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Li S, Li B, Guo S. Chromosome-Level Assembly Reveals a Fifteen-Chromosome Aneuploid Genome and Environmental Adaptation Strategy of Chinese Traditional Medical Fungus Wolfiporia hoelen. Int J Mol Sci 2024; 25:8786. [PMID: 39201472 PMCID: PMC11354754 DOI: 10.3390/ijms25168786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/30/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
The sclerotia of Wolfiporia hoelen are one of the most important traditional Chinese medicines and foods commonly used in China, Japan, Korea, and other Asian countries. To provide a high-quality reference genome and deepen our understanding of the genome of W. hoelen to elucidate various biological phenomena. In this study, we assembled three genomes of W. hoelen using a combination of Nanopore and Illumina sequencing strategies. The fifteen-chromosome genome L7 of W. hoelen was assembled with two-sided telomere and rDNA sequences for the first time. The chromosome count was subsequently confirmed through collinearity analysis, correcting the previous belief that W. hoelen had only fourteen chromosomes. Moreover, the aneuploid genome was discovered in W. hoelen for the first time through sequencing depth analysis of different chromosomes, and only some strains of W. hoelen exhibit aneuploid genomes. According to the genome analysis of homokaryotic offspring and protoplast-isolated strains, a potential variation in chromosome allocation patterns was revealed. Moreover, the gene function enrichment analysis of genes on reduplicated chromosomes demonstrated that aneuploidy in the genome may be the result of environmental adaptation for W. hoelen. The discovery of an aneuploid genome also provides new ideas for genetic improvement of W. hoelen.
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Affiliation(s)
| | | | - Shunxing Guo
- The Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (S.L.); (B.L.)
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Yan K, Guo L, Zhang B, Chang M, Meng J, Deng B, Liu J, Hou L. MAC Family Transcription Factors Enhance the Tolerance of Mycelia to Heat Stress and Promote the Primordial Formation Rate of Pleurotus ostreatus. J Fungi (Basel) 2023; 10:13. [PMID: 38248923 PMCID: PMC10816978 DOI: 10.3390/jof10010013] [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: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/10/2023] [Indexed: 01/23/2024] Open
Abstract
Pleurotus ostreatus is a typical tetrapolar heterologous edible mushroom, and its growth and development regulatory mechanism has become a research hotspot in recent years. The MAC1 protein is a transcription factor that perceives copper and can regulate the expression of multiple genes, thereby affecting the growth and development of organisms. However, its function in edible mushrooms is still unknown. In this study, two transcription factor genes, PoMCA1a and PoMAC1b, were identified. Afterwards, PoMAC1 overexpression (OE) and RNA interference (RNAi) strains were constructed to further explore gene function. The results showed that the PoMAC1 mutation had no significant effect on the growth rate of mycelia. Further research has shown that OE-PoMAC1a strains and RNAi-PoMAC1b strains exhibit strong tolerance under 32 °C heat stress. However, under 40 °C heat stress, the OE of PoMAC1a and PoMAC1b promoted the recovery of mycelial growth after heat stress. Second, the OE of PoMAC1a can promote the rapid formation of primordia and shorten the cultivation cycle. In summary, this study indicated that there are functional differences between PoMAC1a and PoMAC1b under different heat stresses during the vegetative growth stage, and PoMAC1a has a positive regulatory effect on the formation of primordia during the reproductive growth stage.
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Affiliation(s)
- Kexing Yan
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
| | - Lifeng Guo
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
| | - Benfeng Zhang
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
| | - Mingchang Chang
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
- Shanxi Research Center for Engineering Technology of Edible Fungi, Jinzhong 030801, China
| | - Junlong Meng
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
- Shanxi Research Center for Engineering Technology of Edible Fungi, Jinzhong 030801, China
| | - Bing Deng
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
- Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Jinzhong 030801, China
| | - Jingyu Liu
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
- Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Jinzhong 030801, China
| | - Ludan Hou
- College of Food Science and Engineering, Shanxi Agricultural University, Jinzhong 030801, China; (K.Y.); (L.G.); (B.Z.); (M.C.); (J.M.); (B.D.)
- Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Jinzhong 030801, China
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3
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Hou L, Yan K, Dong S, Guo L, Liu J, Wang S, Chang M, Meng J. Transcriptome Analysis Revealed That Hydrogen Peroxide-Regulated Oxidative Phosphorylation Plays an Important Role in the Formation of Pleurotus ostreatus Cap Color. J Fungi (Basel) 2023; 9:823. [PMID: 37623594 PMCID: PMC10455351 DOI: 10.3390/jof9080823] [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: 06/14/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Pleurotus ostreatus is widely cultivated in China. H2O2, as a signaling molecule, can regulate the formation of cap color, but its regulatory pathway is still unclear, severely inhibiting the breeding of dark-colored strains. In this study, 614 DEGs specifically regulated by H2O2 were identified by RNA-seq analysis. GO-enrichment analysis shows that DEGs can be significantly enriched in multiple pathways related to ATP synthesis, mainly including proton-transporting ATP synthesis complex, coupling factor F(o), ATP biosynthetic process, nucleoside triphosphate metabolic processes, ATP metabolic process, purine nucleoside triphosphate biosynthetic and metabolic processes, and purine ribonuclease triphosphate biosynthetic metabolic processes. Further KEGG analysis revealed that 23 DEGs were involved in cap color formation through the oxidative phosphorylation pathway. They were enriched in Complexes I, III, IV, and V in the respiratory chain. Further addition of exogenous uncoupling agents and ATP synthase inhibitors clarifies the important role of ATP synthesis in color formation. In summary, H2O2 may upregulate the expression of complex-encoding genes in the respiratory chain and promote ATP synthesis, thereby affecting the formation of cap color. The results of this study lay the foundation for the breeding of dark-colored strains of P. ostreatus and provide a basis for the color-formation mechanism of edible fungi.
