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Li W, Chen WC, Wang JB, Feng J, Wu D, Zhang Z, Zhang JS, Yang Y. Screening candidate genes related to volatile synthesis in shiitake mushrooms and construction of regulatory networks to effectively improve mushroom aroma. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:5618-5626. [PMID: 33709431 DOI: 10.1002/jsfa.11213] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Metabolite formation is a physiological stress response during the growth and development of shiitake mushrooms (Lentinula edodes). The characteristic flavor metabolites are important quality components in shiitake mushrooms. To investigate the formation mechanisms of characteristic flavor metabolites, transcriptome analyses were performed on shiitake mushrooms harvested at different growth stages. RESULTS In total, 30 genes related to the synthesis of characteristic volatiles of mushrooms were identified via screening. Through KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis of the selected genes and correlation analyses of gene expressions, the main volatile synthesis pathways were determined as histidine metabolism, glutathione metabolism and biosynthesis of unsaturated fatty acids. Gene cluster and correlation analyses were performed to clarify the combined effects of different genes in the enzymatic reactions. Further, a correlation network of candidate genes was built based on the gene expression levels. CONCLUSION The activities of flavor synthases and the content of characteristic flavor metabolites were analyzed; the enzyme activity changes and metabolic product distribution sites were clarified. A synthesis and regulation network was constructed for the candidate genes and characteristic volatiles, and information was obtained for 16 hub genes. Moreover, it was essential to identify and characterize the key genes and synthases involved in the synthesis of the characteristic volatiles of mushrooms. This information provides us with a better understanding of the biosynthesis and regulation of the volatiles, which will lay the foundation for improving the quality of shiitake mushrooms. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Wen Li
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, People's Republic of China, Shanghai Guosen Bio-tech Co. Ltd, 1000 Jinqi Road, Shanghai, China
| | - Wan-Chao Chen
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, People's Republic of China, Shanghai Guosen Bio-tech Co. Ltd, 1000 Jinqi Road, Shanghai, China
| | - Jin-Bin Wang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Key Laboratory of Agricultural Genetics and Breeding, 2901 Beidi Road, Shanghai, China
| | - Jie Feng
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, People's Republic of China, Shanghai Guosen Bio-tech Co. Ltd, 1000 Jinqi Road, Shanghai, China
| | - Di Wu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, People's Republic of China, Shanghai Guosen Bio-tech Co. Ltd, 1000 Jinqi Road, Shanghai, China
| | - Zhong Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, People's Republic of China, Shanghai Guosen Bio-tech Co. Ltd, 1000 Jinqi Road, Shanghai, China
| | - Jing-Song Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, People's Republic of China, Shanghai Guosen Bio-tech Co. Ltd, 1000 Jinqi Road, Shanghai, China
| | - Yan Yang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, People's Republic of China, Shanghai Guosen Bio-tech Co. Ltd, 1000 Jinqi Road, Shanghai, China
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Jiang WZ, Yao FJ, Fang M, Lu LX, Zhang YM, Wang P, Meng JJ, Lu J, Ma XX, He Q, Shao KS, Khan AA, Wei YH. Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map. MYCOBIOLOGY 2021; 49:406-420. [PMID: 34512084 PMCID: PMC8409960 DOI: 10.1080/12298093.2021.1954321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1-SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.
