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Zhang J, Shen N, Li C, Xiang X, Liu G, Gui Y, Patev S, Hibbett DS, Barry K, Andreopoulos W, Lipzen A, Riley R, He G, Yan M, Grigoriev IV, Shan Kwan H, Kit Cheung M, Bian Y, Xiao Y. Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes. J Adv Res 2021; 38:91-106. [PMID: 35572413 PMCID: PMC9091725 DOI: 10.1016/j.jare.2021.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 02/08/2023] Open
Abstract
We detected three subgroups of L. edodes with robust phenotypic differentiation. The three subgroups were diverged 36,871 generations ago. L. edodes cultivars in China might originate from the vicinity of Northeast China. We dissected the genetic basis of adaptive evolution in L. edodes. Genes related to fruiting body development are involved in adaptive evolution.
Introduction Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi. Objectives This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution. Methods We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution. Results We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation. Conclusion Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.
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Zhang L, Gong W, Li C, Shen N, Gui Y, Bian Y, Kwan HS, Cheung MK, Xiao Y. RNA-Seq-based high-resolution linkage map reveals the genetic architecture of fruiting body development in shiitake mushroom, Lentinula edodes. Comput Struct Biotechnol J 2021; 19:1641-1653. [PMID: 33868600 PMCID: PMC8026754 DOI: 10.1016/j.csbj.2021.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/07/2021] [Accepted: 03/12/2021] [Indexed: 01/21/2023] Open
Abstract
We constructed a reference genetic map of Lentinula edodes. We re-assembled a chromosome-level genome of L. edodes. We disclosed three hotspots regions for fruiting body-related traits in shiitake. We scanned candidate genes for fruiting body-related traits.
Fruiting body development (FBD) of mushroom-forming fungi has attracted tremendous interest. However, the genetic and molecular basis of FBD is poorly known. Here, using Lentinula edodes (shiitake) as a model, we deciphered the genetic architecture underlying fruiting body-related traits (FBRTs) by combined genomic, genetic and phenotypic data. Using RNA-Seq of fruiting bodies from 110 dikaryons in a bi-parental mapping population, we constructed an ultra-high-density genetic map of L. edodes (Lemap2.0) with a total length of 810.14 cM, which covered 81.7% of the shiitake genome. A total of 94 scaffolds of the shiitake genome were aligned to Lemap2.0 and re-anchored into nine pseudo-chromosomes. Then via quantitative trait locus (QTL) analysis, we disclosed an outline of the genetic architecture of FBD in shiitake. Twenty-nine QTLs and three main genomic regions associated with FBD of shiitake were identified. Using meta-QTL analysis, seven pleiotropic QTLs for multiple traits were detected, which contributed to the correlations of FBRTs. In the mapped QTLs, the expression of 246 genes were found to significantly correlate with the phenotypic traits. Thirty-three of them were involved in FBD and could represent candidate genes controlling the shape and size of fruiting bodies. Collectively, our findings have advanced our understanding of the genetic regulation of FBD in shiitake and mushroom-forming fungi at large.