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Affiliation(s)
- Ludan Hou
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
- Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Taigu 030801, China
| | - Kexing Yan
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
| | - Shuai Dong
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
| | - Lifeng Guo
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
| | - Jingyu Liu
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
- Shanxi Key Laboratory of Edible Fungi for Loess Plateau, Taigu 030801, China
| | - Shurong Wang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
- Shanxi Research Center for Engineering Technology of Edible Fungi, Taigu 030801, China
| | - Mingchang Chang
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
- Shanxi Research Center for Engineering Technology of Edible Fungi, Taigu 030801, China
| | - Junlong Meng
- College of Food Science and Engineering, Shanxi Agricultural University, Taigu 030801, China; (L.H.); (K.Y.); (S.D.); (L.G.); (J.L.); (S.W.)
- Shanxi Research Center for Engineering Technology of Edible Fungi, Taigu 030801, China
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Ma X, Lu L, Yao F, Fang M, Wang P, Meng J, Shao K, Sun X, Zhang Y. High-quality genome assembly and multi-omics analysis of pigment synthesis pathway in Auricularia cornea. Front Microbiol 2023; 14:1211795. [PMID: 37396365 PMCID: PMC10308021 DOI: 10.3389/fmicb.2023.1211795] [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: 04/25/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023] Open
Abstract
Owing to its great market potential for food and health care, white Auricularia cornea, a rare edible fungus, has received increased attention in recent years. This study presents a high-quality genome assembly of A. cornea and multi-omics analysis of its pigment synthesis pathway. Continuous Long Reads libraries, combined with Hi-C-assisted assembly were used to assemble of white A. cornea. Based on this data, we analyzed the transcriptome and metabolome of purple and white strains during the mycelium, primordium, and fruiting body stages. Finally, we obtained the genome of A.cornea assembled from 13 clusters. Comparative and evolutionary analysis suggests that A.cornea is more closely related to Auricularia subglabra than to Auricularia heimuer. The divergence of white/purple A.cornea occurred approximately 40,000 years ago, and there were numerous inversions and translocations between homologous regions of the two genomes. Purple strain synthesized pigment via the shikimate pathway. The pigment in the fruiting body of A. cornea was γ-glutaminyl-3,4-dihydroxy-benzoate. During pigment synthesis, α-D-glucose-1P, citrate, 2-Oxoglutarate, and glutamate were four important intermediate metabolites, whereas polyphenol oxidase and other 20 enzyme genes were the key enzymes. This study sheds light on the genetic blueprint and evolutionary history of the white A.cornea genome, revealing the mechanism of pigment synthesis in A.cornea. It has important theoretical and practical implications for understanding the evolution of basidiomycetes, molecular breeding of white A.cornea, and deciphering the genetic regulations of edible fungi. Additionally, it provides valuable insights for the study of phenotypic traits in other edible fungi.
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Affiliation(s)
- Xiaoxu Ma
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
- Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Edible Fungi Breeding, Guiyang, China
| | - Lixin Lu
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Fangjie Yao
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
- Country Engineering Research Centre of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Ming Fang
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Peng Wang
- Economic Plants Research Insitute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jingjing Meng
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Kaisheng Shao
- Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Edible Fungi Breeding, Guiyang, China
| | - Xu Sun
- Guizhou Academy of Agricultural Sciences, Guizhou Key Laboratory of Edible Fungi Breeding, Guiyang, China
| | - Youmin Zhang
- Lab of Genetic Breeding of Edible Fungi, Horticultural, College of Horticulture, Jilin Agricultural University, Changchun, China
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Jiang N, Li Z, Dai Y, Liu Z, Han X, Li Y, Li Y, Xiong H, Xu J, Zhang G, Xiao S, Yuan X, Fu Y. Massive genome investigations reveal insights of prevalent introgression for environmental adaptation and triterpene biosynthesis in Ganoderma. Mol Ecol Resour 2022. [PMID: 36214617 DOI: 10.1111/1755-0998.13718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/26/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022]
Abstract
Genome introgression is one of the driving forces that can increase species and genetic diversity and facilitate the adaptive evolution of organisms and biodiversity conservation. However, the genomic introgression and its contribution to biodiversity of macrofungi are still unclear. The genus Ganoderma is a typical macrofungal group that plays crucial roles in forest ecosystem as saprophytic organisms and plant pathogens, and is also involved in human health as medicinal mushrooms. Most public Ganoderma genomes are fragmented, and reference genomes and whole-genome information of diverse germplasm resources for many Ganoderma species are lacking, thus hindering functional and evolutionary genomic investigations among Ganoderma species. In this study, we provide high-quality genomes of 10 Ganoderma species and whole-genome variants data of 224 individuals from various ecoregions, enabling us to infer the phylogeny of Ganoderma species and their historical population dynamics. Based on whole-genome variants, widespread and genome-wide introgression among Ganoderma species is revealed. Genes with significant introgression signals were related to stress response, digestive absorption, and secondary metabolite synthesis, factors that may contribute to environmental adaptation and important biocomponent metabolism. CYP512U6, an essential functional gene in the CYP450 family related to Ganoderma triterpene synthesis, was detected with significant introgression and selection signals combined with Ganoderma metabolomic analysis, indicating that both ancient gene exchange and recent domestication have contributed to the categories and content of secondary metabolites of Ganoderma. The reference genomes, whole-genome variants, and metabolite profiles could serve as abundant and valuable genetic resources for evolution, ecology, and conservation investigations of Ganoderma species and other macrofungi.