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Affiliation(s)
- Wan-Zhu Jiang
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Fang-Jie Yao
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Ming Fang
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Li-Xin Lu
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - You-Min Zhang
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Peng Wang
- Economic Plants Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Jing-Jing Meng
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Jia Lu
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Xiao-Xu Ma
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Qi He
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Kai-Sheng Shao
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Asif Ali Khan
- International Cooperation Research Center of China for New Germplasm Breeding of Edible Mushrooms, Jilin Agricultural University, Changchun, China
| | - Yun-Hui Wei
- Institute of Agricultural Applied Microbiology, Jiangxi Academy of Agricultural Sciences, Nanchang, China
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Liu M, Yu T, Singh PK, Liu Q, Liu H, Zhu Q, Xiao Z, Xu J, Peng Y, Fu S, Chen S, He H. A Comparative Transcriptome Analysis of Volvariella volvacea Identified the Candidate Genes Involved in Fast Growth at the Mycelial Growth Stage. Genes (Basel) 2020; 11:genes11020161. [PMID: 32033161 PMCID: PMC7074523 DOI: 10.3390/genes11020161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 02/01/2020] [Indexed: 01/13/2023] Open
Abstract
The edible straw mushroom, Volvariella volvacea, is one of the most important cultivated mushrooms in tropical and sub-tropical regions. Strain improvement for V. volvacea is difficult because of the unknown mechanisms involved in its growth regulation and substrate utilization. A comparative physiological and transcriptomic study was conducted between two commercially available straw mushroom strains (v9 and v26) to explore their fast-growth regulation mechanism(s). The physiological study showed that V. volvacea v9 had a shorter growth cycle and higher biological efficiency (4% higher) than that in v26. At least 14,556 unigenes were obtained from the four cDNA libraries (two replicates per strain). Among them, the expression of 1597 unigenes was up-regulated while 1352 were down-regulated. Four heat-shock proteins were highly expressed in v9, showing that v9 has the better ability to handle stresses and/or environmental changes. Moreover, up to 14 putative transporter genes were expressed at a higher level in v9 than those in v26, implying that v9 has a better ability to transport nutrients or export xenobiotics efficiently. Our report allows to identify the candidate genes involved in the fast growth requirement of V. volvacea, which represents a valuable resource for strain improvement in this commercially important edible mushroom.
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Affiliation(s)
- Ming Liu
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China; (M.L.); (Z.X.); (J.X.); (Y.P.)
| | - Ting Yu
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (T.Y.); (Q.L.); (Q.Z.)
| | - Puneet Kumar Singh
- School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China; (P.K.S.); (H.L.); (S.F.)
| | - Qinjian Liu
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (T.Y.); (Q.L.); (Q.Z.)
| | - Hao Liu
- School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China; (P.K.S.); (H.L.); (S.F.)
| | - Qingfeng Zhu
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (T.Y.); (Q.L.); (Q.Z.)
| | - Zitian Xiao
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China; (M.L.); (Z.X.); (J.X.); (Y.P.)
| | - Jiang Xu
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China; (M.L.); (Z.X.); (J.X.); (Y.P.)
| | - Yangyang Peng
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China; (M.L.); (Z.X.); (J.X.); (Y.P.)
| | - Shiyu Fu
- School of Light Industry and Engineering, South China University of Technology, Guangzhou 510640, China; (P.K.S.); (H.L.); (S.F.)
| | - Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (S.C.); (H.H.); Tel.: +1-517-884-5383 (S.C.); +86-20-38469598 (H.H.); Fax: +1-517-884-5384 (S.C.); +86-20-38469598 (H.H.)
| | - Huanqing He
- Vegetables Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China; (M.L.); (Z.X.); (J.X.); (Y.P.)
- Correspondence: (S.C.); (H.H.); Tel.: +1-517-884-5383 (S.C.); +86-20-38469598 (H.H.); Fax: +1-517-884-5384 (S.C.); +86-20-38469598 (H.H.)
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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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Sakurai K, Yuasa M, Ohji S, Hosoyama A, Sato M, Fujita N, Kawasaki H. Gene Mutations in Ganoderma lucidum During Long-Term Preservation by Repeated Subculturing. Biopreserv Biobank 2019; 17:395-400. [PMID: 30938541 DOI: 10.1089/bio.2018.0149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Subculturing is frequently used for the preservation of basidiomycetes. In this study, to assess and verify the risks of repeated subculturing on the long-term preservation of strains of culture collections, we performed single nucleotide polymorphism (SNP) analysis in genes encoding enzymes of the mevalonate pathway, 1,3-β-glucan synthesis, lignin degradation, and the tricarboxylic acid (TCA) cycle of mycelia before and after preserving for a 4-year period by the subculturing 30 times every 45 days of Ganoderma lucidum NBRC 8346. As a result of analyzing 60 genes of the strain, SNPs were found in 18 genes, and 14 of them were found in the exon region. Nonsynonymous coding SNPs were found in two genes (atoB_2, hmgr) encoding enzymes of mevalonate pathway and five genes (lcc1_9, lcc1_11, lcc1_13, dslcc6, aa5_1_9) encoding enzymes of lignin degradation after subculturing of G. lucidum NBRC 8346.