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Affiliation(s)
- Lin Zhang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Wenbing Gong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Chuang Li
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Nan Shen
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Ying Gui
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong, China
| | - Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong, China
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
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Dwivedi S, Singh S, Chauhan U, Tiwari MK. Inter and intraspecific genetic diversity (RAPD) among three most frequent species of macrofungi ( Ganoderma lucidum, Leucoagricus sp. and Lentinus sp.) of Tropical forest of Central India. J Genet Eng Biotechnol 2018; 16:133-141. [PMID: 30647715 PMCID: PMC6296601 DOI: 10.1016/j.jgeb.2017.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 11/09/2017] [Accepted: 11/20/2017] [Indexed: 11/03/2022]
Abstract
In present study seven RAPD primers were used to access the diversity within and among twelve populations of three mushroom species Ganoderma lucidum, leucoagaricus sp. and Lentinus sp. Total of 111 bands were scored by 7 RAPD primers in 30 accessions of three mushroom species collected from different sampling sites of central India. Total 111 bands were generated using seven primers which were F-1, OPG-06, OPC-07, OPD-08, OPA-02, OPD-02, OPB-10. All 111 bands were polymorphic in nature (100%). Therefore, it revealed that the used primers had sufficient potency for population studies and 30 accessions had higher genetic differences among each other. In best of the knowledge, this is the first report, which accesses the genetic diversity between three mushroom species (Gd Ganoderma lucidum, Lg Leucoagaricus sp., Ls Lentinus). The polymorphic percentage ranged from 3.60 to 23% within twelve populations, while polymorphic percentage among group was 40.56, among population within groups was 41.12 and within population was 18.32. This indicated that the genetic diversity within the population was very low, but slightly higher in the populations of three species. Among three groups representing Gd., Lg and Ls, Among populations within groups shown highest percentage of variation (Pv = 41.12) while within populations, the lowest percentage of variation (18.32) was observed. This result also support that the highest genetic variation was present among groups in comparison to among the population within a species and lowest genetic variation was observed within the population.
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Affiliation(s)
- Sandhya Dwivedi
- Department of Post Graduate Studies and Research in Biological Science, Rani Durgawati University, Jabalpur 480221, India
| | - Surendra Singh
- Department of Post Graduate Studies and Research in Biological Science, Rani Durgawati University, Jabalpur 480221, India
| | - U.K. Chauhan
- School of Environmental Biology and Biotechnology, Awadhesh Pratap Singh University, 486003, India
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Li C, Gong W, Zhang L, Yang Z, Nong W, Bian Y, Kwan HS, Cheung MK, Xiao Y. Association Mapping Reveals Genetic Loci Associated with Important Agronomic Traits in Lentinula edodes, Shiitake Mushroom. Front Microbiol 2017; 8:237. [PMID: 28261189 PMCID: PMC5314409 DOI: 10.3389/fmicb.2017.00237] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/03/2017] [Indexed: 12/28/2022] Open
Abstract
Association mapping is a robust approach for the detection of quantitative trait loci (QTLs). Here, by genotyping 297 genome-wide molecular markers of 89 Lentinula edodes cultivars in China, the genetic diversity, population structure and genetic loci associated with 11 agronomic traits were examined. A total of 873 alleles were detected in the tested strains with a mean of 2.939 alleles per locus, and the Shannon's information index was 0.734. Population structure analysis revealed two robustly differentiated groups among the Chinese L. edodes cultivars (FST = 0.247). Using the mixed linear model, a total of 43 markers were detected to be significantly associated with four traits. The number of markers associated with traits ranged from 9 to 26, and the phenotypic variations explained by each marker varied from 12.07% to 31.32%. Apart from five previously reported markers, the remaining 38 markers were newly reported here. Twenty-one markers were identified as simultaneously linked to two to four traits, and five markers were associated with the same traits in cultivation tests performed in two consecutive years. The 43 traits-associated markers were related to 97 genes, and 24 of them were related to 10 traits-associated markers detected in both years or identified previously, 13 of which had a >2-fold expression change between the mycelium and primordium stages. Our study has provided candidate markers for marker-assisted selection (MAS) and useful clues for understanding the genetic architecture of agronomic traits in the shiitake mushroom.
