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Ma L, Yang C, Xiao D, Liu X, Jiang X, Lin H, Ying Z, Lin Y. Chromosome-level assembly of Dictyophora rubrovolvata genome using third-generation DNA sequencing and Hi-C analysis. G3 (BETHESDA, MD.) 2023; 13:jkad102. [PMID: 37178144 PMCID: PMC10411574 DOI: 10.1093/g3journal/jkad102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 01/15/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023]
Abstract
Dictyophora rubrovolvata, a rare edible mushroom with both nutritional and medicinal values, was regarded as the "queen of the mushroom" for its attractive appearance. Dictyophora rubrovolvata has been widely cultivated in China in recent years, and many researchers were focusing on its nutrition, culture condition, and artificial cultivation. Due to a lack of genomic information, research on bioactive substances, cross breeding, lignocellulose degradation, and molecular biology is limited. In this study, we report a chromosome-level reference genome of D. rubrovolvata using the PacBio single-molecule real-time-sequencing technique and high-throughput chromosome conformation capture (Hi-C) technologies. A total of 1.83 Gb circular consensus sequencing reads representing ∼983.34 coverage of the D. rubrovolvata genome were generated. The final genome was assembled into 136 contigs with a total length of 32.89 Mb. The scaffold and contig N50 length were 2.71 and 2.48 Mb, respectively. After chromosome-level scaffolding, 11 chromosomes with a total length of 28.24 Mb were constructed. Genome annotation further revealed that 9.86% of the genome was composed of repetitive sequences, and a total of 508 noncoding RNA (rRNA: 329, tRNA: 150, ncRNA: 29) were annotated. In addition, 9,725 protein-coding genes were predicted, among which 8,830 (90.79%) genes were predicted using homology or RNA-seq. Benchmarking Universal Single-Copy Orthologs results further revealed that there were 80.34% complete single-copy fungal orthologs. In this study, a total of 360 genes were annotated as belonging to the carbohydrate-active enzymes family. Further analysis also predicted 425 cytochromes P450 genes, which can be classified into 41 families. This highly accurate, chromosome-level reference genome of D. rubrovolvata will provide essential genomic information for understanding the molecular mechanism in its fruiting body formation during morphological development and facilitate the exploitation of medicinal compounds produced by this mushroom.
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Affiliation(s)
- Lu Ma
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Chi Yang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Donglai Xiao
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Xiaoyu Liu
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Xiaoling Jiang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Hui Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Zhenghe Ying
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Yanquan Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
- National and Local Joint Engineering Research Center for Breeding and Cultivation of Featured Edible Muhsroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
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Nagy L, Vonk P, Künzler M, Földi C, Virágh M, Ohm R, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu X, Nan S, Pareek M, Sahu N, Szathmári B, Varga T, Wu H, Yang X, Merényi Z. Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Stud Mycol 2023; 104:1-85. [PMID: 37351542 PMCID: PMC10282164 DOI: 10.3114/sim.2022.104.01] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/02/2022] [Indexed: 01/09/2024] Open
Abstract
Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01.
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Affiliation(s)
- L.G. Nagy
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - P.J. Vonk
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - M. Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland;
| | - C. Földi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - M. Virágh
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - R.A. Ohm
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;
| | - F. Hennicke
- Project Group Genetics and Genomics of Fungi, Chair Evolution of Plants and Fungi, Ruhr-University Bochum, 44780, Bochum, North Rhine-Westphalia, Germany;
| | - B. Bálint
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Á. Csernetics
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Hegedüs
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - Z. Hou
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X.B. Liu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - S. Nan
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - M. Pareek
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - N. Sahu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - B. Szathmári
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - T. Varga
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - H. Wu
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
| | - X. Yang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Z. Merényi
- Synthetic and Systems Biology Unit, Biological Research Center, Szeged, 6726, Hungary;
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Proteomic characterization of Shiitake (Lentinula edodes) post-harvest fruit bodies grown on hardwood logs and isolation of an antibacterial serine protease inhibitor. Fungal Biol 2023; 127:881-890. [PMID: 36746560 DOI: 10.1016/j.funbio.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/23/2022]
Abstract
Lentinula edodes (Shiitake) is one of the most heavily cultivated mushrooms in the world with proven antioxidant and antibacterial properties, among others. Evidence indicates that the choice of mushroom cultivation technique strongly influences the production of bioactive compounds, but to date the nature of many of these compounds has not been fully established. This work focuses on the proteomic characterization of L. edodes to highlight the main active processes two days after harvest and elucidates the proteins involved in the known antioxidant and antibacterial proprieties of Shiitake fruit bodies cultivated on oak logs. A label-free approach allowed us to identify a total of 2702 proteins which were mainly involved in carbohydrate and protein metabolism, cell growth and replication, indicating that several developmental processes remain active in fruit bodies post-harvest. Proteins with antioxidant activities were identified, indicating the contribution of proteins to the antioxidant properties of L. edodes extracts. Antibacterial assays also reveal the activity of a serine protease inhibitor that strongly accumulates in the post-harvest fruit body grown on oak logs. Overall, this study contributes to the understanding of the impact of the log cultivation method on the production of Shiitake mushrooms richest in high-value bioactive compounds.
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Kim S, Eom H, Nandre R, Choi YJ, Lee H, Ryu H, Ro HS. Comparative structural analysis on the mitochondrial DNAs from various strains of Lentinula edodes. Front Microbiol 2022; 13:1034387. [DOI: 10.3389/fmicb.2022.1034387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/09/2022] [Indexed: 11/30/2022] Open
Abstract
The evolution of mitochondria through variations in mitochondrial DNA (mtDNA) is one of the intriguing questions in eukaryotic cells. In order to assess the causes of the variations in mitochondria, the mtDNAs of the 21 strains of Lentinula edodes were assembled for this study, and analyzed together with four published mtDNA sequences. The mtDNAs were within the sizes of 117 kb ~ 122 kb. The gene number was observed consistent except for two mtDNAs, which carry a duplicated trnG1-trnG2 unit or a putative gene deletion. The size variation was largely attributed to the number of introns, repeated sequences, transposable elements (TEs), and plasmid-related sequences. Intron loss and gain were found from cox1, rnl, and rns of three mtDNAs. Loss of two introns in cox1 of KY217797.1 reduced its size by 2.7 kb, making it the smallest cox1 gene (8.4 kb) among the cox1s of the 25 mtDNAs, whereas gain of a Group II intron (2.65 kb) and loss of a Group I intron (1.7 kb) in cox1 of MF774813.1 resulted in the longest cox1 (12 kb). In rnl of L. edodes, we discovered four intron insertion consensus sequences which were unique to basidiomycetes but not ascomycetes. Differential incorporation of introns was the primary cause of the rnl size polymorphism. Homing endonucleases (HEGs) were suggestively involved in the mobilization of the introns because all of the introns have HEG genes of the LAGRIDADG or GIY-YIG families with the conserved HEG cleavage sites. TEs contributed to 11.04% of the mtDNA size in average, of which 7.08% was LTR-retrotransposon and 3.96% was DNA transposon, whereas the repeated sequences covered 4.6% of the mtDNA. The repeat numbers were variable in a strain-dependent manner. Both the TEs and repeated sequences were mostly found in the intronic and intergenic regions. Lastly, two major deletions were found in the plasmid-related sequence regions (pol2-pol3 and pol1-atp8) in the five mtDNAs. Particularly, the 6.8 kb-long deletion at pol2-pol3 region made MF774813.1 the shortest mtDNA of all. Our results demonstrate that mtDNA is a dynamic molecule that persistently evolves over a short period of time by insertion/deletion and repetition of DNA segments at the strain level.
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UVB Irradiation-Induced Transcriptional Changes in Lignin- and Flavonoid Biosynthesis and Indole/Tryptophan-Auxin-Responsive Genes in Rice Seedlings. PLANTS 2022; 11:plants11121618. [PMID: 35736769 PMCID: PMC9229965 DOI: 10.3390/plants11121618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022]
Abstract
Global warming accelerates the destruction of the ozone layer, increasing the amount of UVB reaching the Earth’s surface, which in turn alters plant growth and development. The effects of UVB-induced alterations of plant secondary and cell wall metabolism were previously documented; however, there is little knowledge of its effects on rice seedlings during the developmental phase of leaves. In this study, we examined secondary metabolic responses to UVB stress using a transcriptomic approach, focusing on the biosynthetic pathways for lignin, flavonoid, and indole/tryptophan-auxin responses. As new leaves emerged, they were irradiated with UVB for 5 days (for 3 h/day−1). The genes encoding the enzymes related to lignin (4CL, CAD, and POD) and flavonoid biosynthesis (CHS, CHI, and FLS) were highly expressed on day 1 (younger leaves) and day 5 (older leaves) after UVB irradiation. The expression of the genes encoding the enzymes related to tryptophan biosynthesis (AS, PRT, PRAI, IGPS, and TS) increased on day 3 of UVB irradiation, and the level of tryptophan increased and showed the same temporal pattern of occurrence as the expression of the cognate gene. Interestingly, the genes encoding BBX4 and BBX11, negative regulators of UVB signaling, and SAUR27 and SAUR55, auxin response enzymes, were downregulated on day 3 of UVB irradiation. When these results are taken together, they suggest that secondary metabolic pathways in rice seedlings are influenced by the interaction between UVB irradiation and the leaf developmental stage. Thus, the strategies of protection against, adaptation to, and mitigation of UVB might be delicately regulated, and, in this context, our data provide valuable information to understand UVB-induced secondary metabolism in rice seedlings.