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Affiliation(s)
- Kenta Sakurai
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Munemitsu Yuasa
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Syoko Ohji
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Akira Hosoyama
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Masanori Sato
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Nobuyuki Fujita
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
| | - Hiroko Kawasaki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Tokyo, Japan
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An Q, Wu XJ, Dai YC. Comparative genomics of 40 edible and medicinal mushrooms provide an insight into the evolution of lignocellulose decomposition mechanisms. 3 Biotech 2019; 9:157. [PMID: 30944804 DOI: 10.1007/s13205-019-1689-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/19/2019] [Indexed: 11/28/2022] Open
Abstract
Diversity comparison and phylogenetic analyses of carbohydrate-active enzymes (CAZymes), auxiliary activities (AAs) and cytochromes P450 among 40 fungi, which are based on different nutritional pathways, help clarify and explain their divergence and improvement of various life-styles. Molecular clock analyses allow us to understand the evolutionary and developmental rules in decomposition gene families. Our results suggested that fungi in different ecological types acquired an obvious preference on specific decomposing gene families during evolutionary selection. White rot and litter saprotrophic fungi possessed more complete types of varied degradation gene families and were superior in quantities. With evolution and development of lignocellulose decomposition mechanism, certain families (like CBM1, GH6, GH7, GH10, and CYP53) disappeared in brown rot fungi and symbiotic fungi. In addition, the earlier time of phylogenetic divergence determined the more integrated and larger decomposition families. And various gains and losses in gene quantity of varied decomposition families led in particularly phylogenetic clades or nodes, then accelerated in forming varied ecotypes of species.
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Affiliation(s)
- Qi An
- 1Institute of Microbiology, Beijing Forestry University, Beijing, 100083 People's Republic of China
- 2Edible and Medicinal Fungi Research and Development Center, Universities/Colleges in Hebei Province, Langfang Normal University, Langfang, 065000 Hebei People's Republic of China
| | - Xue-Jun Wu
- 1Institute of Microbiology, Beijing Forestry University, Beijing, 100083 People's Republic of China
| | - Yu-Cheng Dai
- 1Institute of Microbiology, Beijing Forestry University, Beijing, 100083 People's Republic of China
- 3Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing, 100083 People's Republic of China
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Wan J, Li Y, Wang H, Tang L, Li Z, Zhou C, Tan Q, Bao D, Yang R. Three complete mitochondrial genomes of straw-rotting edible fungus Volvariella volvacea using next generation sequencing. Mitochondrial DNA B Resour 2018; 3:1054-1056. [PMID: 33474412 PMCID: PMC7799644 DOI: 10.1080/23802359.2018.1511849] [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: 07/23/2018] [Accepted: 08/10/2018] [Indexed: 11/01/2022] Open
Abstract
The straw-rotting edible fungus Volvariella volvacea is a widely cultivated edible fungus across China and Southeast Asian countries. Three complete mitochondrial genomes of V. volvacea from China, Thailand, and India were determined using the next-generation sequencing technology. The genome sizes of the three strains (China, Thailand, and India) were 62,541 bp, 64,531 bp, and 65,668 bp with GC contents of 38.46%, 38.56%, and 38.52%, respectively. All the genomes encoded 14 conserved protein-coding genes, the small ribosomal RNA subunits (rns), large ribosomal RNA subunits (rnl), and 23 tRNAs were located on the same strand. In the putative protein-coding genes, four introns were distributed in cox1 in the genomes of V23-1 and V8. 5 introns (four introns invaded into cox1and one intron invaded into cob) were detected in Tai8. The phylogenetic analysis confirmed that V. volvacea was a number of Agaricales. This mitochondrial genome may open new avenues for understanding the phylogeny and evolution of Pluteaceae and Agaricales.
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Affiliation(s)
- Jianing Wan
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Li
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hong Wang
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Lihua Tang
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhengpeng Li
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Chenli Zhou
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Qi Tan
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ruiheng Yang
- National Engineering Research Center of Edible Fungi, Ministry of Science and Technology (MOST), Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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Qian J, Gao Y, Wáng Y, Wu Y, Wāng Y, Zhao Y, Chen H, Bao D, Xu J, Bian X. Selection and Evaluation of Appropriate Reference Genes for RT-qPCR Normalization of Volvariella volvacea Gene Expression under Different Conditions. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6125706. [PMID: 30079349 PMCID: PMC6069580 DOI: 10.1155/2018/6125706] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 06/10/2018] [Indexed: 11/18/2022]
Abstract
Volvariella volvacea (V. volvacea), commonly referred to as Chinese (paddy straw) mushroom, is a basidiomycete with a protein-rich volva and pileus. Selecting appropriate reference genes is a crucial step in the normalization of quantitative real-time PCR data. Therefore, 12 candidate reference genes were selected from the V. volvacea transcriptome based on previous studies and then BestKeeper, geNorm, and NormFinder were used to identify reference genes stably expressed during different developmental stages and conditions. Of the 12 candidate reference genes, SPRY domain protein (SPRYp), alpha-tubulin (TUBα), cyclophilin (CYP), L-asparaginase (L-asp), and MSF1-domain-containing protein (MSF1) were the most stably expressed under different experimental conditions, while 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), and beta-actin (ACTB) were the least stably expressed. This investigation not only revealed potential factors influencing the suitability of reference genes, but also identified optimal reference genes from a pool of candidate genes under a wide range of conditions.