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Affiliation(s)
- Chuang Li
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
| | - Wenbing Gong
- Institute of Applied Mycology, Huazhong Agricultural UniversityHubei, China; Institute of Bast Fiber Crops, Chinese Academy of Agricultural SciencesChangsha, China
| | - Lin Zhang
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
| | - Zhiquan Yang
- College of Informatics, Huazhong Agricultural University Hubei, China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
| | - Hoi-Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong
| | - Man-Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong Hong Kong, Hong Kong
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University Hubei, China
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Antimicrobial Potential, Identification and Phylogenetic Affiliation of Wild Mushrooms from Two Sub-Tropical Semi-Evergreen Indian Forest Ecosystems. PLoS One 2016; 11:e0166368. [PMID: 27902725 PMCID: PMC5130189 DOI: 10.1371/journal.pone.0166368] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/27/2016] [Indexed: 12/01/2022] Open
Abstract
The diversity of wild mushrooms was investigated from two protected forest areas in India and 231 mushroom specimens were morphologically identified. Among them, 76 isolates were screened for their antimicrobial potential against seven bacterial and fungal pathogens. Out of 76 isolates, 45 isolates which displayed significant antimicrobial activities were identified using ITS rRNA gene amplification and subsequently phylogenetically characterized using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) markers. Sequencing of the ITS rRNA region classified the isolates into 16 genera belonging to 11 families. In total, 11 RAPD and 10 ISSR primers were selected to evaluate genetic diversity based on their banding profile produced. In total 337 RAPD and 312 ISSR bands were detected, among which percentage of polymorphism ranges from 34.2% to 78.8% and 38.6% to 92.4% by using RAPD and ISSR primers respectively. Unweighted Pair-Group Method with Arithmetic Mean (UPGMA) trees of selected two methods were structured similarly, grouping the 46 isolates into two clusters which clearly showed a significant genetic distance among the different strains of wild mushroom, with an similarity coefficient ranges from 0.58 to 1.00 and 0.59 to 1.00 with RAPD and ISSR analysis respectively. This reporthas highlighted both DTR and MNP forests provide a habitat for diverse macrofungal species, therefore having the potential to be used for the discovery of antimicrobials. The report has also demonstrated that both RAPD and ISSR could efficiently differentiate wild mushrooms and could thus be considered as efficient markers for surveying genetic diversity. Additionally, selected six wild edible mushroom strains (Schizophyllum commune BPSM01, Panusgiganteus BPSM27, Pleurotussp. BPSM34, Lentinussp. BPSM37, Pleurotusdjamor BPSM41 and Lentinula sp. BPSM45) were analysed for their nutritional (proteins, carbohydrates, fat and ash content), antioxidant potential. The present findings also suggested that the wild edible mushroom strains do not have only nutritional values but also can be used as an accessible source of natural antioxidants.
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Xiao Y, Cheng X, Liu J, Li C, Nong W, Bian Y, Cheung MK, Kwan HS. Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China. Sci Rep 2016; 6:36789. [PMID: 27830835 PMCID: PMC5103288 DOI: 10.1038/srep36789] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/26/2016] [Indexed: 01/06/2023] Open
Abstract
The elucidation of genome-wide variations could help reveal aspects of divergence, domestication, and adaptation of edible mushrooms. Here, we resequenced the whole genomes of 39 wild and 21 cultivated strains of Chinese Lentinula edodes, the shiitake mushroom. We identified three distinct genetic groups in the Chinese L. edodes population with robust differentiation. Results of phylogenetic and population structure analyses suggest that the cultivated strains and most of the wild trains of L. edodes in China possess different gene pools and two outlier strains show signatures of hybridization between groups. Eighty-four candidate genes contributing to population divergence were detected in outlier analysis, 18 of which are involved in response to environmental stresses. Gene enrichment analysis of group-specific single nucleotide polymorphisms showed that the cultivated strains were genetically diversified in biological processes related to stress response. As the formation of fruiting bodies is a stress-response process, we postulate that environment factors, such as temperature, drove the population divergence of L. edodes in China by natural or artificial selection. We also found phenotypic variations between groups and identified some wild strains that have potential to diversify the genetic pool for improving agricultural traits of L. edodes cultivars in China.