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Menolli N, Sánchez-Ramírez S, Sánchez-García M, Wang C, Patev S, Ishikawa NK, Mata JL, Lenz AR, Vargas-Isla R, Liderman L, Lamb M, Nuhn M, Hughes KW, Xiao Y, Hibbett DS. Global phylogeny of the Shiitake mushroom and related Lentinula species uncovers novel diversity and suggests an origin in the Neotropics. Mol Phylogenet Evol 2022; 173:107494. [PMID: 35490968 DOI: 10.1016/j.ympev.2022.107494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 01/18/2023]
Abstract
Lentinula (Basidiomycota, Agaricales) includes the most widely cultivated mushroom in the world, Lentinula edodes, also known as shiitake (Japanese) or xiang-gu (Chinese). At present, nine species are recognized in the genus, based on morphology, mating criteria, and geographic distributions. However, analyses of internal transcribed spacers (ITS) of ribosomal RNA genes have suggested that there are cryptic lineages. We analyzed a global-scale phylogenetic dataset from 325 Lentinula individuals from 24 countries in Asia-Australasia and the Americas plus Madagascar, with 325 sequences of ITS, 80 LSU sequences, and 111 sequences of translation elongation factor (tef1-α) genes. We recovered 15 independent lineages (Groups 1-15) that may correspond to species. Lineages in Asia-Australasia (Groups 1-5) and the Americas plus Madagascar (Groups 6-15) formed sister clades. Four lineages are represented only by sequences from single individuals and require further molecular sampling, including L. aff. raphanica (Group 7), L. ixodes (Group 8), L. boryana (Group 12), and L. aff. aciculospora (Group 14). Groups 1 and 5 are here referred to L. edodes and L. aff. edodes, respectively. However, these groups most likely represent the same species and are only recognized as (unsupported) monophyletic lineages by maximum likelihood analyses of ITS alone. Other putative species resolved here include L. lateritia (Group 2), L. novae-zelandieae (Group 3), L. aff. lateritia (Group 4), L. raphanica (Group 6), L. aff. detonsa (Group 9), L. detonsa (Group 10), L. guzmanii sp. nov. (Group 11), L. aciculospora (Group 13), and L. madagasikarensis (Group 15). Groups 9-12 represent the "L. boryana complex". Molecular clock and historical biogeographic analyses suggest that the most recent common ancestor (MRCA) of Lentinula can be placed in the middle Oligocene, ca. 30 million years ago (Ma), and had a likely presence in neotropical America. The MRCA of Lentinula in the Americas and Madagascar lived ca. 22 Ma in the Neotropics and the MRCA of Lentinula in Asia-Australasia lived ca. 6 Ma in Oceania. Given the current knowledge about plate tectonics and paleoclimatic models of the last 30 Myr, our phylogenetic hypothesis suggests that the extant distribution of Lentinula is likely to have arisen, in large part, due to long-distance dispersal. Lentinula collections include at least four dubious taxa that need further taxonomic studies: L. reticeps from the USA (Ohio); L. guarapiensis from Paraguay; Lentinus puiggarii from Brazil (São Paulo); and "L. platinedodes" from Vietnam. Approximately ten of the fifteen Groups are reported on Fagaceae, which appears to be the ancestral substrate of Lentinula.
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Affiliation(s)
- Nelson Menolli
- IFungiLab, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Câmpus São Paulo (SPO), Departamento de Ciências da Natureza e Matemática (DCM) / Subárea de Biologia (SAB), Rua Pedro Vicente 625, São Paulo, SP 01109-010, Brazil.
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2, Canada
| | - Marisol Sánchez-García
- Uppsala Biocentre, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-75005, Sweden
| | - Chaoqun Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Institute of Microbiology, Guangdong Academy of Science, Guangzhou 510070, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sean Patev
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Noemia Kazue Ishikawa
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil
| | - Juan L Mata
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Alexandre Rafael Lenz
- Departamento de Ciências Exatas e da Terra, Colegiado de Sistemas de Informação, Campus I, Universidade do Estado da Bahia (UNEB), Salvador, BA, Brazil
| | - Ruby Vargas-Isla
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia (INPA), Av. André Araújo, 2936, Petrópolis, Manaus, AM 69067-375, Brazil
| | - Lauren Liderman
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Meriel Lamb
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Mitchell Nuhn
- Biology Department, Clark University, Worcester, MA 01610, USA
| | - Karen W Hughes
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - David S Hibbett
- Biology Department, Clark University, Worcester, MA 01610, USA
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Improved Foods Using Enzymes from Basidiomycetes. Processes (Basel) 2022. [DOI: 10.3390/pr10040726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
Within the kingdom of fungi, the division Basidiomycota represents more than 30,000 species, some with huge genomes indicating great metabolic potential. The fruiting bodies of many basidiomycetes are appreciated as food (“mushrooms”). Solid-state and submerged cultivation processes have been established for many species. Specifically, xylophilic fungi secrete numerous enzymes but also form smaller metabolites along unique pathways; both groups of compounds may be of interest to the food processing industry. To stimulate further research and not aim at comprehensiveness in the broad field, this review describes some recent progress in fermentation processes and the knowledge of fungal genetics. Processes with potential for food applications based on lipases, esterases, glycosidases, peptidases and oxidoreductases are presented. The formation and degradation of colourants, the degradation of harmful food components, the formation of food ingredients and particularly of volatile and non-volatile flavours serve as examples. In summary, edible basidiomycetes are foods—and catalysts—for food applications and rich donors of genes to construct heterologous cell factories for fermentation processes. Options arise to support the worldwide trend toward greener, more eco-friendly and sustainable processes.
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Tang L, Chu T, Shang J, Yang R, Song C, Bao D, Tan Q, Jian H. Oxidative Stress and Autophagy Are Important Processes in Post Ripeness and Brown Film Formation in Mycelium of Lentinula edodes. Front Microbiol 2022; 13:811673. [PMID: 35283832 PMCID: PMC8908433 DOI: 10.3389/fmicb.2022.811673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/18/2022] [Indexed: 11/17/2022] Open
Abstract
Lentinula edodes (Berk.) Pegler, the shiitake mushroom, is one of the most important mushrooms in the global mushroom industry. Although mycelium post ripeness and brown film (BF) formation are crucial for fruiting body initiation, the underlying molecular mechanisms of BF formation are largely unknown. In this study, proteomic quantification (relative and absolute) and metabolomic profiling of L. edodes were performed using isobaric tags and gas chromatography-mass spectroscopy, respectively. A total of 2,474 proteins were identified, which included 239 differentially expressed proteins. Notably, several proteins associated with autophagy were upregulated, including RPD3, TOR1, VAC8, VPS1, and VPS27. Transmission electron microscopy also indicated that autophagy occurred in post ripeness and BF formation. In time-dependent analysis of the metabolome, metabolites associated with oxidative stress and autophagy changed significantly, including mannitol, trehalose, myo-inositol, glucose, leucine, valine, glutamine, and 4-aminobutyric acid. Thus, oxidative stress and autophagy were important processes in post ripeness and BF formation in L. edodes, and new insights were gained into molecular mechanisms at proteome and metabolome levels.