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Affiliation(s)
- Jiang Qian
- School of Life Science and Technology, China Pharmaceutical University, No. 24, Tongjiaxiang, Gulou District, Nanjing 210009, China
| | - Yingnv Gao
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Ying Wáng
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Yingying Wu
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Ying Wāng
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Yucheng Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Hongyu Chen
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Dapeng Bao
- National Engineering Research Center of Edible Fungi and Key Laboratory of Applied Mycological Resources and Utilization, Ministry of Agriculture and Shanghai Key Laboratory of Agricultural Genetics and Breeding and Institute of Edible Fungi, Shanghai Academy of Agriculture Science, Shanghai, China
| | - Jiyang Xu
- School of Life Science and Technology, China Pharmaceutical University, No. 24, Tongjiaxiang, Gulou District, Nanjing 210009, China
| | - Xiaohong Bian
- School of Life Science and Technology, China Pharmaceutical University, No. 24, Tongjiaxiang, Gulou District, Nanjing 210009, China
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Gao W, Qu J, Zhang J, Sonnenberg A, Chen Q, Zhang Y, Huang C. A genetic linkage map of Pleurotus tuoliensis integrated with physical mapping of the de novo sequenced genome and the mating type loci. BMC Genomics 2018; 19:18. [PMID: 29304732 PMCID: PMC5755439 DOI: 10.1186/s12864-017-4421-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/27/2017] [Indexed: 11/21/2022] Open
Abstract
Background Pleurotus tuoliensis (Bailinggu) is a commercially cultivated mushroom species with an increasing popularity in China and other Asian countries. Commercial profits are now low, mainly due to a low yield, long cultivation period and sensitivity to diseases. Breeding efforts are thus required to improve agronomical important traits. Developing saturated genetic linkage and physical maps is a start for applying genetic and molecular approaches to accelerate the precise breeding programs. Results Here we present a genetic linkage map for P. tuoliensis constructed by using 115 haploid monokaryons derived from a hybrid strain H6. One thousand one hundred and eighty-two SNP markers developed by 2b–RAD (type IIB restriction-site associated DNA) approach were mapped to 12 linkage groups. The map covers 1073 cM with an average marker spacing of 1.0 cM. The genome of P. tuoliensis was de novo sequenced as 40.8 Mb and consisted of 500 scaffolds (>500 bp), which showed a high level of colinearity to the genome of P. eryngii var. eryngii. A total of 97.4% SNP markers (1151) were physically localized on 78 scaffolds, and the physical length of these anchored scaffolds were 33.9 Mb representing 83.1% of the whole genome. Mating type loci A and B were mapped on separate linkage groups and identified physically on the assembled genomes. Five putative pheromone receptors and two putative pheromone precursors were identified for the mating type B locus. Conclusions This study reported a first genetic linkage map integrated with physical mapping of the de novo sequenced genome and the mating type loci of an important cultivated mushroom in China, P. tuoliensis. The de novo sequenced and annotated genome, assembled using a 2b–RAD generated linkage map, provides a basis for marker-assisted breeding of this economic important mushroom species. Electronic supplementary material The online version of this article (10.1186/s12864-017-4421-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Gao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Jibin Qu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Jinxia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Anton Sonnenberg
- Plant Breeding, Wageningen University & Research Centre, 6708, PB, Wageningen, The Netherlands
| | - Qiang Chen
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Yan Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, 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, Beijing, China.