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Affiliation(s)
- Nan Jiang
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
- College of Plant Protection, Jilin Agricultural University, Jilin, Changchun, China
| | - Zhenhao Li
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Yueting Dai
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Zhenhua Liu
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Xuerong Han
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yu Li
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yong Li
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Hui Xiong
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Jing Xu
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Guoliang Zhang
- ShouXianGu Botanical Drug Institute Co., Ltd., Jinhua, Zhejiang, China
| | - Shijun Xiao
- Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing, Zhejiang, China
| | - Xiaohui Yuan
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, Jilin, China
| | - Yongping Fu
- College of Plant Protection, Jilin Agricultural University, Jilin, Changchun, China
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6
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Whole-Genome Sequencing and Comparative Genomics Analysis of the Wild Edible Mushroom ( Gomphus purpuraceus) Provide Insights into Its Potential Food Application and Artificial Domestication. Genes (Basel) 2022; 13:genes13091628. [PMID: 36140797 PMCID: PMC9498453 DOI: 10.3390/genes13091628] [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: 08/23/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Gomphus purpuraceus (Iwade) Yokoyama is a species of wild fungi that grows in southwest China, considered an edible and medicinal fungus with potential commercial prospects. However, the detailed mechanisms related to the development of mycelium and the formation of the fruiting body are unclear. To obtain a comprehensive overview of genetic features, whole-genome and comparative genomics analyses of G. purpuraceus were performed. High-quality DNA was extracted from the mycelium, which was isolated from a fresh fruiting body of G. purpuraceus. The DNA sample was subjected to sequencing using Illumina and Oxford Nanopore sequencing platforms. A genome assembly totaling 40.15 Mb in 50 contigs with an N50 length of 2.06 Mb was generated, and 8705 putative predicted genes were found. Subsequently, phylogenetic analysis revealed a close evolutionary relationship between G. purpuraceus and Gomphus bonarii. Moreover, a total of 403 carbohydrate-active enzymes (CAZymes) were identified in G. purpuraceus, which included 147 glycoside hydrolases (GHs), 85 glycosyl transferases (GTs), 8 polysaccharide lyases (PLs), 76 carbohydrate esterases (CEs), 57 auxiliary activities (AAs) and 30 carbohydrate-binding modules (CBMs). Compared with the other 13 fungi (Laccaria bicolor, Russula virescens, Boletus edulis, etc.), the number and distribution of CAZymes in G. purpuraceus were similar to other mycorrhizal fungi. Furthermore, the optimization of culture medium for G. purpuraceus showed the efficient utilization of disaccharides such as sucrose and maltose. The genome of G. purpuraceus provides new insights into its niche, food applications and potential artificial domestication.
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Sun X, Wu J, Zhang S, Luo L, Mo C, Sheng L, Ma A. Genome and Comparative Transcriptome Dissection Provide Insights Into Molecular Mechanisms of Sclerotium Formation in Culinary-Medicinal Mushroom Pleurotus tuber-regium. Front Microbiol 2022; 12:815954. [PMID: 35250915 PMCID: PMC8891965 DOI: 10.3389/fmicb.2021.815954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
Pleurotus tuber-regium is an edible and medicinal sclerotium-producing mushroom. The sclerotia of this mushroom also serve as food and folk medicine. Based on the description of its monokaryon genome, sequenced with Illumina and PacBio sequencing technologies, comparative transcriptomic analysis using RNA sequencing (RNA-seq) was employed to study its mechanism of sclerotium formation. The de novo assembled genome is 35.82 Mb in size with a N50 scaffold size of 4.29 Mb and encodes 12,173 putative proteins. Expression analysis demonstrated that 1,146 and 1,249 genes were upregulated and downregulated with the formation of sclerotia, respectively. The differentially expressed genes were associated with substrate decomposition, the oxidation-reduction process, cell wall synthesis, and other biological processes in P. tuber-regium. These genomic and transcriptomic resources provide useful information for the mechanism underlying sclerotium formation in P. tuber-regium.
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Affiliation(s)
- Xueyan Sun
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junyue Wu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuhui Zhang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lu Luo
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Cuiyuan Mo
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Li Sheng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agro-Microbial Resources and Utilization, Ministry of Agriculture, Wuhan, China
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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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Munhoz da Rocha IF, Martins ST, Amatuzzi RF, Zamith-Miranda D, Nosanchuk JD, Rodrigues ML, Alves LR. Cellular and Extracellular Vesicle RNA Analysis in the Global Threat Fungus Candida auris. Microbiol Spectr 2021; 9:e0153821. [PMID: 34908466 PMCID: PMC8672890 DOI: 10.1128/spectrum.01538-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/03/2021] [Indexed: 12/18/2022] Open
Abstract
Emerging and reemerging pathogens are a worldwide concern, and it is predicted that these microbes will cause severe outbreaks. Candida auris affects people with weakened immune systems, particularly those who are hospitalized or are in health care facilities. Extracellular vesicles (EVs) are lipid bilayer structures released by organisms from all domains of life. EVs can deliver functional molecules to target cells, including proteins and nucleic acids, especially RNA molecules. EVs from several pathogenic fungi species play diverse biological roles related to cell-cell communication and pathogen-host interaction. In this study, we describe a data set which we produced by sequencing the RNA content of EVs from C. auris under normal growth conditions and in the presence of the antifungal caspofungin, a first-line drug to treat this fungus. To generate a more complete data set for future comparative studies, we also sequenced the RNA cellular content of EVs under the same conditions. This data set addresses a previously unexplored area of fungal biology regarding cellular small RNA and EV RNA. Our data will provide a molecular basis for the study of the aspects associated with antifungal treatment, gene expression response, and EV composition in C. auris. These data will also allow the exploration of small RNA content in the fungal kingdom and might serve as an informative basis for studies on the mechanisms by which molecules are directed to fungal EVs. IMPORTANCE Candida auris, a relevant emerging human-pathogenic yeast, is the first fungus to be called a global public health threat by the WHO. This is because of its rapid spread on all inhabited continents, together with its extremely high frequency of drug and multidrug resistance. In our study, we generated a large data set for 3 distinct strains of C. auris and obtained cellular small RNA fraction as well as extracellular vesicle RNA (EV-RNA) during normal growth conditions and after treatment with caspofungin, the first-line drug used to treat C. auris infection.