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Affiliation(s)
- Lihua Tang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Ting Chu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China.,School of Food Sciences and Technology, Shanghai Ocean University, Shanghai, China
| | - Junjun Shang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Ruiheng Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Chunyan Song
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Dapeng Bao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Qi Tan
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture and Rural Affairs (China), National Engineering Research Center of Edible Fungi, Shanghai, China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Yu H, Zhang L, Shang X, Peng B, Li Y, Xiao S, Tan Q, Fu Y. Chromosomal genome and population genetic analyses to reveal genetic architecture, breeding history and genes related to cadmium accumulation in Lentinula edodes. BMC Genomics 2022; 23:120. [PMID: 35144543 PMCID: PMC8832684 DOI: 10.1186/s12864-022-08325-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/19/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Lentinula edodes (Berk.) is the second most productive mushroom in the world. It contains compounds effective for antiviral, antitumor, antioxidant and immune regulation. Although genomes have previously been reported for this species, a high-quality chromosome-level reference for L. edodes is unavailable. This hinders detailed investigation of population genetics, breeding history of strains and genes related to environmental stress responses. RESULTS A high-quality chromosome-level genome was constructed. We separated a monokaryon from protoplasts of the commercial L. edodes strain L808 and assembled the genome of L. edodes using PacBio long-read and Illumina short-read sequencing, along with the high-throughput chromatin conformation capture (Hi-C) technique. We assembled a 45.87 Mb genome, and 99% of the sequences were anchored onto 10 chromosomes. The contig and scaffold N50 length were 2.17 and 4.94 Mb, respectively. Over 96% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) were identified, and 9853 protein-coding genes were predicted. We performed population genome resequencing using 34 wild strains and 65 commercial cultivars of L. edodes originating from China, Japan, the United States and Australia. Based on whole-genome variants, we showed substantial differences in the Chinese wild population, which divided into different branches according to the main areas of their geographical distribution. We also determined the breeding history of L. edodes at the molecular level, and demonstrated that the cultivated strains in China mainly originated from wild strains from China and Northeast Asia. Phenotypic analysis showed that 99 strains exhibited differences on the Cd accumulation. Three significant loci in the of L. edodes genome were identified using the genome-wide association study (GWAS) of Cd accumulation traits. Functional genes associated with Cd accumulation traits were related to DNA ligase and aminoacyl tRNA synthetase, indicating that DNA damage repair and in vivo protein translation may be responses to Cd stress. CONCLUSIONS A high-quality chromosome-level genome and population genetic data of L. edodes provide genetic resources for functional genomic, evolutionary and artificial breeding studies for L. edodes.
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Affiliation(s)
- Hailong Yu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Lujun Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
| | - Xiaodong Shang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
| | - Bing Peng
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Yu Li
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China
| | - Shijun Xiao
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China.
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing, 314000, China.
| | - Qi Tan
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, 201403, China.
| | - Yongping Fu
- Internationally Cooperative Research Center of China for New Germplasm Breading of Edible Mushroom, Jilin Agricultural University, Changchun, 130018, China.
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10
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Gao Q, Yan D, Song S, Fan Y, Wang S, Liu Y, Huang Y, Rong C, Guo Y, Zhao S, Qin W, Xu J. Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. J Fungi (Basel) 2022; 8:jof8020167. [PMID: 35205921 PMCID: PMC8877449 DOI: 10.3390/jof8020167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 01/02/2023] Open
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.
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Affiliation(s)
- Qi Gao
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Dong Yan
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- Correspondence: (D.Y.); (J.X.)
| | - Shuang Song
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yangyang Fan
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Shouxian Wang
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yu Liu
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yu Huang
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- College of Agriculture and Food Engineering, Baise University, 21 Zhongshan Second Street, Youjiang District, Baise 533000, China
| | - Chengbo Rong
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yuan Guo
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Shuang Zhao
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
| | - Wentao Qin
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
- Correspondence: (D.Y.); (J.X.)
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11
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Dong Y, Miao R, Feng R, Wang T, Yan J, Zhao X, Han X, Gan Y, Lin J, Li Y, Gan B, Zhao J. Edible and medicinal fungi breeding techniques, a review: Current status and future prospects. Curr Res Food Sci 2022; 5:2070-2080. [DOI: 10.1016/j.crfs.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/06/2022] Open
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12
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Whole Genome Sequencing and Annotation of Naematelia aurantialba (Basidiomycota, Edible-Medicinal Fungi). J Fungi (Basel) 2021; 8:jof8010006. [PMID: 35049946 PMCID: PMC8777972 DOI: 10.3390/jof8010006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 12/26/2022] Open
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.
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13
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Lee YJ, Kim E, Eom H, Yang SH, Choi YJ, Ro HS. Discovery and Functional Study of a Novel Genomic Locus Homologous to Bα-Mating-Type Sublocus of Lentinula edodes. MYCOBIOLOGY 2021; 49:582-588. [PMID: 35035249 PMCID: PMC8725915 DOI: 10.1080/12298093.2021.2001906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/26/2021] [Accepted: 10/30/2021] [Indexed: 06/14/2023]
Abstract
The interaction of mating pheromone and pheromone receptor from the B mating-type locus is the first step in the activation of the mushroom mating signal transduction pathway. The B mating-type locus of Lentinula edodes is composed of Bα and Bβ subloci, each of which contains genes for mating pheromone and pheromone receptor. Allelic variations in both subloci generate multiple B mating-types through which L. edodes maintains genetic diversity. In addition to the B mating-type locus, our genomic sequence analysis revealed the presence of a novel chromosomal locus 43.3 kb away from the B mating-type locus, containing genes for a pair of mating pheromones (PHBN1 and PHBN2) and a pheromone receptor (RCBN). The new locus (Bα-N) was homologous to the Bα sublocus, but unlike the multiallelic Bα sublocus, it was highly conserved across the wild and cultivated strains. The interactions of RcbN with various mating pheromones from the B and Bα-N mating-type loci were investigated using yeast model that replaced endogenous yeast mating pheromone receptor STE2 with RCBN. The yeast mating signal transduction pathway was only activated in the presence of PHBN1 or PHBN2 in the RcbN producing yeast, indicating that RcbN interacts with self-pheromones (PHBN1 and PHBN2), not with pheromones from the B mating-type locus. The biological function of the Bα-N locus was suggested to control the expression of A mating-type genes, as evidenced by the increased expression of two A-genes HD1 and HD2 upon the treatment of synthetic PHBN1 and PHBN2 peptides to the monokaryotic strain of L. edodes.
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Affiliation(s)
- Yun Jin Lee
- Department of Bio & Medical Big Data (BK4 program) and Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Eunbi Kim
- Department of Bio & Medical Big Data (BK4 program) and Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Hyerang Eom
- Department of Bio & Medical Big Data (BK4 program) and Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Seong-Hyeok Yang
- Department of Bio & Medical Big Data (BK4 program) and Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Yeon Jae Choi
- Department of Bio & Medical Big Data (BK4 program) and Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Hyeon-Su Ro
- Department of Bio & Medical Big Data (BK4 program) and Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
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14
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Moon S, An JY, Choi YJ, Oh YL, Ro HS, Ryu H. Construction of a CRISPR/Cas9-Mediated Genome Editing System in Lentinula edodes. MYCOBIOLOGY 2021; 49:599-603. [PMID: 35035251 PMCID: PMC8725921 DOI: 10.1080/12298093.2021.2006401] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 10/13/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
CRISPR/Cas9 genome editing systems have been established in a broad range of eukaryotic species. Herein, we report the first method for genetic engineering in pyogo (shiitake) mushrooms (Lentinula edodes) using CRISPR/Cas9. For in vivo expression of guide RNAs (gRNAs) targeting the mating-type gene HD1 (LeA1), we identified an endogenous LeU6 promoter in the L. edodes genome. We constructed a plasmid containing the LeU6 and glyceraldehyde-3-phosphate dehydrogenase (LeGPD) promoters to express the Cas9 protein. Among the eight gRNAs we tested, three successfully disrupted the LeA1 locus. Although the CRISPR-Cas9-induced alleles did not affect mating with compatible monokaryotic strains, disruption of the transcription levels of the downstream genes of LeHD1 and LeHD2 was detected. Based on this result, we present the first report of a simple and powerful genetic manipulation tool using the CRISPR/Cas9 toolbox for the scientifically and industrially important edible mushroom, L. edodes.
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Affiliation(s)
- Suyun Moon
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Korea
| | | | - Yeon-Jae Choi
- Department of Bio & Medical Big Data and Research Institute of Life Sciences, Gyeongsang National University, Jinju, Korea
| | - Youn-Lee Oh
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
| | - Hyeon-Su Ro
- Department of Bio & Medical Big Data and Research Institute of Life Sciences, Gyeongsang National University, Jinju, Korea
| | - Hojin Ryu
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Korea
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15
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Liu Z, Lu H, Zhang X, Chen Q. The Genomic and Transcriptomic Analyses of Floccularia luteovirens, a Rare Edible Fungus in the Qinghai-Tibet Plateau, Provide Insights into the Taxonomy Placement and Fruiting Body Formation. J Fungi (Basel) 2021; 7:jof7110887. [PMID: 34829176 PMCID: PMC8618933 DOI: 10.3390/jof7110887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 12/13/2022] Open
Abstract
Floccularia luteovirens is a famous and precious edible mushroom (Huang Mogu) on the Qinghai–Tibet plateau that has a unique flavor and remarkable medical functions. Herein, we report a reference-grade 27 Mb genome of F. luteovirens containing 7068 protein-coding genes. The genome component and gene functions were predicted. Genome ontology enrichment and pathway analyses indicated the potential production capacity for terpenoids, polyketides and polysaccharides. Moreover, 16 putative gene clusters and 145 genes coding for secondary metabolites were obtained, including guadinomine and melleolides. In addition, phylogenetic and comparative genomic analyses shed light on the precise classification of F. luteovirens suggesting that it belongs to the genus Floccularia instead of Armillaria. RNA-sequencing and comparative transcriptomic analysis revealed differentially expressed genes during four developmental stages of F. luteovirens, that of which helps to identify important genes regulating fruiting body formation for strain modification. This study will provide insight into artificial cultivation and increase the production of useful metabolites.