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10
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Lu T, Bau T. De novo assembly and characterization of the transcriptome of a wild edible mushroom Leucocalocybe mongolica and identification of SSR markers. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1383187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Tie Lu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Institute of Mycology, Jilin Agricultural University, Changchun, PR China
| | - Tolgor Bau
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Institute of Mycology, Jilin Agricultural University, Changchun, PR China
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11
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Yan JJ, Xie B, Zhang L, Li SJ, van Peer AF, Wu TJ, Chen BZ, Xie BG. Small GTPases and Stress Responses of vvran1 in the Straw Mushroom Volvariella volvacea. Int J Mol Sci 2016; 17:ijms17091527. [PMID: 27626406 PMCID: PMC5037802 DOI: 10.3390/ijms17091527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/05/2016] [Accepted: 09/07/2016] [Indexed: 12/11/2022] Open
Abstract
Small GTPases play important roles in the growth, development and environmental responses of eukaryotes. Based on the genomic sequence of the straw mushroom Volvariella volvacea, 44 small GTPases were identified. A clustering analysis using human small GTPases as the references revealed that V. volvacea small GTPases can be grouped into five families: nine are in the Ras family, 10 are in the Rho family, 15 are in the Rab family, one is in the Ran family and nine are in the Arf family. The transcription of vvran1 was up-regulated upon hydrogen peroxide (H2O2) stress, and could be repressed by diphenyleneiodonium chloride (DPI), a NADPH oxidase-specific inhibitor. The number of vvran1 transcripts also increased upon cold stress. Diphenyleneiodonium chloride, but not the superoxide dismutase (SOD) inhibitor diethy dithiocarbamate (DDC), could suppress the up-regulation of vvran1 gene expression to cold stress. These results combined with the high correlations between gene expression and superoxide anion (O2−) generation indicated that vvran1 could be one of the candidate genes in the downstream of O2− mediated pathways that are generated by NADPH oxidase under low temperature and oxidative stresses.
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Affiliation(s)
- Jun-Jie Yan
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Bin Xie
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Lei Zhang
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Shao-Jie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China.
| | - Arend F van Peer
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ta-Ju Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China.
| | - Bing-Zhi Chen
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Bao-Gui Xie
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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12
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Chen L, Gong Y, Cai Y, Liu W, Zhou Y, Xiao Y, Xu Z, Liu Y, Lei X, Wang G, Guo M, Ma X, Bian Y. Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation. PLoS One 2016; 11:e0160336. [PMID: 27500531 PMCID: PMC4976891 DOI: 10.1371/journal.pone.0160336] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/18/2016] [Indexed: 01/09/2023] Open
Abstract
Lentinula edodes, one of the most popular, edible mushroom species with a high content of proteins and polysaccharides as well as unique aroma, is widely cultivated in many Asian countries, especially in China, Japan and Korea. As a white rot fungus with lignocellulose degradation ability, L. edodes has the potential for application in the utilization of agriculture straw resources. Here, we report its 41.8-Mb genome, encoding 14,889 predicted genes. Through a phylogenetic analysis with model species of fungi, the evolutionary divergence time of L. edodes and Gymnopus luxurians was estimated to be 39 MYA. The carbohydrate-active enzyme genes in L. edodes were compared with those of the other 25 fungal species, and 101 lignocellulolytic enzymes were identified in L. edodes, similar to other white rot fungi. Transcriptome analysis showed that the expression of genes encoding two cellulases and 16 transcription factor was up-regulated when mycelia were cultivated for 120 minutes in cellulose medium versus glucose medium. Our results will foster a better understanding of the molecular mechanism of lignocellulose degradation and provide the basis for partial replacement of wood sawdust with agricultural wastes in L. edodes cultivation.