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Affiliation(s)
| | - Sharon T. Martins
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
| | - Rafaela F. Amatuzzi
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
| | - Daniel Zamith-Miranda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Joshua D. Nosanchuk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Marcio L. Rodrigues
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
- Microbiology Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lysangela R. Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, Fiocruz Paraná, Curitiba, Brazil
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10
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Jiang N, Hu S, Peng B, Li Z, Yuan X, Xiao S, Fu Y. Genome of Ganoderma Species Provides Insights Into the Evolution, Conifers Substrate Utilization, and Terpene Synthesis for Ganoderma tsugae. Front Microbiol 2021; 12:724451. [PMID: 34603250 PMCID: PMC8481371 DOI: 10.3389/fmicb.2021.724451] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 08/16/2021] [Indexed: 12/30/2022] Open
Abstract
Ganoderma tsugae is an endemic medicinal mushroom in Northeast China, providing important source of pharmaceutical product. Comparing with other Ganoderma species, wild G. tsugae can utilize coniferous wood. However, functional genes related to medicinal component synthesis and the genetic mechanism of conifer substrate utilization is still obscure. Here, we assembled a high-quality G. tsugae genome with 18 contigs and 98.5% BUSCO genes and performed the comparative genomics with other Ganoderma species. G. tsugae diverged from their common ancestor of G. lingzhi and G. sinense about 21 million years ago. Genes in G. tsugae-specific and G. tsugae-expanded gene families, such as salh, phea, cyp53a1, and cyp102a, and positively selected genes, such as glpk and amie, were functionally enriched in plant-pathogen interaction, benzoate degradation, and fanconi anemia pathway. Those functional genes might contribute to conifer substrate utilization of G. tsugae. Meanwhile, gene families in the terpene synthesis were identified and genome-wide SNP variants were detected in population. Finally, the study provided valuable genomic resources and offered useful hints for the functional gene mapping and investigation of key gene contributing to conifer cultivation substrate utilization and medicinal component biosynthesis.
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Affiliation(s)
- Nan Jiang
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Shuang Hu
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Bing Peng
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Zhenhao Li
- Shouxiangu Botanical Drug Institute Co., Ltd., Jinhua, China
| | - Xiaohui Yuan
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China.,Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology, Jiaxing, China
| | - Shijun Xiao
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Yongping Fu
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
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11
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Wang L, Liao B, Gong L, Xiao S, Huang Z. Haploid Genome Analysis Reveals a Tandem Cluster of Four HSP20 Genes Involved in the High-Temperature Adaptation of Coriolopsis trogii. Microbiol Spectr 2021; 9:e0028721. [PMID: 34406871 PMCID: PMC8552761 DOI: 10.1128/spectrum.00287-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 01/16/2023] Open
Abstract
Coriolopsis trogii is a typical thermotolerant basidiomycete fungus, but its thermotolerance mechanisms are currently unknown. In this study, two monokaryons of C. trogii strain Ct001 were assembled: Ct001_29 had a genome assembly size of 38.85 Mb and encoded 13,113 genes, while Ct001_31 was 40.19 Mb in length and encoded 13,309 genes. Comparative intra- and interstrain genomic analysis revealed the rich genetic diversity of C. trogii, which included more than 315,194 single-nucleotide polymorphisms (SNPs), 30,387 insertion/deletions (indels), and 1,460 structural variations. Gene family analysis showed that the expanded families of C. trogii were functionally enriched in lignocellulose degradation activities. Furthermore, a total of 14 allelic pairs of heat shock protein 20 (HSP20) genes were identified in the C. trogii genome. The expression profile obtained from RNA sequencing (RNA-Seq) showed that four tandem-duplicated allelic pairs, HSP20.5 to HSP20.8, had more than 5-fold higher expression at 35°C than at 25°C. In particular, HSP20.5 and HSP20.8 were the most highly expressed HSP20 genes. Allelic expression bias was found for HSP20.5 and HSP20.8; the expression of Ct29HSP20.8 was at least 1.34-fold higher than that of Ct31HSP20.8, and that of Ct31HSP20.5 was at least 1.5-fold higher than that of Ct29HSP20.5. The unique structural and expression profiles of the HSP20 genes revealed by these haplotype-resolved genomes provide insight into the molecular mechanisms of high-temperature adaptation in C. trogii. IMPORTANCE Heat stress is one of the most frequently encountered environmental stresses for most mushroom-forming fungi. Currently available fungal genomes are mostly haploid because high heterozygosity hinders diploid genome assembly. Here, two haplotype genomes of C. trogii, a thermotolerant basidiomycete, were assembled separately. A conserved tandem cluster of four HSP20 genes showing allele-specific expression was found to be closely related to high-temperature adaptation in C. trogii. The obtained haploid genomes and their comparison offer a more thorough understanding of the genetic background of C. trogii. In addition, the responses of HSP20 genes at 35°C, which may contribute to the growth and survival of C. trogii at high temperatures, could inform the selection and breeding of elite strains in the future.
