. The optimized transformation efficiency reached 72.7 CFU/μg, which is higher than the average level of Pleurotus sp. (10–40 CFU/μg). Moreover, three endogenous promoters (P_pfgpd1, P_pfgpd2, and P_pfsar1) were screened and evaluated for different transcription initiation characteristics. A controllable overexpression system was established using these three promoters that satisfied various heterologous gene expression requirements, such as strong or weak, varied, or stable expression levels. This study lays the foundation for recombinant protein expression in P. eryngii var. ferulae and provides a method to investigate the underlying molecular mechanisms and secondary metabolic pathway modifications. Full article

(This article belongs to the Special Issue Genetics and Breeding of Basidiomycetes for Biotechnology)

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19 pages, 5033 KiB

Open AccessArticle

Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes

by Qi Gao, Dong Yan, Shuang Song, Yangyang Fan, Shouxian Wang, Yu Liu, Yu Huang, Chengbo Rong, Yuan Guo, Shuang Zhao, Wentao Qin and Jianping Xu

J. Fungi 2022, 8(2), 167; https://doi.org/10.3390/jof8020167 - 9 Feb 2022

Cited by 8 | Viewed by 3291 | Correction

Abstract

Lentinula edodes is a tetrapolar basidiomycete with two haploid nuclei in each cell during most of their life cycle. Understanding the two haploid nuclei genome structures and their interactions on growth and fruiting body development has significant practical implications, especially for commercial cultivars. In this study, we isolated and assembled the two haploid genomes from a commercial strain of L. edodes using Illumina, HiFi, and Hi-C technologies. The total genome lengths were 50.93 Mb and 49.80 Mb for the two monokaryons SP3 and SP30, respectively, with each assembled into 10 chromosomes with 99.63% and 98.91% anchoring rates, respectively, for contigs more than 100 Kb. Genome comparisons suggest that two haploid nuclei likely derived from distinct genetic ancestries, with ~30% of their genomes being unique or non-syntenic. Consistent with a tetrapolar mating system, the two mating-type loci A (matA) and B (matB) of L. edodes were found located on two different chromosomes. However, we identified a new but incomplete homeodomain (HD) sublocus at ~2.8 Mb from matA in both monokaryons. Our study provides a solid foundation for investigating the relationships among cultivars and between cultivars and wild strains and for studying how two genetically divergent nuclei coordinate to regulate fruiting body formation in L. edodes. Full article

(This article belongs to the Special Issue Genetics and Breeding of Basidiomycetes for Biotechnology)

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15 pages, 22411 KiB

Open AccessArticle

Whole Genome Sequence of an Edible Mushroom Stropharia rugosoannulata (Daqiugaigu)

by Shuwen Li, Shuxue Zhao, Chunhui Hu, Chengzhi Mao, Lizhong Guo, Hailong Yu and Hao Yu

J. Fungi 2022, 8(2), 99; https://doi.org/10.3390/jof8020099 - 20 Jan 2022

Cited by 24 | Viewed by 4566

Abstract

Stropharia rugosoannulata, also known as Daqiugaigu in China, is a well-known edible mushroom that has been widely cultivated in China in recent years. Many studies have focused on its nutrients, bioactive compounds, and lignin degradation capacity, although there are few molecular and genetic breeding studies due to the lack of genomic information. Here, we present the 47.9 Mb genome sequence of an S. rugosoannulata monokaryotic strain (A15), which has 20 contigs and an N50 of 3.64 Mb, which was obtained by a combination of Illumina and Nanopore sequencing platforms. Further analysis predicted 12,752 protein-coding genes, including 486 CAZyme-encoding genes. Phylogenetic analysis revealed a close evolutionary relationship between S. rugosoannulata and Hypholoma sublateritium, Psilocybe cyanescens, and Galerina marginata based on single-copy orthologous genes. Proteomic analysis revealed different protein expression profiles between the cap and the stipe of the S. rugosoannulata fruiting body. The proteins of the stipe associated with carbon metabolism, energy production, and stress-response-related biological processes had higher abundance, whereas proteins involved in fatty acid synthesis and mRNA splicing showed higher expression in the cap than in the stipe. The genome of S. rugosoannulata will provide valuable genetic resources not only for comparative genomic analyses and evolutionary studies among Basidiomycetes but also for alleviating the bottlenecks that restrict the molecular breeding of this edible mushroom. Full article

(This article belongs to the Special Issue Genetics and Breeding of Basidiomycetes for Biotechnology)

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21 pages, 3047 KiB

Open AccessArticle

Effect of Nutritional Factors and Copper on the Regulation of Laccase Enzyme Production in Pleurotus ostreatus

by Dinary Durán-Sequeda, Daniela Suspes, Estibenson Maestre, Manuel Alfaro, Gumer Perez, Lucía Ramírez, Antonio G. Pisabarro and Rocío Sierra