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Affiliation(s)
- Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China.,School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Xuanjin Cheng
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Jun Liu
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China
| | - Chuang Li
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China
| | - Wenyan Nong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, 430070, Hubei Province, P. R. China
| | - Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P. R. China
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7
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Genetic diversity and population structure of Chinese Lentinula edodes revealed by InDel and SSR markers. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1183-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Enhanced Specificity for Detection of Frauds by Fusion of Multi-class and One-Class Partial Least Squares Discriminant Analysis: Geographical Origins of Chinese Shiitake Mushroom. FOOD ANAL METHOD 2015. [DOI: 10.1007/s12161-015-0213-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kim KH, Ka KH, Kang JH, Kim S, Lee JW, Jeon BK, Yun JK, Park SR, Lee HJ. Identification of Single Nucleotide Polymorphism Markers in the Laccase Gene of Shiitake Mushrooms (Lentinula edodes). MYCOBIOLOGY 2015; 43:75-80. [PMID: 25892919 PMCID: PMC4397384 DOI: 10.5941/myco.2015.43.1.75] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 11/17/2014] [Accepted: 12/14/2014] [Indexed: 05/15/2023]
Abstract
We identified single nucleotide polymorphism (SNP) markers in the laccase gene to establish a line-diagnostic system for shiitake mushrooms. A total of 89 fungal isolates representing four lines, including Korean registered, Korean wild type, Chinese, and Japanese lines, were analyzed. The results suggest that SNP markers in the laccase gene can be useful for line typing in shiitake mushrooms.
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Affiliation(s)
| | - Kang-Hyeon Ka
- Korea Forest Research Institute, Seoul 130-712, Korea
| | - Ji Hyoun Kang
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz 78457, Germany
| | - Sangil Kim
- Estuarine & Coastal Ecology Laboratory, Department of Marine Life Sciences, Jeju National University, Jeju 690-756, Korea
| | | | | | - Jung-Kuk Yun
- Department of Medicine, Graduate School, Chungbuk National University, Cheongju 362-763, Korea
| | - Sang Rul Park
- Estuarine & Coastal Ecology Laboratory, Department of Marine Life Sciences, Jeju National University, Jeju 690-756, Korea
| | - Hyuk Je Lee
- Department of Biological Science, College of Science and Engineering, Sangji University, Wonju 220-702, Korea
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Liu J, Wang ZR, Li C, Bian YB, Xiao Y. Evaluating genetic diversity and constructing core collections of ChineseLentinula edodescultivars using ISSR and SRAP markers. J Basic Microbiol 2015; 55:749-60. [DOI: 10.1002/jobm.201400774] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/07/2014] [Indexed: 01/27/2023]
Affiliation(s)
- Jun Liu
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture); Huazhong Agricultural University; Wuhan Hubei Province P.R. China
- Institute of Applied Mycology; Huazhong Agricultural University; Wuhan Hubei Province P.R. China
| | - Zhuo-Ren Wang
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture); Huazhong Agricultural University; Wuhan Hubei Province P.R. China
- Institute of Applied Mycology; Huazhong Agricultural University; Wuhan Hubei Province P.R. China
| | - Chuang Li
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture); Huazhong Agricultural University; Wuhan Hubei Province P.R. China
- Institute of Applied Mycology; Huazhong Agricultural University; Wuhan Hubei Province P.R. China
| | - Yin-Bing Bian
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture); Huazhong Agricultural University; Wuhan Hubei Province P.R. China
- Institute of Applied Mycology; Huazhong Agricultural University; Wuhan Hubei Province P.R. China
| | - Yang Xiao
- Key Laboratory of Agro-Microbial Resource and Development (Ministry of Agriculture); Huazhong Agricultural University; Wuhan Hubei Province P.R. China
- Institute of Applied Mycology; Huazhong Agricultural University; Wuhan Hubei Province P.R. China
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Du P, Cui BK, Dai YC. Assessment of Genetic Diversity among Wild Auricularia polytrichaPopulations in China using ISSR Markers. CRYPTOGAMIE MYCOL 2012. [DOI: 10.7872/crym.v33.iss2.2012.191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mukhopadhyay K, Haque I, Bandopadhyay R, Covert S, Porter D. AFLP based assessment of genetic relationships among shiitake (Lentinula ssp.) mushrooms. Mol Biol Rep 2012; 39:6059-65. [PMID: 22215213 DOI: 10.1007/s11033-011-1420-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 12/19/2011] [Indexed: 11/25/2022]
Abstract
