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Liu JJ, Hou YK, Wang X, Zhou XT, Yin JY, Nie SP. Recent advances in the biosynthesis of fungal glucan structural diversity. Carbohydr Polym 2024; 329:121782. [PMID: 38286552 DOI: 10.1016/j.carbpol.2024.121782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/31/2024]
Abstract
Glucans are the most abundant class of macromolecule polymers in fungi, which are commonly found in Ascomycota and Basidiomycota. Fungal glucans are not only essential for cell integrity and function but also crucial for the immense industrial interest in high value applications. They present a variety of structural characteristics at the nanoscale due to the high regulation of genes and the involvement of stochastic processes in synthesis. However, although recent findings have demonstrated the genes of glucans synthesis are relatively conserved across diverse fungi, the formation and organization of diverse glucan structures is still unclear in fungi. Here, we summarize the structural features of fungal glucans and the recent developments in the mechanisms of glucans biosynthesis. Furthermore, we propose the engineering strategies of targeted glucan synthesis and point out the remaining challenges in the synthetic process. Understanding the synthesis process of diverse glucans is necessary for tailoring high value glucan towards specific applications. This engineering strategy contributes to enable the sustainable and efficient production of glucan diversity.
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Affiliation(s)
- Jin-Jin Liu
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province 330047, China
| | - Yu-Ke Hou
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province 330047, China
| | - Xin Wang
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province 330047, China
| | - Xing-Tao Zhou
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province 330047, China
| | - Jun-Yi Yin
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province 330047, China.
| | - Shao-Ping Nie
- State Key Laboratory of Food Science and Resources, China-Canada Joint Lab of Food Science and Technology (Nanchang), Nanchang University, Nanchang, Jiangxi Province 330047, China; Food Laboratory of Zhongyuan, Luo he 462300, Henan, China.
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2
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Wu X, Du Z, Liu L, Chen Z, Li Y, Fu S. Integrative Analysis of Transcriptome and Metabolome Sheds Light on Flavonoid Biosynthesis in the Fruiting Body of Stropharia rugosoannulata. J Fungi (Basel) 2024; 10:254. [PMID: 38667925 PMCID: PMC11051051 DOI: 10.3390/jof10040254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
Flavonoids are a diverse family of natural compounds that are widely distributed in plants and play a critical role in plant growth, development, and stress adaptation. In recent years, the biosynthesis of flavonoids in plants has been well-researched, with the successive discovery of key genes driving this process. However, the regulation of flavonoid biosynthesis in fungi remains unclear. Stropharia rugosoannulata is an edible mushroom known for its high nutritional and pharmacological value, with flavonoids being one of its main active components. To investigate the flavonoid content of S. rugosoannulata, a study was conducted to extract and determine the total flavonoids at four stages: young mushroom (Ym), gill (Gi), maturation (Ma), and parachute-opening (Po). The findings revealed a gradual increase in total flavonoid concentration as the fruiting body developed, with significant variations observed between the Ym, Gi, and Ma stages. Subsequently, we used UPLC-MS/MS and transcriptome sequencing (RNA-seq) to quantify the flavonoids and identify regulatory genes of Ym, Gi, and Ma. In total, 53 flavonoid-related metabolites and 6726 differentially expressed genes (DEGs) were identified. Through KEGG pathway enrichment analysis, we identified 59 structural genes encoding flavonoid biosynthesis-related enzymes, most of which were up-regulated during the development of the fruiting body, consistent with the accumulation of flavonoids. This research led to the establishment of a comprehensive transcriptional metabolic regulatory network encompassing flavonoids, flavonoid synthases, and transcription factors (TFs). This represents the first systematic exploration of the molecular mechanism of flavonoids in the fruiting of fungi, offering a foundation for further research on flavonoid mechanisms and the breeding of high-quality S. rugosoannulata.