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Affiliation(s)
- Zhengjie Liu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (Z.L.); (H.L.); (X.Z.)
- College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Hongyun Lu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (Z.L.); (H.L.); (X.Z.)
| | - Xinglin Zhang
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (Z.L.); (H.L.); (X.Z.)
| | - Qihe Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (Z.L.); (H.L.); (X.Z.)
- Correspondence: ; Tel.: +86-0571-8698-4316
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16
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Liu Y, Huang L, Hu H, Cai M, Liang X, Li X, Zhang Z, Xie Y, Xiao C, Chen S, Chen D, Yong T, Pan H, Gao X, Wu Q. Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China. G3-GENES GENOMES GENETICS 2021; 11:6377781. [PMID: 34586388 PMCID: PMC8664445 DOI: 10.1093/g3journal/jkab337] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022]
Abstract
Ganoderma leucocontextum, a newly discovered species of Ganodermataceae in China, has diverse pharmacological activities. G. leucocontextum was widely cultivated in southwest China, but the systematic genetic study has been impeded by the lack of a reference genome. Herein, we present the first whole-genome assembly of G. leucocontextum based on the Illumina and Nanopore platform from high-quality DNA extracted from a monokaryon strain (DH-8). The generated genome was 50.05 Mb in size with a N50 scaffold size of 3.06 Mb, 78,206 coding sequences and 13,390 putative genes. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 96.55% of the 280 Fungi BUSCO genes. Furthermore, differences in functional genes of secondary metabolites (terpenoids) were analyzed between G. leucocontextum and G. lucidum. G. leucocontextum has more genes related to terpenoids synthesis compared to G. lucidum, which may be one of the reasons why they exhibit different biological activities. This is the first genome assembly and annotation for G. leucocontextum, which would enrich the toolbox for biological and genetic studies in G. leucocontextum.
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Affiliation(s)
- Yuanchao Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.,Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.,Guangdong Yuewei Edible Mushroom Technology Co., Ltd., Guangzhou, 510663, China
| | - Longhua Huang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Huiping Hu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Manjun Cai
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Xiaowei Liang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Xiangmin Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Zhi Zhang
- Guangdong Yuewei Edible Mushroom Technology Co., Ltd., Guangzhou, 510663, China
| | - Yizhen Xie
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.,Guangdong Yuewei Edible Mushroom Technology Co., Ltd., Guangzhou, 510663, China
| | - Chun Xiao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Shaodan Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Diling Chen
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Tianqiao Yong
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Honghui Pan
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Xiong Gao
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Qingping Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.,Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
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17
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Smith CA. Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes. Sci Rep 2021; 11:9845. [PMID: 33972587 PMCID: PMC8110776 DOI: 10.1038/s41598-021-89146-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/08/2021] [Indexed: 12/03/2022] Open
Abstract
The basidiomycete fungus Lentinula novae-zelandiae is endemic to New Zealand and is a sister taxon to Lentinula edodes, the second most cultivated mushroom in the world. To explore the biology of this organism, a high-quality chromosome level reference genome of L. novae-zelandiae was produced. Macrosyntenic comparisons between the genome assembly of L. novae-zelandiae, L. edodes and a set of three genome assemblies of diverse species from the Agaricomycota reveal a high degree of macrosyntenic restructuring within L. edodes consistent with signal of domestication. These results show L. edodes has undergone significant genomic change during the course of its evolutionary history, likely a result of its cultivation and domestication over the last 1000 years.
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18
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Orban A, Weber A, Herzog R, Hennicke F, Rühl M. Transcriptome of different fruiting stages in the cultivated mushroom Cyclocybe aegerita suggests a complex regulation of fruiting and reveals enzymes putatively involved in fungal oxylipin biosynthesis. BMC Genomics 2021; 22:324. [PMID: 33947322 PMCID: PMC8097960 DOI: 10.1186/s12864-021-07648-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/19/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Cyclocybe aegerita (syn. Agrocybe aegerita) is a commercially cultivated mushroom. Its archetypal agaric morphology and its ability to undergo its whole life cycle under laboratory conditions makes this fungus a well-suited model for studying fruiting body (basidiome, basidiocarp) development. To elucidate the so far barely understood biosynthesis of fungal volatiles, alterations in the transcriptome during different developmental stages of C. aegerita were analyzed and combined with changes in the volatile profile during its different fruiting stages. RESULTS A transcriptomic study at seven points in time during fruiting body development of C. aegerita with seven mycelial and five fruiting body stages was conducted. Differential gene expression was observed for genes involved in fungal fruiting body formation showing interesting transcriptional patterns and correlations of these fruiting-related genes with the developmental stages. Combining transcriptome and volatilome data, enzymes putatively involved in the biosynthesis of C8 oxylipins in C. aegerita including lipoxygenases (LOXs), dioxygenases (DOXs), hydroperoxide lyases (HPLs), alcohol dehydrogenases (ADHs) and ene-reductases could be identified. Furthermore, we were able to localize the mycelium as the main source for sesquiterpenes predominant during sporulation in the headspace of C. aegerita cultures. In contrast, changes in the C8 profile detected in late stages of development are probably due to the activity of enzymes located in the fruiting bodies. CONCLUSIONS In this study, the combination of volatilome and transcriptome data of C. aegerita revealed interesting candidates both for functional genetics-based analysis of fruiting-related genes and for prospective enzyme characterization studies to further elucidate the so far barely understood biosynthesis of fungal C8 oxylipins.
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Affiliation(s)
- Axel Orban
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, 35392, Giessen, Hesse, Germany
| | - Annsophie Weber
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, 35392, Giessen, Hesse, Germany
| | - Robert Herzog
- International Institute Zittau, Technical University Dresden, 02763, Zittau, Saxony, Germany
| | - Florian Hennicke
- Project Group Genetics and Genomics of Fungi, Ruhr-University Bochum, Chair Evolution of Plants and Fungi, 44780, Bochum, North Rhine-Westphalia, Germany.
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, 35392, Giessen, Hesse, Germany. .,Fraunhofer Institute for Molecular Biology and Applied Ecology IME Branch for Bioresources, 35392, Giessen, Hesse, Germany.
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19
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Transcriptional Changes of Cell Wall Organization Genes and Soluble Carbohydrate Alteration during Leaf Blade Development of Rice Seedlings. PLANTS 2021; 10:plants10050823. [PMID: 33919078 PMCID: PMC8143110 DOI: 10.3390/plants10050823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 11/16/2022]
Abstract
Plant cell walls have two constituent parts with different components and developmental stages. Much of the mystery concerning the mechanisms of synthesis, decomposition, modification, and so forth, has been resolved using omics and microscopic techniques. However, it still remains to be determined how cell wall development progresses over time after leaf emergence. Our focus in the present study was to expand our knowledge of the molecular mechanisms associated with cell wall synthesis in rice leaf blade during three distinct stages (sink, sink-to-source transition, and source). The RNA-seq, quantitative reverse transcription PCR (qRT-PCR) and carbohydrate concentrations were evaluated using developing fifth leaf blades harvested at different time points. The results revealed that some of the essential genes for the primary cell wall (PCW) were highly upregulated in the sink-to-source transition compared to the sink stage, whereas those essential to the secondary cell wall (SCW) displayed relatively higher levels (p < 0.05) during the source stage. The concentrations of soluble carbohydrates differed via type rather than stage; we observed higher monosaccharides during the sink stage and higher di- and oligo-saccharides during the sink-to-source transition and source stages. In conclusion, our findings suggest that the transcriptional regulation of plant cell wall biosynthesis genes are both synchronistic with and independent of, and directly and indirectly governed by, the abundance of soluble carbohydrates in the developing leaf blade, and, finally, raffinose is likely to play a transport role comparable to sucrose.