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Affiliation(s)
- Lining Wang
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, People’s Republic of China
| | - Baosheng Liao
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Lu Gong
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Shuiming Xiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Zhihai Huang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
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12
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Hou L, Zhao M, Huang C, He Q, Zhang L, Zhang J. Alternative oxidase gene induced by nitric oxide is involved in the regulation of ROS and enhances the resistance of Pleurotus ostreatus to heat stress. Microb Cell Fact 2021; 20:137. [PMID: 34281563 PMCID: PMC8287771 DOI: 10.1186/s12934-021-01626-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 07/04/2021] [Indexed: 12/13/2022] Open
Abstract
Background In China, during the cultivation process of Pleurotus ostreatus, the yield and quality of fruiting bodies are easily affected by high temperatures in summer. Nitric oxide (NO) plays an important regulatory role in the response to abiotic stress, and previous studies have found that NO can induce alternative oxidase (aox) experssion in response to heat stress (HS) by regulating aconitase. However, the regulatory pathway of NO is complex, and the function and regulation of the aox gene in the response to HS remain unclear. Results In this study, we found that NO affected nicotinamide adenine dinucleotide (NADH) and adenosine triphosphate (ATP) levels, reduced hydrogen peroxide (H2O2) and superoxide anion (O2−) contents, and slowed O2− production. Further RNA-Seq results showed that NO regulated the oxidation-reduction process and oxidoreductase activity, affected the cellular respiration pathway and activated aox gene expression. The function of aox was determined by constructing overexpression (OE) and RNA interference (RNAi) strains. The results showed that the OE-aox strains exhibited obviously improved growth recovery after exposure to HS. During exposure to HS, the OE-aox strains exhibited reduced levels of NADH, the product of the tricarboxylic acid (TCA) cycle, and decreased synthesis of ATP, which reduced the production and accumulation of reactive oxygen species (ROS), whereas the RNAi-aox strains exhibited the opposite result. In addition, aox mediated the expression of antioxidant enzyme genes in the mycelia of P. ostreatus under HS through the retrograde signaling pathway. Conclusions This study shows that the expression of the aox gene in P. ostreatus mycelia can be induced by NO under HS, that it regulates the TCA cycle and cell respiration to reduce the production of ROS, and that it can mediate the retrograde signaling pathway involved in the mycelial response to HS. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01626-y.
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Affiliation(s)
- Ludan Hou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 10081, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, 10081, Beijing, China
| | - Mengran Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 10081, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, 10081, Beijing, China
| | - Chenyang Huang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 10081, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, 10081, Beijing, China
| | - Qi He
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 10081, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, 10081, Beijing, China.,Jilin Agricultural University, 130118, Jilin, China
| | - Lijiao Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 10081, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, 10081, Beijing, China
| | - Jinxia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 10081, Beijing, China. .,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, 10081, Beijing, China.
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13
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Tian F, Li C, Li Y. Genomic Analysis of Sarcomyxa edulis Reveals the Basis of Its Medicinal Properties and Evolutionary Relationships. Front Microbiol 2021; 12:652324. [PMID: 34276589 PMCID: PMC8281127 DOI: 10.3389/fmicb.2021.652324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/26/2021] [Indexed: 11/24/2022] Open
Abstract
Yuanmo [Sarcomyxa edulis (Y.C. Dai, Niemelä & G.F. Qin) T. Saito, Tonouchi & T. Harada] is an important edible and medicinal mushroom endemic to Northeastern China. Here we report the de novo sequencing and assembly of the S. edulis genome using single-molecule real-time sequencing technology. The whole genome was approximately 35.65 Mb, with a G + C content of 48.31%. Genome assembly generated 41 contigs with an N50 length of 1,772,559 bp. The genome comprised 9,364 annotated protein-coding genes, many of which encoded enzymes involved in the modification, biosynthesis, and degradation of glycoconjugates and carbohydrates or enzymes predicted to be involved in the biosynthesis of secondary metabolites such as terpene, type I polyketide, siderophore, and fatty acids, which are responsible for the pharmacodynamic activities of S. edulis. We also identified genes encoding 1,3-β-glucan synthase and endo-1,3(4)-β-glucanase, which are involved in polysaccharide and uridine diphosphate glucose biosynthesis. Phylogenetic and comparative analyses of Basidiomycota fungi based on a single-copy orthologous protein indicated that the Sarcomyxa genus is an independent group that evolved from the Pleurotaceae family. The annotated whole-genome sequence of S. edulis can serve as a reference for investigations of bioactive compounds with medicinal value and the development and commercial production of superior S. edulis varieties.
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Affiliation(s)
- Fenghua Tian
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China.,Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China
| | - Changtian Li
- 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
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14
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Wang G, Chen L, Tang W, Wang Y, Zhang Q, Wang H, Zhou X, Wu H, Guo L, Dou M, Liu L, Wang B, Lin J, Xie B, Wang Z, Liu Z, Ming R, Zhang J. Identifying a melanogenesis-related candidate gene by a high-quality genome assembly and population diversity analysis in Hypsizygus marmoreus. J Genet Genomics 2021; 48:75-87. [PMID: 33744162 DOI: 10.1016/j.jgg.2021.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 12/15/2022]
Abstract
Hypsizygus marmoreus is one of the most important edible fungi in Basidiomycete division and includes white and gray strains. However, very limited knowledge is known about the genomic structures and the genetic basis for the white/gray diversity of this mushroom. Here, we report the near-complete high-quality H. marmoreus genome at the chromosomal level. Comparative genomics analysis indicates that chromosome structures were relatively conserved, and variations in collinearity and chromosome number were mainly attributed by chromosome split/fusion events in Aragicales, whereas the fungi genome experienced many genomic chromosome fracture, fusion, and genomic replication events after the split of Aragicales from Basidiomycetes. Resequencing of 57 strains allows us to classify the population into four major groups and associate genetic variations with morphological features, indicating that white strains were not originated independently. We further generated genetic populations and identified a cytochrome P450 as the candidate causal gene for the melanogenesis in H. marmoreus based on bulked segregant analysis (BSA) and comparative transcriptome analysis. The high-quality H. marmoreus genome and diversity data compiled in this study provide new knowledge and resources for the molecular breeding of H. marmoreus as well as the evolution of Basidiomycete.