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Affiliation(s)
- Xian Wu
- School of Pharmacy, Zunyi Medical University, Zunyi 563000, China;
| | - Zhihui Du
- Guizhou Horticulture Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China; (Z.D.); (L.L.); (Z.C.)
| | - Lian Liu
- Guizhou Horticulture Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China; (Z.D.); (L.L.); (Z.C.)
| | - Zhilin Chen
- Guizhou Horticulture Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China; (Z.D.); (L.L.); (Z.C.)
| | - Yurong Li
- Guizhou Horticulture Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550009, China; (Z.D.); (L.L.); (Z.C.)
| | - Shaobin Fu
- School of Pharmacy, Zunyi Medical University, Zunyi 563000, China;
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3
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Jin C, Ma JX, Wang H, Tang LX, Ye YF, Li X, Si J. First genome assembly and annotation of Sanghuangporus weigelae uncovers its medicinal functions, metabolic pathways, and evolution. Front Cell Infect Microbiol 2024; 13:1325418. [PMID: 38264724 PMCID: PMC10803629 DOI: 10.3389/fcimb.2023.1325418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
Sanghuangporus, also known as "Sanghuang" in China, is a well-known genus of traditional Chinese medicinal macrofungi. To make more effective use of Sanghuangporus resources, we completed the first genome assembly and annotation of a monokaryon strain of S. weigelae in the present study. A 33.96-Mb genome sequence was assembled as 13 contigs, leading to prediction of 9377 protein-coding genes. Phylogenetic and average nucleotide identity analyses indicated that the S. weigelae genome is closely related to those of other Sanghuangporus species in evolutionary tree, which clustered in one clade. Collinearity analysis revealed a high level of collinearity of S. weigelae with S. baumii, S. vaninii, and S. sanghuang. Biosynthesis pathways potentially involved in medicinal properties, including terpenoid and polysaccharide synthesis, were identified in S. weigelae, while polysaccharides were identified as the main medicinal metabolites in S. weigelae, with flavonoids more important in Sanghuangporus than other medicinal mushroom groups. Genes encoding 332 carbohydrate-active enzymes were identified in the S. weigelae genome, including major glycoside hydrolases and glycosyltransferases predicted, revealing the robust lignocellulose degradation capacity of S. weigelae. Further, 130 genes, clustered in seven classes were annotated to encode cytochromes P450 in the S. weigelae genome. Overall, our results reveal the remarkably medicinal capacity of S. weigelae and provide new insights that will inform the study of evolution and medicinal application of S. weigelae. The data are a reference resource for the formulation of scientific and rational ecological protection policies for Sanghuangporus species.
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Affiliation(s)
| | | | | | | | | | | | - Jing Si
- Institute of Microbiology, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
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4
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Zhu L, Gao X, Zhang M, Hu C, Yang W, Guo L, Yang S, Yu H, Yu H. Whole Genome Sequence of an Edible Mushroom Oudemansiella raphanipes (Changgengu). J Fungi (Basel) 2023; 9:jof9020266. [PMID: 36836380 PMCID: PMC9961838 DOI: 10.3390/jof9020266] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/09/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Oudemansiella raphanipes, considered as a well-known culinary edible mushroom with a high content of natural bioactive substances, is widely cultivated in China with the commercial name Changgengu. However, due to the lack of genomic data, molecular and genetic study on O. raphanipes is rare. To obtain a comprehensive overview of genetic characteristics and enhance the value of O. raphanipes, two mating-compatible monokaryons isolated from the dikaryon were applied for de novo genome sequencing and assembly using Nanopore and /or Illumina sequencing platforms. One of the monokaryons, O. raphanipes CGG-A-s1, was annotated with 21,308 protein-coding genes, of which 56 were predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I PKS, NRPS, and siderophore. Phylogenetic and comparative analysis of multiple fungi genomes revealed a close evolutionary relationship between O. raphanipes and Mucidula mucid based on single-copy orthologous protein genes. Significant collinearity was detected between O. raphanipes and Flammulina velutipes on the synteny of inter-species genomes. 664 CAZyme genes in CGG-A-s1 were identified with GHs and AAs families significantly elevated when compared with the other 25 sequenced fungi, indicating a strong wood degradation ability. Furthermore, the mating type locus analysis revealed that CGG-A-s1 and CGG-A-s2 were conserved in the gene organization of the mating A locus but various in that of the mating B locus. The genome resource of O. raphanipes will provide new insights into its development of genetic studies and commercial production of high-quality varieties.