Despite the economical importance of shiitake (Lentinula ssp.) mushrooms, until the present date little information exists on cultivated and wild species in correlation with geographic origin applying molecular techniques. Use of a high resolution molecular tool like AFLP for assessing genetic similarity and geographical diversity would be an important step towards understanding of different Lentinula species. Thirteen wild and 17 cultivated accessions of 3 Lentinula species were analysed with 64 EcoRI-MseI primer combinations and finally 32 reproducible and polymorphic primer combinations were considered for the analysis. A total of 816 informative AFLP markers were generated and scored as binary data. These data were analysed using various method packages for cluster analysis, genetic diversity and genetic differentiation. Percentage polymorphism was high (62.99%) among the species studied. Different clustering analysis segregated the wild and the cultivated species into two major branches, with the wild samples being further grouped according to their geographic location. Overall polymorphisms among cultivated strains in the USA were higher than that of the cultivated strains in Japan (58.9%).
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Affiliation(s)
- Kunal Mukhopadhyay
- Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India.
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Molecular characterization and mating type analysis of oyster mushroom (Pleurotus spp.) using single basidiospores for strain improvement. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0419-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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SCAR makers and multiplex PCR-based rapid molecular typing of Lentinula edodes strains. Curr Microbiol 2010; 61:381-9. [PMID: 20358374 DOI: 10.1007/s00284-010-9623-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 03/16/2010] [Indexed: 10/19/2022]
Abstract
Lentinula edodes is the second most important cultivated mushroom worldwide, the most commercial strains have been identified only through traditional phenotypic analysis. In this study, a simple rapid PCR-based molecular method was developed for distinguishing commercial strains of L. edodes by developing specific sequence characterized amplified region (SCAR) markers and establishing multiplex PCR assays with the SCAR primers. Derived from the randomly amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) techniques, 10 informative SCAR markers were generated from 10 polymorphic RAPD and SRAP bands. The differences in SCAR phenotypes among different strains made these SCAR markers potentially useful to characterize 6 strains and identify them from other studied strains. Moreover, different SCAR phenotypes also made the other 17 studied strains to be divided into four distinguishable groups. The multiplex PCR assays were further established for the joint use of some SCAR markers efficiently. Compared with some identification methods reported previously, the special feature of this new molecular method is technically rapid and convenient in the practical use and suitable for analyzing large numbers of samples. Thus, the simple rapid PCR-based molecular method can be used as a helpful assistant tool for the lentinula industry. To our knowledge, this study is the first to describe a development of a new SCAR maker-based multiplex PCR assay for rapid molecular typing of edible mushroom.
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Kim KH, Kim YY, Ka KH, Lee HS, Bak WC, Jeong SJ, Seong JY, Suh DS. Microsatellite markers for population-genetic studies of shiitake (Lentinula edodes) strains. Genes Genomics 2009. [DOI: 10.1007/bf03191853] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Urbanelli S, Della Rosa V, Punelli F, Porretta D, Reverberi M, Fabbri AA, Fanelli C. DNA-fingerprinting (AFLP and RFLP) for genotypic identification in species of the Pleurotus eryngii complex. Appl Microbiol Biotechnol 2007; 74:592-600. [PMID: 17268785 DOI: 10.1007/s00253-006-0684-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 09/11/2006] [Accepted: 09/26/2006] [Indexed: 11/28/2022]
Abstract
Wild populations of edible species are important source of genetic variability for cultivated lines that can undergo a drastic loss of diversity resulting from man's selection. The development of tools aimed at the clear-cut and safe identification and assessment of genetic variability of the wild and cultivated strains is thus a fundamental goal of molecular genetic research. In this study, we used two polymerase chain reaction (PCR)-based fingerprinting methods-amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) of laccase and manganese peroxidase genes-to assess genetic differences among strains and independently evolving lineages belonging to the Pleurotus eryngii complex. Both laccase RFLP and AFLP have been proved to distinguish unambiguously the three taxa studied: Pleurotus ferulae, P. eryngii, and P. eryngii var. nebrodensis. AFLP also showed enough sensitivity to detect polymorphisms among the strains, proving to be an efficient DNA fingerprinting tool in studies of strain assignment. The divergent RFLP laccase and manganese peroxidase patterns are also discussed in relation to the role played by these genes in the interaction between these fungi and their host plants.
