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Weike W, Na L, Jiayao L, Liqin L, Guanping C. Transcriptome analysis reveals key genes and pathways associated with heat stress in Pleurotus pulmonarius. Int Microbiol 2025; 28:165-172. [PMID: 38750284 DOI: 10.1007/s10123-024-00536-4] [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: 04/01/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 01/29/2025]
Abstract
Pleurotus pulmonarius is a medium temperature edible mushroom, and its yield and quality are severely affected by high temperature. However, the molecular mechanism of Pleurotus pulmonarius response to heat stress remains unknown. In this study, transcriptome sequencing and analysis of Pleurotus pulmonarius mycelia under heat stress were performed, related differentially expressed genes (DEGs) were verified by fluorescence quantitative PCR (qPCR) and the reduced glutathione content was detected. 5906 DEGs, including 1086 upregulated and 4820 downregulated, were identified by RNA-Seq. GO analysis revealed that DEGs were mainly enriched in the pathways of Aminoacyl-tRNA biosynthesis, pyrimidine metabolism, arginine and proline metabolism, fructose and mannose metabolism, and glutathione metabolism. qPCR analysis showed that the expression of ggt decreased after heat stress treatment, while gst2 and gst3 increased. The glutathione content in mycelia after heat stress was significantly higher than that in the control group. These results suggest that glutathione metabolism may play an important role in the response to heat stress. Our study will provide a molecular-level perspective on fungal response to heat stress and a basis for research on fungal environmental response and molecular breeding.
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Affiliation(s)
- Wang Weike
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Lu Na
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Lin Jiayao
- Hangzhou Academy of Agricultural Sciences, Hangzhou, China
| | - Lai Liqin
- Pathology Department, Tongde Hospital of Zhejiang Province, Hangzhou, China
| | - Chen Guanping
- Cancer Institute of Integrated Traditional Chinese and Western Medicine, Zhejiang Academy of Traditional Chinese Medicine, Tongde Hospital of Zhejiang Province, Hangzhou, China.
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Wang F, Li F, Han L, Wang J, Ding X, Liu Q, Jiang M, Li H. High-Yield-Related Genes Participate in Mushroom Production. J Fungi (Basel) 2024; 10:767. [PMID: 39590686 PMCID: PMC11595646 DOI: 10.3390/jof10110767] [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: 09/12/2024] [Revised: 10/24/2024] [Accepted: 11/04/2024] [Indexed: 11/28/2024] Open
Abstract
In recent years, the increasing global demand for mushrooms has made the enhancement of mushroom yield a focal point of research. Currently, the primary methods for developing high-yield mushroom varieties include mutation- and hybridization-based breeding. However, due to the long breeding cycles and low predictability associated with these approaches, they no longer meet the demands for high-yield and high-quality varieties in the expansive mushroom market. Modern molecular biology technologies such as RNA interference (RNAi) and gene editing, including via CRISPR-Cas9, can be used to precisely modify target genes, providing a new solution for mushroom breeding. The high-yield genes of mushrooms can be divided into four categories based on existing research results: the genes controlling mycelial growth are very suitable for genetic modification; the genes controlling primordium formation are directly or indirectly regulated by the genes controlling mycelial growth; the genes controlling button germination are more difficult to modify; and the genes controlling fruiting body development can be regulated during the mycelial stage. This article reviews the current research status for the four major categories of high-yield-related genes across the different stages of mushroom growth stages, providing a foundation and scientific basis for using molecular biology to improve mushroom yield and promote the economic development of the global edible-mushroom industry.
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Affiliation(s)
- Fang Wang
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; (F.W.); (F.L.); (L.H.); (J.W.); (X.D.)
| | - Fengzhu Li
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; (F.W.); (F.L.); (L.H.); (J.W.); (X.D.)
| | - Luyang Han
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; (F.W.); (F.L.); (L.H.); (J.W.); (X.D.)
| | - Jingzi Wang
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; (F.W.); (F.L.); (L.H.); (J.W.); (X.D.)
| | - Xupo Ding
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; (F.W.); (F.L.); (L.H.); (J.W.); (X.D.)
| | - Qinhong Liu
- Department of Vegetables, College of Horticulture, China Agricultural University, Beijing 100193, China;
| | - Mingguo Jiang
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; (F.W.); (F.L.); (L.H.); (J.W.); (X.D.)
| | - Hailin Li
- Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning 530008, China; (F.W.); (F.L.); (L.H.); (J.W.); (X.D.)