J. Fungi 2022, 8(1), 7; https://doi.org/10.3390/jof8010007 - 22 Dec 2021

Cited by 23 | Viewed by 4412

Abstract

This research aimed to establish the relationship between carbon–nitrogen nutritional factors and copper sulfate on laccase activity (LA) by Pleurotus ostreatus. Culture media composition was tested to choose the nitrogen source. Yeast extract (YE) was selected as a better nitrogen source than ammonium sulfate. Then, the effect of glucose and YE concentrations on biomass production and LA as response variables was evaluated using central composite experimental designs with and without copper. The results showed that the best culture medium composition was glucose 45 gL⁻¹and YE 15 gL⁻¹, simultaneously optimizing these two response variables. The fungal transcriptome was obtained in this medium with or without copper, and the differentially expressed genes were found. The main upregulated transcripts included three laccase genes (lacc2, lacc6, and lacc10) regulated by copper, whereas the principal downregulated transcripts included a copper transporter (ctr1) and a regulator of nitrogen metabolism (nmr1). These results suggest that Ctr1, which facilitates the entry of copper into the cell, is regulated by nutrient-sufficiency conditions. Once inside, copper induces transcription of laccase genes. This finding could explain why a 10–20-fold increase in LA occurs with copper compared to cultures without copper when using the optimal concentration of YE as nitrogen sources. Full article

(This article belongs to the Special Issue Genetics and Breeding of Basidiomycetes for Biotechnology)

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18 pages, 3868 KiB

Open AccessArticle

Whole Genome Sequencing and Annotation of Naematelia aurantialba (Basidiomycota, Edible-Medicinal Fungi)

by Tao Sun, Yixuan Zhang, Hao Jiang, Kai Yang, Shiyu Wang, Rui Wang, Sha Li, Peng Lei, Hong Xu, Yibin Qiu and Dafeng Sun

J. Fungi 2022, 8(1), 6; https://doi.org/10.3390/jof8010006 - 22 Dec 2021

Cited by 14 | Viewed by 4715

Abstract

Naematelia aurantialba is a rare edible fungus with both nutritional and medicinal values and especially rich in bioactive polysaccharides. However, due to the lack of genomic information, researches on the mining of active compounds, artificial breeding and cultivation, genetics, and molecular biology are limited. To facilitate the medicinal and food applications of N. aurantialba, we sequenced and analyzed the whole genome of N. aurantialba for the first time. The 21-Mb genome contained 15 contigs, and a total of 5860 protein-coding genes were predicted. The genome sequence shows that 296 genes are related to polysaccharide synthesis, including 15 genes related to nucleoside-activated sugar synthesis and 11 genes related to glucan synthesis. The genome also contains genes and gene clusters for the synthesis of other active substances, including terpenoids, unsaturated fatty acids, and bioactive proteins. In addition, it was also found that N. aurantialba was more closely related to Naematelia encephala than to Tremella fuciformis. In short, this study provides a reference for molecular cognition of N. aurantialba and related researches. Full article

(This article belongs to the Special Issue Genetics and Breeding of Basidiomycetes for Biotechnology)

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26 pages, 3400 KiB

Open AccessArticle

Strain Degeneration in Pleurotus ostreatus: A Genotype Dependent Oxidative Stress Process Which Triggers Oxidative Stress, Cellular Detoxifying and Cell Wall Reshaping Genes

by Gumer Pérez, Federico Lopez-Moya, Emilia Chuina, María Ibañez-Vea, Edurne Garde, Luis V. López-Llorca, Antonio G. Pisabarro and Lucía Ramírez

J. Fungi 2021, 7(10), 862; https://doi.org/10.3390/jof7100862 - 14 Oct 2021

Cited by 17 | Viewed by 4077

Abstract

Strain degeneration has been defined as a decrease or loss in the yield of important commercial traits resulting from subsequent culture, which ultimately leads to Reactive Oxygen Species (ROS) production. Pleurotus ostreatus is a lignin-producing nematophagous edible mushroom. Mycelia for mushroom production are usually maintained in subsequent culture in solid media and frequently show symptoms of strain degeneration. The dikaryotic strain P. ostreatus (DkN001) has been used in our lab as a model organism for different purposes. Hence, different tools have been developed to uncover genetic and molecular aspects of this fungus. In this work, strain degeneration was studied in a full-sib monokaryotic progeny of the DkN001 strain with fast (F) and slow (S) growth rates by using different experimental approaches (light microscopy, malondialdehyde levels, whole-genome transcriptome analysis, and chitosan effect on monokaryotic mycelia). The results obtained showed that: (i) strain degeneration in P. ostreatus is linked to oxidative stress, (ii) the oxidative stress response in monokaryons is genotype dependent, (iii) stress and detoxifying genes are highly expressed in S monokaryons with symptoms of strain degeneration, (iv) chitosan addition to F and S monokaryons uncovered the constitutive expression of both oxidative stress and cellular detoxifying genes in S monokaryon strains which suggest their adaptation to oxidative stress, and (v) the overexpression of the cell wall genes, Uap1 and Cda1, in S monokaryons with strain degeneration phenotype indicates cell wall reshaping and the activation of High Osmolarity Glycerol (HOG) and Cell Wall Integrity (CWI) pathways. These results could constitute a hallmark for mushroom producers to distinguish strain degeneration in commercial mushrooms. Full article