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Affiliation(s)
- Lianfu Chen
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuhua Gong
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yingli Cai
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wei Liu
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yan Zhou
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yang Xiao
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhangyi Xu
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yin Liu
- Food Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaoyu Lei
- Food Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Gangzheng Wang
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Mengpei Guo
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaolong Ma
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yinbing Bian
- Institute of Applied Mycology, Plant Science and Technology College, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
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13
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Fruiting Body Formation in Volvariella volvacea Can Occur Independently of Its MAT-A-Controlled Bipolar Mating System, Enabling Homothallic and Heterothallic Life Cycles. G3-GENES GENOMES GENETICS 2016; 6:2135-46. [PMID: 27194800 PMCID: PMC4938666 DOI: 10.1534/g3.116.030700] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Volvariella volvacea is an important crop in Southeast Asia, but erratic fruiting presents a serious challenge for its production and breeding. Efforts to explain inconsistent fruiting have been complicated by the multinucleate nature, typical lack of clamp connections, and an incompletely identified sexual reproductive system. In this study, we addressed the life cycle of V. volvacea using whole genome sequencing, cloning of MAT loci, karyotyping of spores, and fruiting assays. Microscopy analysis of spores had previously indicated the possible coexistence of heterothallic and homothallic life cycles. Our analysis of the MAT loci showed that only MAT-A, and not MAT-B, controlled heterokaryotization. Thus, the heterothallic life cycle was bipolar. Karyotyping of single spore isolates (SSIs) using molecular markers supported the existence of heterokaryotic spores. However, most SSIs were clearly not heterokaryotic, yet contained structural variation (SV) markers relating to both alleles of both parents. Heterokaryons from crossed, self-sterile homokaryons could produce fruiting bodies, agreeing with bipolar heterothallism. Meanwhile, some SSIs with two different MAT-A loci also produced fruiting bodies, which supported secondary homothallism. Next, SSIs that clearly contained only one MAT-A locus (homothallism) were also able to fruit, demonstrating that self-fertile SSIs were not, per definition, secondary homothallic, and that a third life cycle or genetic mechanism must exist. Finally, recombination between SV markers was normal, yet 10 out of 24 SV markers showed 1:2 or 1:3 distributions in the spores, and large numbers of SSIs contained doubled SV markers. This indicated selfish genes, and possibly partial aneuploidy.
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14
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The Accordant Trend of Both Parameters (rgs Expression and cAMP Content) Follows the Pattern of Development of Fruiting Body in Volvariella volvacea. Curr Microbiol 2015; 71:579-84. [PMID: 26264785 DOI: 10.1007/s00284-015-0885-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/29/2015] [Indexed: 10/23/2022]
Abstract
The formation of fruiting body in Volvariella volvacea is affected by endogenous genes and environmental factors. However, its regulation at a molecular level is still poorly understood. To study the genes involved in the formation of fruiting body, we cloned a new regulator of the G protein signaling (RGS) encoding gene (rgs) from V. volvacea. Phylogenetic analysis showed that RGS in V. volvacea and other basidiomycete RGS proteins from Schizophyllum commune and Coprinus cinereus belong to the same clade. In addition, we assayed intracellular cAMP content in the three developmental stages (mycelium, fruiting body primordia, and button). We also found that the expression of rgs was highly positively correlated to the content of intracellular cAMP during fruiting body formation. The conserved protein sequences and expression of rgs, together with high concent of cAMP at primordia tissue, suggested that rgs gene and cAMP may play a crucial role in fruiting body formation in V. volvacea.
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15
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Structural Variation (SV) Markers in the Basidiomycete Volvariella volvacea and Their Application in the Construction of a Genetic Map. Int J Mol Sci 2015. [PMID: 26204838 PMCID: PMC4519972 DOI: 10.3390/ijms160716669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Molecular markers and genetic maps are useful tools in genetic studies. Novel molecular markers and their applications have been developed in recent years. With the recent advancements in sequencing technology, the genomic sequences of an increasingly great number of fungi have become available. A novel type of molecular marker was developed to construct the first reported linkage map of the edible and economically important basidiomycete Volvariella volvacea by using 104 structural variation (SV) markers that are based on the genomic sequences. Because of the special and simple life cycle in basidiomycete, SV markers can be effectively developed by genomic comparison and tested in single spore isolates (SSIs). This stable, convenient and rapidly developed marker may assist in the construction of genetic maps and facilitate genomic research for other species of fungi.
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16
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Rytioja J, Hildén K, Yuzon J, Hatakka A, de Vries RP, Mäkelä MR. Plant-polysaccharide-degrading enzymes from Basidiomycetes. Microbiol Mol Biol Rev 2014; 78:614-49. [PMID: 25428937 PMCID: PMC4248655 DOI: 10.1128/mmbr.00035-14] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
SUMMARY Basidiomycete fungi subsist on various types of plant material in diverse environments, from living and dead trees and forest litter to crops and grasses and to decaying plant matter in soils. Due to the variation in their natural carbon sources, basidiomycetes have highly varied plant-polysaccharide-degrading capabilities. This topic is not as well studied for basidiomycetes as for ascomycete fungi, which are the main sources of knowledge on fungal plant polysaccharide degradation. Research on plant-biomass-decaying fungi has focused on isolating enzymes for current and future applications, such as for the production of fuels, the food industry, and waste treatment. More recently, genomic studies of basidiomycete fungi have provided a profound view of the plant-biomass-degrading potential of wood-rotting, litter-decomposing, plant-pathogenic, and ectomycorrhizal (ECM) basidiomycetes. This review summarizes the current knowledge on plant polysaccharide depolymerization by basidiomycete species from diverse habitats. In addition, these data are compared to those for the most broadly studied ascomycete genus, Aspergillus, to provide insight into specific features of basidiomycetes with respect to plant polysaccharide degradation.