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Affiliation(s)
- Gang Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; School of Geographical Science, Nantong University, Nantong 226001, China
| | - Lianfu Chen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weiqi Tang
- Institute of Oceanography, Marine Biotechnology Center, Minjiang University, Fuzhou 350108, China
| | - Yuanyuan Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongbo Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuan Zhou
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haofeng Wu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lin Guo
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meijie Dou
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Liu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baiyu Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingxian Lin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baogui Xie
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhengchao Wang
- Provincial Key Laboratory for Developmental Biology and Neurosciences, College of Life Sciences, Fujian Normal University, Fuzhou 350007, China
| | - ZhongJian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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15
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Vidal-Diez de Ulzurrun G, Lee YY, Stajich JE, Schwarz EM, Hsueh YP. Genomic analyses of two Italian oyster mushroom Pleurotus pulmonarius strains. G3 (BETHESDA, MD.) 2021; 11:jkaa007. [PMID: 33585863 PMCID: PMC8022975 DOI: 10.1093/g3journal/jkaa007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/14/2020] [Indexed: 11/14/2022]
Abstract
Pleurotus mushrooms are among the most cultivated fungi in the world and are highly valuable for food, medicine, and biotechnology industries. Furthermore, Pleurotus species are carnivorous fungi; they can rapidly paralyze and kill nematodes when nutrient-deprived. The predator-prey interactions between Pleurotus and nematodes are still widely unexplored. Moreover, the molecular mechanisms and the genes involved in the carnivorous behavior of Pleurotus mushrooms remain a mystery. We are attempting to understand the interactions between Pleurotus mushrooms and their nematode prey through genetic and genomic analyses. Two single spores (ss2 and ss5) isolated from a fruiting body of Pleurotus pulmonarius exhibited significant differences in growth and toxicity against nematodes. Thus, using PacBio long reads, we assembled and annotated two high-quality genomes for these two isolates of P. pulmonarius. Each of these assemblies contains 23 scaffolds, including 6 (ss2) and 8 (ss5) telomere-to-telomere scaffolds, and they are among the most complete assembled genomes of the Pleurotus species. Comparative analyses identified the genomic differences between the two P. pulmonarius strains. In sum, this work provides a genomic resource that will be invaluable for better understanding the Italian oyster mushroom P. pulmonarius.
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Affiliation(s)
| | - Yi-Yun Lee
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei 115, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, 900 University Ave. Riverside, CA 92521, USA
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology 351, 526 Campus Road, Ithaca, NY 14853-2703, USA
| | - Yen-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei 115, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Department of Biochemical Science and Technology, National Taiwan University No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
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16
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Zhao S, Gao Q, Rong C, Wang S, Zhao Z, Liu Y, Xu J. Immunomodulatory Effects of Edible and Medicinal Mushrooms and Their Bioactive Immunoregulatory Products. J Fungi (Basel) 2020; 6:E269. [PMID: 33171663 PMCID: PMC7712035 DOI: 10.3390/jof6040269] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 12/19/2022] Open
Abstract
Mushrooms have been valued as food and health supplements by humans for centuries. They are rich in dietary fiber, essential amino acids, minerals, and many bioactive compounds, especially those related to human immune system functions. Mushrooms contain diverse immunoregulatory compounds such as terpenes and terpenoids, lectins, fungal immunomodulatory proteins (FIPs) and polysaccharides. The distributions of these compounds differ among mushroom species and their potent immune modulation activities vary depending on their core structures and fraction composition chemical modifications. Here we review the current status of clinical studies on immunomodulatory activities of mushrooms and mushroom products. The potential mechanisms for their activities both in vitro and in vivo were summarized. We describe the approaches that have been used in the development and application of bioactive compounds extracted from mushrooms. These developments have led to the commercialization of a large number of mushroom products. Finally, we discuss the problems in pharmacological applications of mushrooms and mushroom products and highlight a few areas that should be improved before immunomodulatory compounds from mushrooms can be widely used as therapeutic agents.
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Affiliation(s)
- Shuang Zhao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
| | - Qi Gao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
| | - Chengbo Rong
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
| | - Shouxian Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
| | - Zhekun Zhao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056038, China
| | - Yu Liu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (S.Z.); (Q.G.); (C.R.); (S.W.); (Z.Z.); (Y.L.)
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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17
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Hou Z, Chen Q, Zhao M, Huang C, Wu X. Genome-wide characterization of the Zn(II) 2Cys 6 zinc cluster-encoding gene family in Pleurotus ostreatus and expression analyses of this family during developmental stages and under heat stress. PeerJ 2020; 8:e9336. [PMID: 32566411 PMCID: PMC7295025 DOI: 10.7717/peerj.9336] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/20/2020] [Indexed: 12/13/2022] Open
Abstract
Pleurotus ostreatus is one of the most widely cultivated mushrooms in China. The regulatory mechanisms of fruiting body formation and the response to heat stress in P. ostreatus are main research focuses. The Zn(II)2Cys6 family is one of the largest families of transcriptional factors and plays important roles in multiple biological processes in fungi. In this study, we identified 66 zinc cluster proteins in P. ostreatus (PoZCPs) through a genome-wide search. The PoZCPs were classified into 15 types according to their zinc cluster domain. Physical and chemical property analyses showed a huge diversity among the PoZCPs. Phylogenetic analysis of PoZCPs classified these proteins into six groups and conserved motif combinations and similar gene structures were observed in each group. The expression profiles of these PoZCP genes during different developmental stages and under heat stress were further investigated by RNA-sequencing (RNA-seq), revealing diverse expression patterns. A total of 13 PoZCPs that may participate in development or the heat stress response were selected for validation of their expression levels through real-time quantitative PCR (RT-qPCR) analysis, and some developmental stage-specific and heat stress-responsive candidates were identified. The findings contribute to our understanding of the roles and regulatory mechanisms of ZCPs in P. ostreatus.