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Affiliation(s)
- Liping Zhu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai 201403, China
| | - Xia Gao
- Shandong Agricultural Technology Extending Station, Jinan 250100, China
| | - Meihua Zhang
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
| | - Chunhui Hu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
| | - Wujie Yang
- Shandong Agricultural Technology Extending Station, Jinan 250100, China
| | - Lizhong Guo
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
| | - Song Yang
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
| | - Hailong Yu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai 201403, China
- Correspondence: (H.Y.); or (H.Y.); Tel.: +86-532-58957640 (Hailong Yu)
| | - Hao Yu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao 266109, China
- Correspondence: (H.Y.); or (H.Y.); Tel.: +86-532-58957640 (Hailong Yu)
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Duan M, Long S, Wu X, Feng B, Qin S, Li Y, Li X, Li C, Zhao C, Wang L, Yan Y, Wu J, Zhao F, Chen Z, Wang Z. Genome, transcriptome, and metabolome analyses provide new insights into the resource development in an edible fungus Dictyophora indusiata. Front Microbiol 2023; 14:1137159. [PMID: 36846778 PMCID: PMC9948255 DOI: 10.3389/fmicb.2023.1137159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
Dictyophora indusiata (Vent. Ex Pers.) Fisch. (DI) is an edible and medicinal fungus widely used in East Asian countries. However, during DI cultivation, the formation of fruiting bodies cannot be regulated, which leads to yield and quality losses. The present study performed a combined genome, transcriptome, and metabolome analysis of DI. Using Nanopore and Illumina sequencing approaches, we created the DI reference genome, which was 67.32 Mb long with 323 contigs. We identified 19,909 coding genes on this genome, of which 46 gene clusters were related to terpenoid synthesis. Subsequent transcriptome sequencing using five DI tissues (cap, indusia, mycelia, stipe, and volva) showed high expression levels of genes in the cap, indicating the tissue's importance in regulating the fruiting body formation. Meanwhile, the metabolome analysis identified 728 metabolites from the five tissues. Mycelium was rich in choline, while volva was rich in dendronobilin; stipe had monosaccharides as the primary component, and the cap was the main source of indole acetic acid (IAA) synthesis. We confirmed the importance of tryptophan metabolism for DI fruiting body differentiation based on KEGG pathway analysis. Finally, the combined multiomics analysis identified three new genes related to IAA synthesis of the tryptophan metabolic pathway in the cap, which may regulate DI fruiting body synthesis and improve DI quality. Thus, the study's findings expand our understanding of resource development and the molecular mechanisms underlying DI development and differentiation. However, the current genome is still a rough draft that needs to be strengthened.