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Gomes TG, de Assis Fonseca FC, Alves GSC, de Siqueira FG, Miller RNG. Development of reference genes for RT-qPCR analysis of gene expression in Pleurotus pulmonarius for biotechnological applications. Sci Rep 2023; 13:12296. [PMID: 37516784 PMCID: PMC10387064 DOI: 10.1038/s41598-023-39115-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/20/2023] [Indexed: 07/31/2023] Open
Abstract
Jatropha curcas is an oilseed crop with biorefinery applications. Whilst cake generated following oil extraction offers potential as a protein source for animal feed, inactivation of toxic phorbol esters present in the material is necessary. Pleurotus pulmonarius is a detoxifying agent for jatropha cake with additional potential as animal feed, edible mushroom and for enzyme production. For the characterization of fungal genes involved in phorbol ester degradation, together with other industrial applications, reverse transcription-quantitative PCR (RT-qPCR) is a tool that enables accurate quantification of gene expression. For this, reliable analysis requires reference genes for normalization of mRNA levels validated under conditions employed for target genes. The stability of potential reference genes β-TUB, ACTIN, GAPDH, PHOS, EF1α, TRPHO, LAC, MNP3, MYP and VP were evaluated following growth of P. pulmonarius on toxic, non-toxic jatropha cake and a combined treatment, respectively. NormFinder and geNorm algorithms for expression stability analysis identified PHOS, EF1α and MNP3 as appropriate for normalizing gene expression. Reference gene combinations contrasting in ranking were compared following normalization of relative expression of the CHU_2040 gene, encoding an esterase enzyme potentially involved in phorbol ester degradation. The reference genes for P. pulmonarius will facilitate the elucidation of mechanisms involved in detoxification of phorbol esters as well as analysis of target genes for application in biorefinery models.
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Affiliation(s)
- Taísa Godoy Gomes
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | - Fernando Campos de Assis Fonseca
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
- Instituto Federal de Goiás (IFG), Águas Lindas, GO, 72910-733, Brazil
| | - Gabriel Sergio Costa Alves
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil
| | | | - Robert Neil Gerard Miller
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
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Gao Q, Yan D, Song S, Fan Y, Wang S, Liu Y, Huang Y, Rong C, Guo Y, Zhao S, Qin W, Xu J. Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. J Fungi (Basel) 2022; 8:167. [PMID: 35205921 PMCID: PMC8877449 DOI: 10.3390/jof8020167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/05/2022] [Accepted: 02/06/2022] [Indexed: 01/02/2023] Open
Abstract
Lentinula edodes is a tetrapolar basidiomycete with two haploid nuclei in each cell during most of their life cycle. Understanding the two haploid nuclei genome structures and their interactions on growth and fruiting body development has significant practical implications, especially for commercial cultivars. In this study, we isolated and assembled the two haploid genomes from a commercial strain of L. edodes using Illumina, HiFi, and Hi-C technologies. The total genome lengths were 50.93 Mb and 49.80 Mb for the two monokaryons SP3 and SP30, respectively, with each assembled into 10 chromosomes with 99.63% and 98.91% anchoring rates, respectively, for contigs more than 100 Kb. Genome comparisons suggest that two haploid nuclei likely derived from distinct genetic ancestries, with ~30% of their genomes being unique or non-syntenic. Consistent with a tetrapolar mating system, the two mating-type loci A (matA) and B (matB) of L. edodes were found located on two different chromosomes. However, we identified a new but incomplete homeodomain (HD) sublocus at ~2.8 Mb from matA in both monokaryons. Our study provides a solid foundation for investigating the relationships among cultivars and between cultivars and wild strains and for studying how two genetically divergent nuclei coordinate to regulate fruiting body formation in L. edodes.
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Affiliation(s)
- Qi Gao
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Dong Yan
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Shuang Song
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yangyang Fan
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Shouxian Wang
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yu Liu
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yu Huang
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- College of Agriculture and Food Engineering, Baise University, 21 Zhongshan Second Street, Youjiang District, Baise 533000, China
| | - Chengbo Rong
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Yuan Guo
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Shuang Zhao
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
| | - Wentao Qin
- Beijing Engineering Research Center for Edible Mushroom, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, 9 Shuguang Garden Zhonglu, Haidian District, Beijing 100097, China; (Q.G.); (S.S.); (Y.F.); (S.W.); (Y.L.); (Y.H.); (C.R.); (Y.G.); (S.Z.); (W.Q.)
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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Cowen LE, Heitman J. Showcasing Fungal Genetics & Genomics with the Genetics Society of America. Genetics 2021; 217:6128394. [PMID: 33724422 DOI: 10.1093/genetics/iyaa034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, M5G 1M1, Canada
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University, Durham, 27710, USA
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Cowen LE, Heitman J. Showcasing Fungal Genetics & Genomics with the Genetics Society of America. G3-GENES GENOMES GENETICS 2021; 11:6135027. [PMID: 33585877 PMCID: PMC8022925 DOI: 10.1093/g3journal/jkaa041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 11/14/2022]
Affiliation(s)
- Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, M5G 1M1, Canada
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University, Durham, 27710 USA
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