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20
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Zhang L, Gong W, Li C, Shen N, Gui Y, Bian Y, Kwan HS, Cheung MK, Xiao Y. RNA-Seq-based high-resolution linkage map reveals the genetic architecture of fruiting body development in shiitake mushroom, Lentinula edodes. Comput Struct Biotechnol J 2021; 19:1641-1653. [PMID: 33868600 PMCID: PMC8026754 DOI: 10.1016/j.csbj.2021.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/07/2021] [Accepted: 03/12/2021] [Indexed: 01/21/2023] Open
Abstract
We constructed a reference genetic map of Lentinula edodes. We re-assembled a chromosome-level genome of L. edodes. We disclosed three hotspots regions for fruiting body-related traits in shiitake. We scanned candidate genes for fruiting body-related traits.
Fruiting body development (FBD) of mushroom-forming fungi has attracted tremendous interest. However, the genetic and molecular basis of FBD is poorly known. Here, using Lentinula edodes (shiitake) as a model, we deciphered the genetic architecture underlying fruiting body-related traits (FBRTs) by combined genomic, genetic and phenotypic data. Using RNA-Seq of fruiting bodies from 110 dikaryons in a bi-parental mapping population, we constructed an ultra-high-density genetic map of L. edodes (Lemap2.0) with a total length of 810.14 cM, which covered 81.7% of the shiitake genome. A total of 94 scaffolds of the shiitake genome were aligned to Lemap2.0 and re-anchored into nine pseudo-chromosomes. Then via quantitative trait locus (QTL) analysis, we disclosed an outline of the genetic architecture of FBD in shiitake. Twenty-nine QTLs and three main genomic regions associated with FBD of shiitake were identified. Using meta-QTL analysis, seven pleiotropic QTLs for multiple traits were detected, which contributed to the correlations of FBRTs. In the mapped QTLs, the expression of 246 genes were found to significantly correlate with the phenotypic traits. Thirty-three of them were involved in FBD and could represent candidate genes controlling the shape and size of fruiting bodies. Collectively, our findings have advanced our understanding of the genetic regulation of FBD in shiitake and mushroom-forming fungi at large.
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Affiliation(s)
- Lin Zhang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Wenbing Gong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Chuang Li
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Nan Shen
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Ying Gui
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong, China
| | - Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong, China
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
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21
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Salwan R, Katoch S, Sharma V. Recent Developments in Shiitake Mushrooms and Their Nutraceutical Importance. Fungal Biol 2021. [DOI: 10.1007/978-3-030-64406-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Hong CP, Moon S, Yoo SI, Noh JH, Ko HG, Kim HA, Ro HS, Cho H, Chung JW, Lee HY, Ryu H. Functional Analysis of a Novel ABL ( Abnormal Browning Related to Light) Gene in Mycelial Brown Film Formation of Lentinula edodes. J Fungi (Basel) 2020; 6:E272. [PMID: 33182449 PMCID: PMC7712820 DOI: 10.3390/jof6040272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/30/2022] Open
Abstract
Lentinula edodes is a globally important edible mushroom species that is appreciated for its medicinal properties as well as its nutritional value. During commercial cultivation, a mycelial brown film forms on the surface of the sawdust growth medium at the late vegetative stage. Mycelial film formation is a critical developmental process that contributes to the quantity and quality of the mushroom yield. However, little is known regarding the genetic underpinnings of brown film formation on the surface of mycelial tissue. A novel causal gene associated with the formation of the mycelial brown film, named ABL (Abnormal browning related to light), was identified in this study. The comparative genetic analysis by dihybrid crosses between normal and abnormal browning film cultivars demonstrated that a single dominant allele was responsible for the abnormal mycelium browning phenotype. Whole-genome sequencing analysis of hybrid isolates revealed five missense single-nucleotide polymorphisms (SNPs) in the ABL locus of individuals forming abnormal partial brown films. Additional whole-genome resequencing of a further 16 cultivars showed that three of the five missense SNPs were strongly associated with the abnormal browning phenotype. Overexpression of the dominant abl-D allele in a wild-type background conferred the abnormal mycelial browning phenotype upon transformants, with slender hyphae observed as a general defective mycelial growth phenotype. Our methodology will aid the future discovery of candidate genes associated with favorable traits in edible mushrooms. The discovery of a novel gene, ABL, associated with mycelial film formation will facilitate marker-associated breeding in L. edodes.
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Affiliation(s)
- Chang Pyo Hong
- Department of R&D Planning & Management, Theragen Bio, Suwon 16229, Korea; (C.P.H.); (S.-i.Y.); (H.A.K.)
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea;
| | - Seung-il Yoo
- Department of R&D Planning & Management, Theragen Bio, Suwon 16229, Korea; (C.P.H.); (S.-i.Y.); (H.A.K.)
| | - Jong-Hyun Noh
- Forest Mushroom Research Center, National Forestry Cooperative Federation, Yeoju 12653, Korea; (J.-H.N.); (H.-G.K.)
| | - Han-Gyu Ko
- Forest Mushroom Research Center, National Forestry Cooperative Federation, Yeoju 12653, Korea; (J.-H.N.); (H.-G.K.)
| | - Hyun A. Kim
- Department of R&D Planning & Management, Theragen Bio, Suwon 16229, Korea; (C.P.H.); (S.-i.Y.); (H.A.K.)
| | - Hyeon-Su Ro
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Korea;
| | - Hyunwoo Cho
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea; (H.C.); (J.-W.C.)
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea; (H.C.); (J.-W.C.)
| | - Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea;
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23
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Saito T, Sakuta G, Kobayashi H, Ouchi K, Inatomi S. Genetically Independent Tetranucleotide to Hexanucleotide Core Motif SSR Markers for Identifying Lentinula edodes Cultivars. MYCOBIOLOGY 2019; 47:466-472. [PMID: 32010468 PMCID: PMC6968638 DOI: 10.1080/12298093.2019.1665331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
For the purpose of protecting the rights of Lentinula edodes breeders, we developed a new simple sequence repeat (SSR) marker set consisting only of genetically independent tetranucleotide or longer core motifs. Using available genome sequences for five L. edodes strains, we designed primers for 13 SSR markers that amplified polymorphic sequences in 20 L. edodes cultivars. We evaluated the independence of every possible marker pair based on genotype data. Consequently, eight genetically independent markers were selected. The polymorphic information content values of the markers ranged from 0.269 to 0.764, with an average of 0.409. The markers could distinguish among 20 L. edodes cultivars and produced highly repeatable and reproducible results. The markers developed in this study will enable the precise identification of L. edodes cultivars, and may be useful for protecting breeders' rights.
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Affiliation(s)
- Teruaki Saito
- Mushroom Research Laboratory, Hokuto Corporation, Nagano, Japan
| | - Genki Sakuta
- Mushroom Research Laboratory, Hokuto Corporation, Nagano, Japan
| | | | - Kenji Ouchi
- Mushroom Research Laboratory, Hokuto Corporation, Nagano, Japan
| | - Satoshi Inatomi
- Mushroom Research Laboratory, Hokuto Corporation, Nagano, Japan
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24
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Dai Y, Li X, Song B, Sun L, Yang C, Zhang X, Wang Y, Zhang Z, Fu Y, Li Y. Genomic Analyses Provide Insights Into the Evolutionary History and Genetic Diversity of Auricularia Species. Front Microbiol 2019; 10:2255. [PMID: 31632371 PMCID: PMC6786273 DOI: 10.3389/fmicb.2019.02255] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/17/2019] [Indexed: 12/27/2022] Open
Abstract
Species in the genus Auricularia play important roles for people’s food and nutrition especially Auricularia cornea and A. heimuer. To understand their evolutionary history, genome structure, and population-level genetic variation, we performed a high-quality genome sequencing of Auricularia cornea and the corresponding comparative genomic analysis. The genome size of A. cornea was similar to Auricularia subglabra, but 1.5 times larger than that of A. heimuer. Several factors were responsible for genome size variation including gene numbers, repetitive elements, and gene lengths. Phylogenomic analysis revealed that the estimated divergence time between A. heimuer and other Auricularia is ∼79.1 million years ago (Mya), while the divergence between A. cornea and A. subglabra occurred in ∼54.8 Mya. Population genomic analysis also provided insight into the demographic history of A. cornea and A. heimuer, indicating that their populations fluctuated over time with global climate change during Marine Isotope Stage 5-2. Moreover, despite the highly similar external morphologies of A. cornea and A. heimuer, their genomic properties were remarkably different. The A. cornea genome only shared 14% homologous syntenic blocks with A. heimuer and possessed more genes encoding carbohydrate-active enzymes and secondary metabolite biosynthesis proteins. The cross-taxa transferability rates of simple sequence repeat (SSR) and insertion or deletion (InDel) markers within the genus Auricularia were also lower than that previously observed for species within the same genus. Taken together, these results indicate a high level of genetic differentiation between these two Auricularia species. Consequently, our study provides new insights into the genomic evolution and genetic differentiation of Auricularia species that will facilitate future genetic breeding.