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Affiliation(s)
- Mingzheng Duan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Science/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, China,Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Shengfeng Long
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiaojian Wu
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Bin Feng
- Laibin Branch of Guangxi Academy of Agricultural Sciences, Laihua Center, Laibin, China
| | - Sunqian Qin
- Laibin Branch of Guangxi Academy of Agricultural Sciences, Laihua Center, Laibin, China
| | - Yijie Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Science/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, China
| | - Xiang Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Science/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, China
| | - Changning Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Science/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, China
| | - Chenggang Zhao
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Lingqiang Wang
- Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yong Yan
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jianming Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Science/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, China
| | - Falin Zhao
- Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Zhendong Chen
- Guangxi Academy of Agricultural Sciences, Nanning, China,*Correspondence: Zhendong Chen, ✉
| | - Zeping Wang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/Sugarcane Research Center, Chinese Academy of Agricultural Science/Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Nanning, China,Zeping Wang, ✉
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6
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Xu L, Yang W, Qiu T, Gao X, Zhang H, Zhang S, Cui H, Guo L, Yu H, Yu H. Complete genome sequences and comparative secretomic analysis for the industrially cultivated edible mushroom Lyophyllum decastes reveals insights on evolution and lignocellulose degradation potential. Front Microbiol 2023; 14:1137162. [PMID: 37032898 PMCID: PMC10078946 DOI: 10.3389/fmicb.2023.1137162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/15/2023] [Indexed: 04/11/2023] Open
Abstract
Lyophyllum decastes, also known as Luronggu in China, is a culinary edible and medicinal mushroom that was widely cultivated in China in recent years. In the present study, the complete high-quality genome of two mating compatible L. decastes strain was sequenced. The L. decastes LRG-d1-1 genome consists of 47.7 Mb in 15 contigs with a contig N90 of 2.08 Mb and 14,499 predicted gene models. Phylogenetic analysis revealed that L. decastes exhibits a close evolutionary relationship to the Termitomyces and Hypsizygus genus and was diverged from H. marmoreus ~ 45.53 Mya ago. Mating A loci of L. decastes compose of five and four HD genes in two monokaryotic strains, respectively. Mating B loci compose of five STE genes in both two monokaryotic strains. To accelerate the cross-breeding process, we designed four pairs of specific primers and successfully detected both mating types in L. decastes. As a wood-rotting mushroom, a total of 541 genes accounting for 577 CAZymes were identified in the genome of L. decastes. Proteomic analysis revealed that 1,071 proteins including 182 CAZymes and 258 secreted enzymes were identified from four groups (PDB, PDB + bran, PDB + cotton hull, and PDB + sawdust). Two laccases and a quinone reductase were strongly overproduced in lignin-rich cultures, and the laccases were among the top-3 secreted proteins, suggesting an important role in the synergistic decomposition of lignin. These results revealed the robustness of the lignocellulose degradation capacity of L. decastes. This is the first study to provide insights into the evolution and lignocellulose degradation of L. decastes.
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Affiliation(s)
- Lili Xu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wujie Yang
- Shandong Agricultural Technology Extending Station, Jinan, Shandong, China
| | - Tianmei Qiu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Xia Gao
- Shandong Agricultural Technology Extending Station, Jinan, Shandong, China
| | - Hongyong Zhang
- Dezhou Academy of Agricultural Sciences, Dezhou, Shandong, China
| | - Shuliang Zhang
- Dezhou Academy of Agricultural Sciences, Dezhou, Shandong, China
| | - Hui Cui
- Shandong Agricultural Technology Extending Station, Jinan, Shandong, China
| | - Lizhong Guo
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Hailong Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Hailong Yu,
| | - Hao Yu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, China
- Hao Yu,