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Affiliation(s)
- Johanna Rytioja
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Kristiina Hildén
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jennifer Yuzon
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Annele Hatakka
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Miia R Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Helsinki, Finland
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17
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Omarini AB, Plagemann I, Schimanski S, Krings U, Berger RG. Crosses between monokaryons of Pleurotus sapidus or Pleurotus florida show an improved biotransformation of (+)-valencene to (+)-nootkatone. BIORESOURCE TECHNOLOGY 2014; 171:113-119. [PMID: 25189516 DOI: 10.1016/j.biortech.2014.08.061] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/12/2014] [Accepted: 08/13/2014] [Indexed: 06/03/2023]
Abstract
Several hundred monokaryotic and new dikaryotic strains derived thereof were established from (+)-valencene tolerant Pleurotus species. When grouped according to their growth rate on agar plates and compared to the parental of Pleurotus sapidus 69, the slowly growing monokaryons converted (+)-valencene more efficiently to the grapefruit flavour compound (+)-nootkatone. The fast growing monokaryons and the slow×slow and the fast×fast dikaryotic crosses showed similar or inferior yields. Some slow×fast dikaryons, however, exceeded the biotransformation capability of the parental dikaryon significantly. The activity of the responsible enzyme, lipoxygenase, showed a weak correlation with the yields of (+)-nootkatone indicating that the determination of enzyme activity using the primary substrate linoleic acid may be misleading in predicting the biotransformation efficiency. This exploratory study indicated that a classical genetics approach resulted in altered and partly improved terpene transformation capability (plus 60%) and lipoxygenase activity of the strains.
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Affiliation(s)
- Alejandra B Omarini
- Institut für Lebensmittelchemie, Leibniz Universität Hannover, Callinstraße 5, 30167 Hannover, Germany.
| | - Ina Plagemann
- Institut für Lebensmittelchemie, Leibniz Universität Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Silke Schimanski
- Institut für Lebensmittelchemie, Leibniz Universität Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Ulrich Krings
- Institut für Lebensmittelchemie, Leibniz Universität Hannover, Callinstraße 5, 30167 Hannover, Germany
| | - Ralf G Berger
- Institut für Lebensmittelchemie, Leibniz Universität Hannover, Callinstraße 5, 30167 Hannover, Germany
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18
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Biochemical characteristics of an alkaline pectate lyase PelA from Volvariella volvacea: roles of the highly conserved N-glycosylation site in its secretion and activity. Appl Microbiol Biotechnol 2014; 99:3447-58. [DOI: 10.1007/s00253-014-6146-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 10/06/2014] [Accepted: 10/09/2014] [Indexed: 02/05/2023]
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19
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Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation. PLoS One 2014; 9:e93560. [PMID: 24714189 PMCID: PMC3979922 DOI: 10.1371/journal.pone.0093560] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/07/2014] [Indexed: 12/27/2022] Open
Abstract
Flammulina velutipes is a fungus with health and medicinal benefits that has been used for consumption and cultivation in East Asia. F. velutipes is also known to degrade lignocellulose and produce ethanol. The overlapping interests of mushroom production and wood bioconversion make F. velutipes an attractive new model for fungal wood related studies. Here, we present the complete sequence of the F. velutipes genome. This is the first sequenced genome for a commercially produced edible mushroom that also degrades wood. The 35.6-Mb genome contained 12,218 predicted protein-encoding genes and 287 tRNA genes assembled into 11 scaffolds corresponding with the 11 chromosomes of strain KACC42780. The 88.4-kb mitochondrial genome contained 35 genes. Well-developed wood degrading machinery with strong potential for lignin degradation (69 auxiliary activities, formerly FOLymes) and carbohydrate degradation (392 CAZymes), along with 58 alcohol dehydrogenase genes were highly expressed in the mycelium, demonstrating the potential application of this organism to bioethanol production. Thus, the newly uncovered wood degrading capacity and sequential nature of this process in F. velutipes, offer interesting possibilities for more detailed studies on either lignin or (hemi-) cellulose degradation in complex wood substrates. The mutual interest in wood degradation by the mushroom industry and (ligno-)cellulose biomass related industries further increase the significance of F. velutipes as a new model.