(This article belongs to the Special Issue Genetics and Breeding of Basidiomycetes for Biotechnology)

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18 pages, 2363 KiB

Open AccessArticle

The First Whole Genome Sequencing of Sanghuangporus sanghuang Provides Insights into Its Medicinal Application and Evolution

by Ji-Hang Jiang, Sheng-Hua Wu and Li-Wei Zhou

J. Fungi 2021, 7(10), 787; https://doi.org/10.3390/jof7100787 - 22 Sep 2021

Cited by 21 | Viewed by 4056

Abstract

Sanghuangporus is a medicinal macrofungal genus typified by S. sanghuang, the very species utilized in traditional Chinese medicines by Chinese ancient people. To facilitate the medicinal application of S. sanghuang, we, for the first time, perform its genome sequencing and analyses from a monokaryon strain. A 33.34 Mb genome sequence was assembled to 26 contigs, which lead to the prediction of 8278 protein-coding genes. From these genes, the potential biosynthesis pathway of sesquiterpenoids was, for the first time, identified from Sanghuangporus, besides that of triterpenoids. While polysaccharides are the main medicinal metabolites in S. sanghuang, flavonoids are especially abundant medicinal metabolites comparing with other medicinal macrofungal groups. From the genomic perspective, S. sanghuang has a tetrapolar heterothallic mating system, and has its special nutritional strategy and advantageous medicinal properties compared with S. baumii and S. vaninii. A phylogenomics analysis indicates that Sanghuangporus emerged 15.39 million years ago and S. sanghuang has a closer phylogenetic relationship with S. baumii than S. vaninii. However, S. sanghuang shares a higher region of synteny and more orthologous genes, including carbohydrate-active enzymes with S. vaninii than S. baumii. A comparative genomics analysis with S. baumii and S. vaninii indicates that species diversification within Sanghuangporus may be driven by the translocation and translocation plus inversion of genome sequences, while the expansion and contraction of gene families may contribute to the host specificity of Sanghuangporus species. In general, the genome sequence of S. sanghuang provides insights into its medicinal application and evolution. Full article

(This article belongs to the Special Issue Genetics and Breeding of Basidiomycetes for Biotechnology)

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Review

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21 pages, 1876 KiB

Open AccessReview

Kinesin Motors in the Filamentous Basidiomycetes in Light of the Schizophyllum commune Genome

by Marjatta Raudaskoski

J. Fungi 2022, 8(3), 294; https://doi.org/10.3390/jof8030294 - 12 Mar 2022

Viewed by 2903

Abstract

Kinesins are essential motor molecules of the microtubule cytoskeleton. All eukaryotic organisms have several genes encoding kinesin proteins, which are necessary for various cell biological functions. During the vegetative growth of filamentous basidiomycetes, the apical cells of long leading hyphae have microtubules extending toward the tip. The reciprocal exchange and migration of nuclei between haploid hyphae at mating is also dependent on cytoskeletal structures, including the microtubules and their motor molecules. In dikaryotic hyphae, resulting from a compatible mating, the nuclear location, synchronous nuclear division, and extensive nuclear separation at telophase are microtubule-dependent processes that involve unidentified molecular motors. The genome of Schizophyllum commune is analyzed as an example of a species belonging to the Basidiomycota subclass, Agaricomycetes. In this subclass, the investigation of cell biology is restricted to a few species. Instead, the whole genome sequences of several species are now available. The analyses of the mating type genes and the genes necessary for fruiting body formation or wood degrading enzymes in several genomes of Agaricomycetes have shown that they are controlled by comparable systems. This supports the idea that the genes regulating the cell biological process in a model fungus, such as the genes encoding kinesin motor molecules, are also functional in other filamentous Agaricomycetes. Full article

(This article belongs to the Special Issue Genetics and Breeding of Basidiomycetes for Biotechnology)

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2 pages, 1416 KiB

Open AccessCorrection

Correction: Gao et al. Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. J. Fungi 2022, 8, 167

by Qi Gao, Dong Yan, Shuang Song, Yangyang Fan, Shouxian Wang, Yu Liu, Yu Huang, Chengbo Rong, Yuan Guo, Shuang Zhao, Wentao Qin and Jianping Xu

J. Fungi 2022, 8(5), 496; https://doi.org/10.3390/jof8050496 - 11 May 2022

Cited by 1 | Viewed by 1253

Abstract

In the original article [...] Full article

(This article belongs to the Special Issue Genetics and Breeding of Basidiomycetes for Biotechnology)

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