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Phithakrotchanakoon C, Mayteeworakoon S, Siriarchawatana P, Kitikhun S, Harnpicharnchai P, Wansom S, Eurwilaichitr L, Ingsriswang S. Beneficial bacterial-Auricularia cornea interactions fostering growth enhancement identified from microbiota present in spent mushroom substrate. Front Microbiol 2022; 13:1006446. [PMID: 36299733 PMCID: PMC9589457 DOI: 10.3389/fmicb.2022.1006446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Complex dynamic bacterial-fungal interactions play key roles during mushroom growth, ranging from mutualism to antagonism. These interactions convey a large influence on mushroom’s mycelial and fruiting body formation during mushroom cultivation. In this study, high-throughput amplicon sequencing was conducted to investigate the structure of bacterial communities in spent mushroom substrates obtained from cultivation of two different groups of Auricularia cornea with (A) high yield and (B) low yield of fruiting body production. It was found that species richness and diversity of microbiota in group (A) samples were significantly higher than in group (B) samples. Among the identified 765 bacterial OTUs, 5 bacterial species found to exhibit high differential abundance between group (A) and group (B) were Pseudonocardia mangrovi, Luteimonas composti, Paracoccus pantotrophus, Sphingobium jiangsuense, and Microvirga massiliensis. The co-cultivation with selected bacterial strains showed that A. cornea TBRC 12900 co-cultivated with P. mangrovi TBRC-BCC 42794 promoted a high level of mycelial growth. Proteomics analysis was performed to elucidate the biological activities involved in the mutualistic association between A. cornea TBRC 12900 and P. mangrovi TBRC-BCC 42794. After co-cultivation of A. cornea TBRC 12900 and P. mangrovi TBRC-BCC 42794, 1,616 proteins were detected including 578 proteins of A. cornea origin and 1,038 proteins of P. mangrovi origin. Functional analysis and PPI network construction revealed that the high level of mycelial growth in the co-culture condition most likely resulted from concerted actions of (a) carbohydrate-active enzymes including hydrolases, glycosyltransferases, and carbohydrate esterases important for carbohydrate metabolism and cell wall generation/remodeling, (b) peptidases including cysteine-, metallo-, and serine-peptidases, (c) transporters including the ABC-type transporter superfamily, the FAT transporter family, and the VGP family, and (d) proteins with proposed roles in formation of metabolites that can act as growth-promoting molecules or those normally contain antimicrobial activity (e.g., indoles, terpenes, β-lactones, lanthipeptides, iturins, and ectoines). The findings will provide novel insights into bacterial-fungal interactions during mycelial growth and fruiting body formation. Our results can be utilized for the selection of growth-promoting bacteria to improve the cultivation process of A. cornea with a high production yield, thus conveying potentially high socio-economic impact to mushroom agriculture.
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Affiliation(s)
- Chitwadee Phithakrotchanakoon
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sermsiri Mayteeworakoon
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Paopit Siriarchawatana
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Supattra Kitikhun
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Piyanun Harnpicharnchai
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Supaporn Wansom
- National Energy Technology Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Lily Eurwilaichitr
- National Energy Technology Center, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Supawadee Ingsriswang
- Microbial Systems and Computational Biology Research Team, Thailand Bioresource Research Center, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- *Correspondence: Supawadee Ingsriswang,
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8
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Yu H, Zhang M, Sun Y, Li Q, Liu J, Song C, Shang X, Tan Q, Zhang L, Yu H. Whole-genome sequence of a high-temperature edible mushroom Pleurotus giganteus (zhudugu). Front Microbiol 2022; 13:941889. [PMID: 36051764 PMCID: PMC9424821 DOI: 10.3389/fmicb.2022.941889] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/29/2022] [Indexed: 11/25/2022] Open
Abstract
Most of the sequenced wood-rotting edible mushroom produce fruiting body at relatively low temperatures. Little information has been known about the high-temperature wood-rotting mushroom. Here, we performed de novo sequencing and assembly of the genome of a high-temperature edible mushroom Pleurotus giganteus from a monokaryotic strain zhudugu2 using the Illumina and Pac-Bio CLR sequencing technologies. P. giganteus, also known as Zhudugu in China, is a well-known culinary edible mushroom that has been widely distributed and cultivated in China, Southeast Asia, and South Asia. The genome consists of 40.00 Mb in 27 contigs with a contig N50 of 4.384 Mb. Phylogenetic analysis reveals that P. giganteus and other strains in Pleurotus clustered in one clade. Phylogenetic analysis and average nucleotide identity analysis indicated that the P. giganteus genome showed a closer relationship with other Pleurotus species. Chromosome collinearity analysis revealed a high level of collinearity between P. ostreatus and P. giganteus. There are 12,628 protein-coding genes annotated in this monoploid genome. A total of 481 enzymes accounting for 514 carbohydrate-active enzymes (CAZymes) terms were identified in the P. giganteus genome, including 15 laccases and 10 class II peroxidases predicted in the genome, which revealed the robustness of lignocellulose degradation capacity of P. giganteus. The mating-A type locus of P. giganteus consisted of a pair of homeodomain mating-type genes HD1 and HD2. The mating-B type locus of P. giganteus consisted of at least four pheromone receptor genes and three pheromone genes. The genome is not only beneficial for the genome-assisted breeding of this mushroom but also helps us to understand the high-temperature tolerance of the edible mushroom.