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20
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Siguier B, Haon M, Nahoum V, Marcellin M, Burlet-Schiltz O, Coutinho PM, Henrissat B, Mourey L, O'Donohue MJ, Berrin JG, Tranier S, Dumon C. First structural insights into α-L-arabinofuranosidases from the two GH62 glycoside hydrolase subfamilies. J Biol Chem 2014; 289:5261-73. [PMID: 24394409 DOI: 10.1074/jbc.m113.528133] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
α-L-arabinofuranosidases are glycoside hydrolases that specifically hydrolyze non-reducing residues from arabinose-containing polysaccharides. In the case of arabinoxylans, which are the main components of hemicellulose, they are part of microbial xylanolytic systems and are necessary for complete breakdown of arabinoxylans. Glycoside hydrolase family 62 (GH62) is currently a small family of α-L-arabinofuranosidases that contains only bacterial and fungal members. Little is known about the GH62 mechanism of action, because only a few members have been biochemically characterized and no three-dimensional structure is available. Here, we present the first crystal structures of two fungal GH62 α-L-arabinofuranosidases from the basidiomycete Ustilago maydis (UmAbf62A) and ascomycete Podospora anserina (PaAbf62A). Both enzymes are able to efficiently remove the α-L-arabinosyl substituents from arabinoxylan. The overall three-dimensional structure of UmAbf62A and PaAbf62A reveals a five-bladed β-propeller fold that confirms their predicted classification into clan GH-F together with GH43 α-L-arabinofuranosidases. Crystallographic structures of the complexes with arabinose and cellotriose reveal the important role of subsites +1 and +2 for sugar binding. Intriguingly, we observed that PaAbf62A was inhibited by cello-oligosaccharides and displayed binding affinity to cellulose although no activity was observed on a range of cellulosic substrates. Bioinformatic analyses showed that UmAbf62A and PaAbf62A belong to two distinct subfamilies within the GH62 family. The results presented here provide a framework to better investigate the structure-function relationships within the GH62 family.
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Affiliation(s)
- Béatrice Siguier
- From the Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse
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21
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Kaffenberger JT, Schilling JS. Using a grass substrate to compare decay among two clades of brown rot fungi. Appl Microbiol Biotechnol 2013; 97:8831-40. [PMID: 23917637 DOI: 10.1007/s00253-013-5142-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 07/17/2013] [Accepted: 07/17/2013] [Indexed: 11/30/2022]
Abstract
Interest in the mechanisms of wood-degrading fungi has grown in tandem with lignocellulose bioconversion efforts, yet many potential biomass feedstocks are non-woody. Using corn stover (Zea mays) as a substrate, we tracked degradative capacities among brown rot fungi from the Antrodia clade, including Postia placenta, the first brown rot fungus to have its genome sequenced. Decay dynamics were compared against Gloeophyllum trabeum from the Gloeophyllum clade. Weight loss induced by P. placenta (6.2 %) and five other Antrodia clade isolates (average 7.4 %) on corn stalk after 12 weeks demonstrated inefficiency among these fungi, relative to decay induced by G. trabeum (44.4 %). Using aspen (Populus sp.) as a woody substrate resulted in, on average, a fourfold increase in weight loss induced by Antrodia clade fungi, while G. trabeum results matched those on stover. The sequence and trajectories of chemical constituent losses differed as a function of substrate but not fungal clade. Instead, chemical data suggest that characters unique to stover limit decay by the Antrodia clade, rather than disparities in growth rate or extractives toxicity. High p-coumaryl lignin content, lacking the methoxy groups characteristically cleaved during brown rot, is among potential rate-distinguishing characters in grasses. This ineptitude among Antrodia clade fungi on grasses was supported by meta-analysis of other unrelated studies using grass substrates. Concerning application, results expose a problem if adopting the strategy of the model decay fungus P. placenta to treat corn stover, a widely available plant feedstock. Overall, the results insinuate phylogenetically distinct modes of brown rot and demonstrate the benefit of using non-woody substrates to probe wood degradation mechanisms.
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Affiliation(s)
- Justin T Kaffenberger
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, 2004 Folwell Avenue, Saint Paul, MN, 55108, USA
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