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Affiliation(s)
- Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Xiao Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Bing Song
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Lei Sun
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Chentao Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xin Zhang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yanfeng Wang
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,Internationally Cooperative Research Center of China for New Germplasm Breeding of Edible Mushroom, Jilin Agricultural University, Changchun, China
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25
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Chitinases Play a Key Role in Stipe Cell Wall Extension in the Mushroom Coprinopsis cinerea. Appl Environ Microbiol 2019; 85:AEM.00532-19. [PMID: 31126941 DOI: 10.1128/aem.00532-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/10/2019] [Indexed: 11/20/2022] Open
Abstract
The elongation growth of the mushroom stipe is a characteristic but not well-understood morphogenetic event of basidiomycetes. We found that extending native stipe cell walls of Coprinopsis cinerea were associated with the release of N-acetylglucosamine and chitinbiose and with chitinase activity. Two chitinases among all detected chitinases from C. cinerea, ChiE1 and ChiIII, reconstituted heat-inactivated stipe wall extension and released N-acetylglucosamine and chitinbiose. Interestingly, both ChiE1 and ChiIII hydrolyze insoluble crystalline chitin powder, while other C. cinerea chitinases do not, suggesting that crystalline chitin components of the stipe cell wall are the target of action for ChiE1 and ChiIII. ChiE1- or ChiIII-reconstituted heat-inactivated stipe walls showed maximal extension activity at pH 4.5, consistent with the optimal pH for native stipe wall extension in vitro; ChiE1- or ChiIII-reconstituted heat-inactivated stipe wall extension activities were associated with stipe elongation growth regions; and the combination of ChiE1 and ChiIII showed a synergism to reconstitute heat-inactivated stipe wall extension at a low action concentration. Field emission scanning electron microscopy (FESEM) images showed that the inner surface of acid-induced extended native stipe cell walls and ChiE1- or ChiIII-reconstituted extended heat-inactivated stipe cell walls exhibited a partially broken parallel microfibril architecture; however, these broken transversely arranged microfibrils were not observed in the unextended stipe cell walls that were induced by neutral pH buffer or heat inactivation. Double knockdown of ChiE1 and ChiIII resulted in the reduction of stipe elongation, mycelium growth, and heat-sensitive cell wall extension of native stipes. These results indicate a chitinase-hydrolyzing mechanism for stipe cell wall extension.IMPORTANCE A remarkable feature in the development of basidiomycete fruiting bodies is stipe elongation growth that results primarily from manifold cell elongation. Some scientists have suggested that stipe elongation is the result of enzymatic hydrolysis of cell wall polysaccharides, while other scientists have proposed the possibility that stipe elongation results from nonhydrolytic disruption of the hydrogen bonds between cell wall polysaccharides. Here, we show direct evidence for a chitinase-hydrolyzing mechanism of stipe cell wall elongation in the model mushroom Coprinopsis cinerea that is different from the expansin nonhydrolysis mechanism of plant cell wall extension. We presumed that in the growing stipe cell walls, parallel chitin microfibrils are tethered by β-1,6-branched β-1,3-glucans, and that the breaking of the tether by chitinases leads to separation of these microfibrils to increase their spacing for insertion of new synthesized chitin and β-1,3-glucans under turgor pressure in vivo.
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26
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Variable Number Tandem Repeats in the Mitochondrial DNA of Lentinula edodes. Genes (Basel) 2019; 10:genes10070542. [PMID: 31319586 PMCID: PMC6679062 DOI: 10.3390/genes10070542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/13/2019] [Accepted: 07/15/2019] [Indexed: 11/17/2022] Open
Abstract
Variable number tandem repeats (VNTRs) in mitochondrial DNA (mtDNA) of Lentinula edodes are of interest for their role in mtDNA variation and their application as genetic marker. Sequence analysis of three L. edodes mtDNAs revealed the presence of VNTRs of two categories. Type I VNTRs consist of two types of repeat units in a symmetric distribution, whereas Type II VNTRs contain tandemly arrayed repeats of 7- or 17-bp DNA sequences. The number of repeat units was variable depending on the mtDNA of different strains. Using the variations in VNTRs as a mitochondrial marker and the A mating type as a nuclear type marker, we demonstrated that one of the two nuclei in the donor dikaryon preferentially enters into the monokaryotic cytoplasm to establish a new dikaryon which still retains the mitochondria of the monokaryon in the individual mating. Interestingly, we found 6 VNTRs with newly added repeat units from the 22 mates, indicating that elongation of VNTRs occurs during replication of mtDNA. This, together with comparative analysis of the repeating pattern, enables us to propose a mechanistic model that explains the elongation of Type I VNTRs through reciprocal incorporation of basic repeat units, 5’-TCCCTTTAGGG-3’ and its complementary sequence (5’-CCCTAAAGGGA-3’).
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27
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Yu F, Song J, Liang J, Wang S, Lu J. Whole genome sequencing and genome annotation of the wild edible mushroom, Russula griseocarnosa. Genomics 2019; 112:603-614. [PMID: 31004699 DOI: 10.1016/j.ygeno.2019.04.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 01/30/2023]
Abstract
Russula griseocarnosa is a species of edible ectomycorrhizal fungi with medicinal properties that grows in southern China. Total DNA was isolated from a fresh fruiting body of R. griseocarnosa and subjected to sequencing using Illumina Hiseq with the PacBio RS sequencing platform. Here, we present the 64.81 Mb draft genome map of R. griseocarnosa based on 471 scaffolds and 16,128 coding protein genes. The gene annotation of protein coding genes was used to obtain corresponding annotations by blastp. Phylogenetic analysis revealed a close evolutionary relationship of R. griseocarnosa to Heterobasidion irregulare and Stereum hirsutum in the core Russulales clade. The R. griseocarnosa genome encodes a repertoire of enzymes engaged in carbohydrate and polysaccharide metabolism, along with cytochrome P450s and secondary metabolite biosynthesis. The genome content of R. griseocarnosa provides insights into the genetic basis of its reported medicinal properties and serves as a reference for comparative genomics of fungi.
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Affiliation(s)
- Fei Yu
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China; Nanjing Forestry University, Nanjing 210037, China
| | - Jie Song
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China
| | - Junfeng Liang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Shengkun Wang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China
| | - Junkun Lu
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China
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28
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Wang X, Peng J, Sun L, Bonito G, Wang J, Cui W, Fu Y, Li Y. Genome Sequencing Illustrates the Genetic Basis of the Pharmacological Properties of Gloeostereum incarnatum. Genes (Basel) 2019; 10:genes10030188. [PMID: 30832255 PMCID: PMC6470497 DOI: 10.3390/genes10030188] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/20/2019] [Accepted: 02/22/2019] [Indexed: 12/23/2022] Open
Abstract
Gloeostereum incarnatum is a precious edible mushroom that is widely grown in Asia and known for its useful medicinal properties. Here, we present a high-quality genome of G. incarnatum using the single-molecule real-time (SMRT) sequencing platform. The G. incarnatum genome, which is the first complete genome to be sequenced in the family Cyphellaceae, was 38.67 Mbp, with an N50 of 3.5 Mbp, encoding 15,251 proteins. Based on our phylogenetic analysis, the Cyphellaceae diverged ~174 million years ago. Several genes and gene clusters associated with lignocellulose degradation, secondary metabolites, and polysaccharide biosynthesis were identified in G. incarnatum, and compared with other medicinal mushrooms. In particular, we identified two terpenoid-associated gene clusters, each containing a gene encoding a sesterterpenoid synthase adjacent to a gene encoding a cytochrome P450 enzyme. These clusters might participate in the biosynthesis of incarnal, a known bioactive sesterterpenoid produced by G. incarnatum. Through a transcriptomic analysis comparing the G. incarnatum mycelium and fruiting body, we also demonstrated that the genes associated with terpenoid biosynthesis were generally upregulated in the mycelium, while those associated with polysaccharide biosynthesis were generally upregulated in the fruiting body. This study provides insights into the genetic basis of the medicinal properties of G. incarnatum, laying a framework for future characterization of bioactive proteins and pharmaceutical uses of this fungus.
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Affiliation(s)
- Xinxin Wang
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
- Department of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China.