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Affiliation(s)
- Hailong Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Meiyan Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yating Sun
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Qiaozhen Li
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jianyu Liu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chunyan Song
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xiaodong Shang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qi Tan
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Lujun Zhang
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Lujun Zhang,
| | - Hao Yu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
- Hao Yu,
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9
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Dong H, Zhao X, Cai M, Gu H, E H, Li X, Zhang Y, Lu H, Zhou C. Metabolomics Analysis of Morchella sp. From Different Geographical Origins of China Using UPLC-Q-TOF-MS. Front Nutr 2022; 9:865531. [PMID: 35449541 PMCID: PMC9016275 DOI: 10.3389/fnut.2022.865531] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/14/2022] [Indexed: 01/08/2023] Open
Abstract
The morel mushroom (Morchella sp.) is reputed as one of the most highly-prized edible fungi with mounting cultivated area as well as commercial popularity in China. To date, optimized methods specific for quality evaluation and constituent analysis of Morchella sp. are still non-available, impeding the healthy and sustainable development of this industry. Herein, an untargeted UPLC-Q-TOF-MS-based metabolomics approach was performed to characterize the metabolite profiles of morel samples from four distinct geographical origins of China, viz. Gansu, Guizhou, Liaoning, and Henan province. A total of 32 significantly different metabolites assigned to lipids (19), organic acids (9), amino acids (3), and ketones (1) were identified to distinguish the geographic-segregation samples amenable to multivariate analysis. These metabolites may serve as molecular markers indicative of specific regions. More importantly, the lipid, protein and amino acid metabolism were responsible for geographic differences as revealed by KEGG pathway enrichment analysis. Collectively, this study not only pioneered high-throughput methodology to evaluate quality of Morchella sp. and distinguish geographical origins in a sensitive, rapid and efficient manner, but also shed light on the potential link between physiochemical variation and geological origins from a metabolic perspective, which may be conducive to the advancement of edible fungi industry and establishment of food traceability system.
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Affiliation(s)
- Hui Dong
- Laboratory of Agro-Food Quality and Safety Risk Assessment (Shanghai), Institute of Agro-Food Quality Standard and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xiaoyan Zhao
- Laboratory of Agro-Food Quality and Safety Risk Assessment (Shanghai), Institute of Agro-Food Quality Standard and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Min Cai
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERCLA), Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Haotian Gu
- Shanghai Engineering Research Center of Low-Carbon Agriculture (SERCLA), Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Science, Shanghai, China
| | - Hengchao E
- Laboratory of Agro-Food Quality and Safety Risk Assessment (Shanghai), Institute of Agro-Food Quality Standard and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Xiaobei Li
- Laboratory of Agro-Food Quality and Safety Risk Assessment (Shanghai), Institute of Agro-Food Quality Standard and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yanmei Zhang
- Laboratory of Agro-Food Quality and Safety Risk Assessment (Shanghai), Institute of Agro-Food Quality Standard and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Huan Lu
- National Research Center of Edible Fungi Biotechnology and Engineering, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Changyan Zhou
- Laboratory of Agro-Food Quality and Safety Risk Assessment (Shanghai), Institute of Agro-Food Quality Standard and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
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10
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Li S, Zhao S, Hu C, Mao C, Guo L, Yu H, Yu H. Whole Genome Sequence of an Edible Mushroom Stropharia rugosoannulata (Daqiugaigu). J Fungi (Basel) 2022; 8:jof8020099. [PMID: 35205854 PMCID: PMC8880121 DOI: 10.3390/jof8020099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