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Affiliation(s)
- Zhihao Hou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Qiang Chen
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Mengran Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Chenyang Huang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xiangli Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
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18
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Lu YP, Liao JH, Guo ZJ, Cai ZX, Chen MY. Genome Survey and Transcriptome Analysis on Mycelia and Primordia of Agaricus blazei. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1824183. [PMID: 32025516 PMCID: PMC6983287 DOI: 10.1155/2020/1824183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/14/2019] [Accepted: 09/26/2019] [Indexed: 12/13/2022]
Abstract
Agaricus blazei, a type of edible straw-rotting mushroom with somewhat sweet taste and fragrance of almonds, has attracted considerable scientific and practical attention. High-throughput Illumina PE150 and PacBio RSII platform were employed to generate a genomic sequence. De novo assembly generated 36 contigs with 38,686,133 bp in size, containing 10,119 putative predicted genes. Additionally, we also studied transcriptional regulation of the mycelia and the primordia for exploration of genes involved in fruiting body formation. Expression profiling analysis revealed that 2,164 genes were upregulated in mycelia and 1,557 in primordia. Functional enrichment showed that differentially expressed genes associated with response to stress, ribosome biogenesis, arginine biosynthesis, and steroid biosynthesis pathway were more active in fruiting body. The genome and transcriptome analysis of A. blazei provide valuable sequence resources and contribute to our understanding of genes related to the biosynthesis pathway of polysaccharide and benzaldehyde, as well as the fruiting body formation.
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Affiliation(s)
- Yuan-Ping Lu
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, Fujian Province, China
| | - Jian-Hua Liao
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, Fujian Province, China
| | - Zhong-Jie Guo
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, Fujian Province, China
| | - Zhi-Xin Cai
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, Fujian Province, China
| | - Mei-Yuan Chen
- Institute of Edible Fungi, Fujian Academy of Agricultural Sciences, Fuzhou 350014, Fujian Province, China
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19
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Zhu W, Hu J, Li Y, Yang B, Guan Y, Xu C, Chen F, Chi J, Bao Y. Comparative Proteomic Analysis of Pleurotus ostreatus Reveals Great Metabolic Differences in the Cap and Stipe Development and the Potential Role of Ca 2+ in the Primordium Differentiation. Int J Mol Sci 2019; 20:ijms20246317. [PMID: 31847351 PMCID: PMC6940972 DOI: 10.3390/ijms20246317] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 01/08/2023] Open
Abstract
Pleurotus ostreatus is a widely cultivated edible fungus around the world. At present, studies on the developmental process of the fruiting body are limited. In our study, we compared the differentially expressed proteins (DEPs) in the stipe and cap of the fruiting body by high-throughput proteomics. GO and pathway analysis revealed the great differences in the metabolic levels, including sucrose and starch metabolism, and sphingolipid signaling and metabolism, and the differences of 16 important DEPs were validated further by qPCR analysis in expression level. In order to control the cap and stipe development, several chemical inducers were applied to the primordium of the fruiting body according to the pathway enrichment results. We found that CaCl2 can affect the primordium differentiation through inhibiting the stipe development. EGTA (ethyleneglycol bis (β-aminoethyl ether)-N,N,N′,N′-tetraacetic acid) treatment confirmed the inhibitory role of Ca2+ in the stipe development. Our study not only shows great metabolic differences during the cap and stipe development but also reveals the underlying mechanism directing the primordium differentiation in the early development of the fruiting body for the first time. Most importantly, we provide a reliable application strategy for the cultivation and improvement of the Pleurotus ostreatus, which can be an example and reference for a more edible fungus.
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Affiliation(s)
- Weiwei Zhu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China;
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (Y.L.); (Y.G.); (C.X.); (F.C.); (J.C.)
| | - Jinbo Hu
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (J.H.); (B.Y.)
| | - Yang Li
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (Y.L.); (Y.G.); (C.X.); (F.C.); (J.C.)
| | - Bing Yang
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; (J.H.); (B.Y.)
| | - Yanli Guan
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (Y.L.); (Y.G.); (C.X.); (F.C.); (J.C.)
| | - Chong Xu
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (Y.L.); (Y.G.); (C.X.); (F.C.); (J.C.)
| | - Fei Chen
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (Y.L.); (Y.G.); (C.X.); (F.C.); (J.C.)
| | - Jingliang Chi
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (Y.L.); (Y.G.); (C.X.); (F.C.); (J.C.)