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.
| | - Jingyu Peng
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.
| | - Lei Sun
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Gregory Bonito
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.
| | - Jie Wang
- Department of Plant Biology and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, USA.
| | - Weijie Cui
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
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29
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Yoo SI, Lee HY, Markkandan K, Moon S, Ahn YJ, Ji S, Ko J, Kim SJ, Ryu H, Hong CP. Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes. BMC Genomics 2019; 20:121. [PMID: 30736734 PMCID: PMC6368761 DOI: 10.1186/s12864-019-5509-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 02/05/2019] [Indexed: 12/18/2022] Open
Abstract
Background Lentinula edodes is one of the most popular edible mushroom species in the world and contains useful medicinal components, such as lentinan. The light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process for ensuring the quantity and quality of this edible mushroom. To understand the molecular mechanisms underlying this critical developmental process in L. edodes, we characterized the morphological phenotypic changes in a strain, Chamaram, associated with abnormal brown film formation and compared its genome-wide transcriptional features. Results In the present study, we performed genome-wide transcriptome analyses of different vegetative mycelium growth phenotypes, namely, early white, normal brown, and defective dark yellow partial brown films phenotypes which were exposed to different light conditions. The analysis revealed the identification of clusters of genes specific to the light-induced brown film phenotypes. These genes were significantly associated with light sensing via photoreceptors such as FMN- and FAD-bindings, signal transduction by kinases and GPCRs, melanogenesis via activation of tyrosinases, and cell wall degradation by glucanases, chitinases, and laccases, which suggests these processes are involved in the formation of mycelial browning in L. edodes. Interestingly, hydrophobin genes such as SC1 and SC3 exhibited divergent expression levels in the normal and abnormal brown mycelial films, indicating the ability of these genes to act in fruiting body initiation and formation of dikaryotic mycelia. Furthermore, we identified the up-regulation of glycoside hydrolase domain-containing genes in the normal brown film but not in the abnormal film phenotype, suggesting that cell wall degradation in the normal brown film phenotype is crucial in the developmental processes related to the initiation and formation of fruiting bodies. Conclusions This study systematically analysed the expression patterns of light-induced browning-related genes in L. edodes. Our findings provide information for further investigations of browning formation mechanisms in L. edodes and a foundation for future L. edodes breeding. Electronic supplementary material The online version of this article (10.1186/s12864-019-5509-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seung-Il Yoo
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea
| | - Hwa-Yong Lee
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | | | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Yong Ju Ahn
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea
| | - Sumin Ji
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea
| | - Junsu Ko
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea
| | - Seong-Jin Kim
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea.,Precision Medicine Research Center, Advanced Institutes of Convergence Technology, Suwon, Korea.,Department of Transdisciplinary Studies, Graduate School of Convergence Science and Technology, Seoul National University, Suwon, Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Chang Pyo Hong
- Theragen Etex Bio Institute, Suwon, 16229, Republic of Korea.
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Park SG, Ryu D, Lee H, Ryu H, Ahn YJ, Yoo SI, Ko J, Hong CP. TaF: a web platform for taxonomic profile-based fungal gene prediction. Genes Genomics 2018; 41:337-342. [PMID: 30456524 DOI: 10.1007/s13258-018-0766-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 11/13/2018] [Indexed: 10/27/2022]
Abstract
INTRODUCTION The accurate prediction and annotation of gene structures from the genome sequence of an organism enable genome-wide functional analyses to obtain insight into the biological properties of an organism. OBJECTIVES We recently developed a highly accurate filamentous fungal gene prediction pipeline and web platform called TaF. TaF is a homology-based gene predictor employing large-scale taxonomic profiling to search for close relatives in genome queries. METHODS TaF pipeline consists of four processing steps; (1) taxonomic profiling to search for close relatives to query, (2) generation of hints for determining exon-intron boundaries from orthologous protein sequence data of the profiled species, (3) gene prediction by combination of ab inito and evidence-based prediction methods, and (4) homology search for gene models. RESULTS TaF generates extrinsic evidence that suggests possible exon-intron boundaries based on orthologous protein sequence data, thus reducing false-positive predictions of gene structure based on distantly related orthologs data. In particular, the gene prediction method using taxonomic profiling shows very high accuracy, including high sensitivity and specificity for gene models, suggesting a new approach for homology-based gene prediction from newly sequenced or uncharacterized fungal genomes, with the potential to improve the quality of gene prediction. CONCLUSION TaF will be a useful tool for fungal genome-wide analyses, including the identification of targeted genes associated with a trait, transcriptome profiling, comparative genomics, and evolutionary analysis.
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Affiliation(s)
- Sin-Gi Park
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea
| | - DongSung Ryu
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea
| | - Hyunsung Lee
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Yong Ju Ahn
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea
| | - Seung Il Yoo
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea
| | - Junsu Ko
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea.
| | - Chang Pyo Hong
- TheragenEtex Bio Institute, Suwon, 16229, Republic of Korea.
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Song HY, Kim DH, Kim JM. Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom Lentinula edodes. Sci Rep 2018; 8:8983. [PMID: 29895888 PMCID: PMC5997629 DOI: 10.1038/s41598-018-27318-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/31/2018] [Indexed: 02/08/2023] Open
Abstract
Lentinula edodes is a popular cultivated edible mushroom with high nutritional and medicinal value. To understand the regulation of gene expression in the dikaryotic mycelium and mature fruiting body in the commercially important Korean L. edodes strain, we first performed comparative transcriptomic analysis, using Illumina HiSeq platform. De novo assembly of these sequences revealed 11,675 representative transcripts in two different stages of L. edodes. A total of 9,092 unigenes were annotated and subjected to Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Gene expression analysis revealed that 2,080 genes were differentially expressed, with 1,503 and 577 upregulated in the mycelium and a mature fruiting body, respectively. Analysis of 18 KEGG categories indicated that fruiting body-specific transcripts were significantly enriched in ‘replication and repair’ and ‘transcription’ pathways, which are important for premeiotic replication, karyogamy, and meiosis during maturation. We also searched for fruiting body-specific proteins such as aspartic protease, gamma-glutamyl transpeptidase, and cyclohexanone monooxygenase, which are involved in fruiting body maturation and isolation of functional substances. These transcriptomes will be useful in elucidating the molecular mechanisms of mature fruiting body development and beneficial properties, and contribute to the characterization of novel genes in L. edodes.
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Affiliation(s)
- Ha-Yeon Song
- Department of Bio-Environmental Chemistry, Institute of Life Science and Natural Resources, Wonkwang University, Iksan, Chonbuk, 54538, Korea
| | - Dae-Hyuk Kim
- Institute for Molecular Biology and Genetics, Center for Fungal Pathogenesis, Chonbuk National University, Jeonju, Chonbuk, 54896, Korea
| | - Jung-Mi Kim
- Department of Bio-Environmental Chemistry, Institute of Life Science and Natural Resources, Wonkwang University, Iksan, Chonbuk, 54538, Korea.
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Ha B, Lee S, Kim S, Kim M, Moon YJ, Song Y, Ro HS. Nucleus-Selective Expression of Laccase Genes in the Dikaryotic Strain of Lentinula edodes. MYCOBIOLOGY 2017; 45:379-384. [PMID: 29371806 PMCID: PMC5780370 DOI: 10.5941/myco.2017.45.4.379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/21/2017] [Accepted: 10/22/2017] [Indexed: 06/07/2023]
Abstract
In mating of Lentinula edodes, dikaryotic strains generated from certain monokaryotic strains such as the B2 used in this study tend to show better quality of fruiting bodies regardless of the mated monokaryotic strains. Unlike B2, dikaryotic strains generated from B16 generally show low yields, with deformed or underdeveloped fruiting bodies. This indicates that the two nuclei in the cytoplasm do not contribute equally to the physiology of dikaryotic L. edodes, suggesting an expression bias in the allelic genes of the two nuclei. To understand the role of each nucleus in dikaryotic strains, we investigated single nucleotide polymorphisms (SNPs) in laccase genes of monokaryotic strains to reveal nuclear origin of the expressed mRNAs in dikaryotic strain. We performed reverse transcription PCR (RT-PCR) analysis using total RNAs extracted from dikaryotic strains (A5B2, A18B2, and A2B16) as well as from compatible monokaryotic strains (A5, A18, and B2 for A5B2 and A18B2; A2 and B16 for A2B16). RT-PCR results revealed that Lcc1, Lcc2, Lcc4, Lcc7, and Lcc10 were the mainly expressed laccase genes in the L. edodes genome. To determine the nuclear origin of these laccase genes, the genomic DNA sequences in monokaryotic strains were analyzed, thereby revealing five SNPs in Lcc4 and two in Lcc7. Subsequent sequence analysis of laccase mRNAs expressed in dikaryotic strains revealed that these were almost exclusively expressed from B2-originated nuclei in A5B2 and A18B2 whereas B16 nucleus did not contribute to laccase expression in A2B16 strain. This suggests that B2 nucleus dominates the expression of allelic genes, thereby governing the physiology of dikaryons.