Stropharia rugosoannulata, also known as Daqiugaigu in China, is a well-known edible mushroom that has been widely cultivated in China in recent years. Many studies have focused on its nutrients, bioactive compounds, and lignin degradation capacity, although there are few molecular and genetic breeding studies due to the lack of genomic information. Here, we present the 47.9 Mb genome sequence of an S. rugosoannulata monokaryotic strain (A15), which has 20 contigs and an N50 of 3.64 Mb, which was obtained by a combination of Illumina and Nanopore sequencing platforms. Further analysis predicted 12,752 protein-coding genes, including 486 CAZyme-encoding genes. Phylogenetic analysis revealed a close evolutionary relationship between S. rugosoannulata and Hypholoma sublateritium, Psilocybe cyanescens, and Galerina marginata based on single-copy orthologous genes. Proteomic analysis revealed different protein expression profiles between the cap and the stipe of the S. rugosoannulata fruiting body. The proteins of the stipe associated with carbon metabolism, energy production, and stress-response-related biological processes had higher abundance, whereas proteins involved in fatty acid synthesis and mRNA splicing showed higher expression in the cap than in the stipe. The genome of S. rugosoannulata will provide valuable genetic resources not only for comparative genomic analyses and evolutionary studies among Basidiomycetes but also for alleviating the bottlenecks that restrict the molecular breeding of this edible mushroom.
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Affiliation(s)
- Shuwen Li
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Shuxue Zhao
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Chunhui Hu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Chengzhi Mao
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Lizhong Guo
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Hailong Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
- Correspondence: (H.Y.); (H.Y.); Tel.: +86-532-58957640 (Hao Yu)
| | - Hao Yu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
- Correspondence: (H.Y.); (H.Y.); Tel.: +86-532-58957640 (Hao Yu)
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11
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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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12
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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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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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14
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Duan M, Bao H, Bau T. Analyses of transcriptomes and the first complete genome of Leucocalocybe mongolica provide new insights into phylogenetic relationships and conservation. Sci Rep 2021; 11:2930. [PMID: 33536487 PMCID: PMC7858605 DOI: 10.1038/s41598-021-81784-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
In this study, we report a de novo assembly of the first high-quality genome for a wild mushroom species Leucocalocybe mongolica (LM). We performed high-throughput transcriptome sequencing to analyze the genetic basis for the life history of LM. Our results show that the genome size of LM is 46.0 Mb, including 26 contigs with a contig N50 size of 3.6 Mb. In total, we predicted 11,599 protein-coding genes, of which 65.7% (7630) could be aligned with high confidence to annotated homologous genes in other species. We performed phylogenetic analyses using genes form 3269 single-copy gene families and showed support for distinguishing LM from the genus Tricholoma (L.) P.Kumm., in which it is sometimes circumscribed. We believe that one reason for limited wild occurrences of LM may be the loss of key metabolic genes, especially carbohydrate-active enzymes (CAZymes), based on comparisons with other closely related species. The results of our transcriptome analyses between vegetative (mycelia) and reproductive (fruiting bodies) organs indicated that changes in gene expression among some key CAZyme genes may help to determine the switch from asexual to sexual reproduction. Taken together, our genomic and transcriptome data for LM comprise a valuable resource for both understanding the evolutionary and life history of this species.
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Affiliation(s)
- Mingzheng Duan
- grid.464353.30000 0000 9888 756XKey Laboratory of Edible Fungi Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, 130118 Jilin China
| | - Haiying Bao
- grid.464353.30000 0000 9888 756XKey Laboratory of Edible Fungi Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, 130118 Jilin China
| | - Tolgor Bau
- grid.464353.30000 0000 9888 756XKey Laboratory of Edible Fungi Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, 130118 Jilin China
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