| | - Yongming Bao
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China;
- School of Food and Environmental Science and Technology, Dalian University of Technology, Panjin 12421, China
- Correspondence: ; Tel.: +86-411-8470-6344; Fax: +86-411-8470-6365
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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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21
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Dai Y, Sun L, Yin X, Gao M, Zhao Y, Jia P, Yuan X, Fu Y, Li Y. Pleurotus eryngii Genomes Reveal Evolution and Adaptation to the Gobi Desert Environment. Front Microbiol 2019; 10:2024. [PMID: 31551962 PMCID: PMC6734163 DOI: 10.3389/fmicb.2019.02024] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/19/2019] [Indexed: 12/30/2022] Open
Abstract
Pleurotus eryngii (King Oyster) is one of the most highly prized edible mushrooms. Among the diverse varieties within P. eryngii, P. eryngii var. eryngii is the commonest one, with a worldwide distribution, while P. eryngii var. ferulae is only distributed in Europe and China, and is especially adapted to the Gobi Desert in Xinjiang Autonomous Region of China. However, little is known about the genome-wide pattern of evolution and adaptation to the divergent environments of P. eryngii. Here, we present the high-quality genome sequences of P. eryngii var. eryngii strain PEE81 originating from Europe and P. eryngii var. ferulae strain PEF12 originating from the Gobi Desert of China. The assembled genome sizes of PEE81 and PEF12 were 53.6 and 48.0 Mbp, respectively, which are larger than other reported genomes in the genus Pleurotus. We propose that the selective amplification of long terminal repeat (LTR) retrotransposons increases the genome size of the genus Pleurotus, and may play a key role in driving their rapid species diversification. Molecular clock analyses of five Pleurotus species, namely PEE81, PEF12, P. tuoliensis, P. ostreatus and P. cf. floridanus suggest that the divergence estimates of the genus Pleurotus over time scales ranged from ∼4 to ∼38 million years ago (Mya), and PEE81 and PEF12 diverged at ∼13 Mya. The whole genome resequencing of 33 geographically diverse strains of P. eryngii var. eryngii and var. ferulae was then performed and the genome variation among and within these two populations were investigated. Comparative analyses of these two populations detected several candidate genes related to stress responses and DNA repair that are putatively involved in adaptation to the Gobi Desert environment. These findings offer insights into genome evolution of the genus Pleurotus and provide valuable genomic resources for King Oyster mushroom 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.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, 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.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Xiaolei Yin
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Meng Gao
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Yitong Zhao
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Peisong Jia
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Xinjiang, China
| | - Xiaohui Yuan
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, China
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, China.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, 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.,International Cooperation Research Center of China for New Germplasm and Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
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22
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Wang L, Gao W, Wu X, Zhao M, Qu J, Huang C, Zhang J. Genome-Wide Characterization and Expression Analyses of Pleurotus ostreatus MYB Transcription Factors during Developmental Stages and under Heat Stress Based on de novo Sequenced Genome. Int J Mol Sci 2018; 19:E2052. [PMID: 30011913 PMCID: PMC6073129 DOI: 10.3390/ijms19072052] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/11/2018] [Accepted: 07/13/2018] [Indexed: 01/02/2023] Open
Abstract
Pleurotus ostreatus is a commercially grown mushroom species in China. However, studies on the mechanisms of the fruiting body development and stress response of P. ostreatus are still at a primary stage. In this study, we report the entire genome sequence of P. ostreatus CCMSSC03989. Then, we performed comprehensive genome-wide characterization and expression analysis of the MYB transcription factor family during a series of developmental stages and under the condition of heat stress. A 34.76 Mb genome was obtained through next-generation sequencing (NGS) and Bionano optical mapping approaches. The genome has a scaffold N50 of 1.1 Mb and contains 10.11% repeats, and 10,936 gene models were predicted. A total of 20 MYB genes (PoMYB) were identified across the genome, and the full-length open reading frames were isolated. The PoMYBs were classified into 1 repeat (1R), 2R, and 3R-MYB groups according to their MYB domain repeat numbers, and 3R-MYBs possessed relatively more introns than 1R and 2R-MYBs. Based on phylogenetic analysis, the PoMYBs were divided into four groups and showed close relationships with the MYB genes of plants and fungi. RNA-sequencing (RNA-Seq) and quantitative PCR (qPCR) analyses revealed that PoMYB expression showed stage-specific patterns in reproductive stages and could be induced by heat stress. The P. ostreatus draft genome will promote genome-wide analysis, and our study of PoMYBs will promote further functional analysis of MYB genes in mushrooms.
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Affiliation(s)
- Lining Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing 100081, China.
| | - Wei Gao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing 100081, China.
| | - Xiangli Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing 100081, China.
| | - Mengran Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing 100081, China.
| | - Jibin Qu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing 100081, China.
| | - Chenyang Huang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing 100081, China.
| | - Jinxia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing 100081, China.
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Differential Expression Patterns of Pleurotus ostreatus Catalase Genes during Developmental Stages and under Heat Stress. Genes (Basel) 2017; 8:genes8110335. [PMID: 29160795 PMCID: PMC5704248 DOI: 10.3390/genes8110335] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/06/2017] [Accepted: 11/17/2017] [Indexed: 01/06/2023] Open
Abstract
Catalases are ubiquitous hydrogen peroxide-detoxifying enzymes. They participate in fungal growth and development, such as mycelial growth and cellular differentiation, and in protecting fungi from oxidative damage under stressful conditions. To investigate the potential functions of catalases in Pleurotus ostreatus, we obtained two catalase genes from a draft genome sequence of P. ostreatus, and cloned and characterized them (Po-cat1 and Po-cat2). Po-cat1 (group II) and Po-cat2 (group III) encoded putative peptides of 745 and 528 amino acids, respectively. Furthermore, the gene structures were variant between Po-cat1 and Po-cat2. Further research revealed that these two catalase genes have divergent expression patterns during different developmental stages. Po-cat1/Po-cat1 was at a barely detectable level in mycelia, accumulated gradually during reproductive growth, and was maximal in separated spores. But no catalase activity of Po-cat1 was detected by native-PAGE during any part of the developmental stages. In contrast, high Po-cat2/Po-cat2 expression and Po-cat2 activity found in mycelia were gradually lost during reproductive growth, and at a minimal level in separated spores. In addition, these two genes responded differentially under 32 °C and 40 °C heat stresses. Po-cat1 was up-regulated under both temperature conditions, while Po-cat2 was up-regulated at 32 °C but down-regulated at 40 °C. The accumulation of catalase proteins correlated with gene expression. These results indicate that the two divergent catalases in P. ostreatus may play different roles during development and under heat stress.
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