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Affiliation(s)
- Byeongsuk Ha
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju 50828, Korea
| | - Sieun Lee
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju 50828, Korea
| | - Sinil Kim
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju 50828, Korea
| | - Minseek Kim
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju 50828, Korea
| | - Yoon Jung Moon
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju 50828, Korea
| | - Yelin Song
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju 50828, Korea
| | - Hyeon-Su Ro
- Division of Applied Life Science and Research Institute of Life Sciences, Gyeongsang National University, Jinju 50828, Korea
- Division of Life Science, Gyeongsang National University, Jinju 50828, Korea
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Park SG, Yoo SI, Ryu DS, Lee H, Ahn YJ, Ryu H, Ko J, Hong CP. Long-read transcriptome data for improved gene prediction in Lentinula edodes. Data Brief 2017; 15:454-458. [PMID: 29845094 PMCID: PMC5961913 DOI: 10.1016/j.dib.2017.09.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 11/28/2022] Open
Abstract
Lentinula edodes is one of the most popular edible mushrooms in the world and contains useful medicinal components such as lentinan. The whole-genome sequence of L. edodes has been determined with the objective of discovering candidate genes associated with agronomic traits, but experimental verification of gene models with correction of gene prediction errors is lacking. To improve the accuracy of gene prediction, we produced 12.6 Gb of long-read transcriptome data of variable lengths using PacBio single-molecule real-time (SMRT) sequencing and generated 36,946 transcript clusters with an average length of 2.2 kb. Evidence-driven gene prediction on the basis of long- and short-read RNA sequencing data was performed; a total of 16,610 protein-coding genes were predicted with error correction. Of the predicted genes, 42.2% were verified to be covered by full-length transcript clusters. The raw reads have been deposited in the NCBI SRA database under accession number PRJNA396788.
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Affiliation(s)
- Sin-Gi Park
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Seung Il Yoo
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Dong Sung Ryu
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Hyunsung Lee
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Yong Ju Ahn
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Junsu Ko
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
| | - Chang Pyo Hong
- Theragen Etex Bio Institute, Suwon 16229, Republic of Korea
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Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis. Appl Environ Microbiol 2017; 83:AEM.02990-16. [PMID: 28314725 DOI: 10.1128/aem.02990-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/07/2017] [Indexed: 12/22/2022] Open
Abstract
Lentinula edodes is a popular, cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems, such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction for Lentinula edodesDe novo assembly was carried out using short reads from paired-end and mate-paired libraries and by using long reads by PacBio, resulting in a contig number of 1,951 and an N50 of 1 Mb. Furthermore, we predicted genes by Augustus using transcriptome sequencing (RNA-seq) data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes. This analysis revealed that Lentinula edodes lacks lignin peroxidase. To reveal genes involved in the loss of quality of Lentinula edodes postharvest fruiting bodies, transcriptome analysis was carried out using serial analysis of gene expression (SuperSAGE). This analysis revealed that many cell wall-related enzymes are upregulated after harvest, such as β-1,3-1,6-glucan-degrading enzymes in glycoside hydrolase (GH) families GH5, GH16, GH30, GH55, and GH128, and thaumatin-like proteins. In addition, we found that several chitin-related genes are upregulated, such as putative chitinases in GH family 18, exochitinases in GH20, and a putative chitosanase in GH family 75. The results suggest that cell wall-degrading enzymes synergistically cooperate for rapid fruiting body autolysis. Many putative transcription factor genes were upregulated postharvest, such as genes containing high-mobility-group (HMG) domains and zinc finger domains. Several cell death-related proteins were also upregulated postharvest.IMPORTANCE Our data collectively suggest that there is a rapid fruiting body autolysis system in Lentinula edodes The genes for the loss of postharvest quality newly found in this research will be targets for the future breeding of strains that keep fresh longer than present strains. De novoLentinula edodes genome assembly data will be used for the construction of a complete Lentinula edodes chromosome map for future breeding.
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Lee HY, Moon S, Shim D, Hong CP, Lee Y, Koo CD, Chung JW, Ryu H. Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars. Genes (Basel) 2017; 8:genes8040109. [PMID: 28338645 PMCID: PMC5406856 DOI: 10.3390/genes8040109] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/28/2017] [Accepted: 03/21/2017] [Indexed: 11/16/2022] Open
Abstract
The shiitake mushroom (Lentinulaedodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms. In this study, we developed 44 novel polymorphic simple sequence repeat (SSR) markers for the determination of shiitake mushroom cultivars based on a whole genome sequencing database of L. edodes. These markers were found to be polymorphic and reliable when screened in 23 shiitake mushroom cultivars. For the 44 SSR markers developed in this study, the major allele frequency ranged from 0.13 to 0.94; the number of genotypes and number of alleles were each 2-11; the observed and expected heterozygosity were 0.00-1.00 and 0.10-0.90, respectively; and the polymorphic information content value ranged from 0.10 to 0.89. These new markers can be used for molecular breeding, the determination of cultivars, and other applications.
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Affiliation(s)
- Hwa-Yong Lee
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea.
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Suyun Moon
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Donghwan Shim
- Department of Forest Genetic Resources, National Institute of Forest Science, Suwon 16631, Korea.
| | | | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea.
| | - Chang-Duck Koo
- Department of Forest Science, Chungbuk National University, Cheongju 28644, Korea.
| | - Jong-Wook Chung
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju 28644, Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
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Zhou Y, Dong X, Li Z, Zou G, Lin L, Wang X, Chen H, Gasser RB, Li J. Predominance of Streptococcus suis ST1 and ST7 in human cases in China, and detection of a novel sequence type, ST658. Virulence 2016; 8:1031-1035. [PMID: 27689249 DOI: 10.1080/21505594.2016.1243193] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Affiliation(s)
- Yang Zhou
- a College of Food Science and Technology, Key Laboratory of Environment Correlative Dietology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, Hubei , P.R. China.,b College of Fisheries, Huazhong Agricultural University , Wuhan, Hubei , P.R. China
| | - Xingxing Dong
- a College of Food Science and Technology, Key Laboratory of Environment Correlative Dietology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, Hubei , P.R. China
| | - Zhiwei Li
- a College of Food Science and Technology, Key Laboratory of Environment Correlative Dietology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, Hubei , P.R. China
| | - Geng Zou
- a College of Food Science and Technology, Key Laboratory of Environment Correlative Dietology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, Hubei , P.R. China
| | - Li Lin
- b College of Fisheries, Huazhong Agricultural University , Wuhan, Hubei , P.R. China
| | - Xiaohong Wang
- a College of Food Science and Technology, Key Laboratory of Environment Correlative Dietology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, Hubei , P.R. China
| | - Huanchun Chen
- a College of Food Science and Technology, Key Laboratory of Environment Correlative Dietology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, Hubei , P.R. China
| | - Robin B Gasser
- a College of Food Science and Technology, Key Laboratory of Environment Correlative Dietology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, Hubei , P.R. China.,c Faculty of Veterinary and Agricultural Sciences, The University of Melbourne , Parkville , Victoria , Australia
| | - Jinquan Li
- a College of Food Science and Technology, Key Laboratory of Environment Correlative Dietology, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, Hubei , P.R. China.,d Jiangsu Key Laboratory of Zoonosis, Yangzhou University , Yangzhou, Jiangsu , P.R. China
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Chen L, Gong Y, Cai Y, Liu W, Zhou Y, Xiao Y, Xu Z, Liu Y, Lei X, Wang G, Guo M, Ma X, Bian Y. Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation. PLoS One 2016; 11:e0160336. [PMID: 27500531 PMCID: PMC4976891 DOI: 10.1371/journal.pone.0160336] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/18/2016] [Indexed: 01/09/2023] Open
Abstract
Lentinula edodes, one of the most popular, edible mushroom species with a high content of proteins and polysaccharides as well as unique aroma, is widely cultivated in many Asian countries, especially in China, Japan and Korea. As a white rot fungus with lignocellulose degradation ability, L. edodes has the potential for application in the utilization of agriculture straw resources. Here, we report its 41.8-Mb genome, encoding 14,889 predicted genes. Through a phylogenetic analysis with model species of fungi, the evolutionary divergence time of L. edodes and Gymnopus luxurians was estimated to be 39 MYA. The carbohydrate-active enzyme genes in L. edodes were compared with those of the other 25 fungal species, and 101 lignocellulolytic enzymes were identified in L. edodes, similar to other white rot fungi. Transcriptome analysis showed that the expression of genes encoding two cellulases and 16 transcription factor was up-regulated when mycelia were cultivated for 120 minutes in cellulose medium versus glucose medium. Our results will foster a better understanding of the molecular mechanism of lignocellulose degradation and provide the basis for partial replacement of wood sawdust with agricultural wastes in L. edodes cultivation.
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Affiliation(s)
- Lianfu Chen
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuhua Gong
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yingli Cai
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wei Liu
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yan Zhou
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yang Xiao
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhangyi Xu
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yin Liu
- Food Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaoyu Lei
- Food Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Gangzheng Wang
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Mengpei Guo
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaolong Ma
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yinbing Bian
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
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