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Affiliation(s)
- S Urbanelli
- Department of Genetics and Molecular Biology, University "La Sapienza" of Rome, Via dei Sardi 70, 00185, Rome, Italy.
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Sánchez C, Moore D, Díaz-Godínez G. Microscopic observations of the early development of Pleurotus pulmonarius fruit bodies. Mycologia 2007; 98:682-9. [PMID: 17256572 DOI: 10.1080/15572536.2006.11832640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
From observations made by light microscopy, transmission electron microscopy, environmental-scanning and cryoscanning electron microscopy we conclude that the expansion of the young fruit body of Pleurotus pulmonarius involves considerable vacuolation of hyphae but no marked inflation of cell dimensions. There is evidence for an extensive extracellular matrix (ECM), the components of which must be under the control of the hyphae which the ECM surrounds. However the ECM in these fruit bodies is a dilute material. It is easily lost during specimen preparation and is evident only when certain techniques are used to preserve the fluid surface of the hyphae. Observations of the hyphal and fruit body structures with a range of conventional microscopic techniques are crucial to complement the information obtained through physiological and molecular studies for understanding the cellular changes that occur during mushroom development.
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Affiliation(s)
- Carmen Sánchez
- Laboratory of Biotechnology, Research Center for Biological Sciences, Universidad Autónoma de Tlaxcala, Apartado postal 129, Tlaxcala, Tlax., CP 90000, México.
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Zhang R, Huang C, Zheng S, Zhang J, Ng TB, Jiang R, Zuo X, Wang H. Strain-typing of Lentinula edodes in China with inter simple sequence repeat markers. Appl Microbiol Biotechnol 2006; 74:140-5. [PMID: 17186239 DOI: 10.1007/s00253-006-0628-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 08/08/2006] [Accepted: 08/09/2006] [Indexed: 11/28/2022]
Abstract
To validate strain typing by inter simple sequence repeat (ISSR) analysis in Lentinula edodes cultivars, 17 Chinese L. edodes strains including 15 cultivated strains cultivated on a large scale and two wild strains were analyzed with the ISSR technique. With the use of two ISSR primers, a total of 32 DNA products were detected, of which, 31 DNA products (96.9% of the detected products) were polymorphic between two or more strains. The profiles of those two primers could be employed to differentiate all of the tested strains. A cluster analysis based on ISSR data revealed that the 17 strains could be classified into two distinct groups. One group consisted of eight strains in which the cultivated strains were H (high-temperature)-type or B (broad-temperature)-type, and the other group comprised cultivated strains that were of the L (low-temperature)-type or M (medium-temperature)-type. In contrast to the two wild strains, the genetic diversity of 15 cultivated strains was very rich based on a similarity coefficient analysis.
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Affiliation(s)
- Ruiying Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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19
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Yan PS, Luo XC, Zhou Q. RAPD molecular differentiation of the cultivated strains of the jelly mushrooms, Auricularia auricula and A. polytricha. World J Microbiol Biotechnol 2004. [DOI: 10.1007/s11274-004-5840-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Terashima K, Matsumoto T. Strain typing of shiitake (Lentinula edodes) cultivars by AFLP analysis, focusing on a heat-dried fruiting body. MYCOSCIENCE 2004. [DOI: 10.1007/s10267-003-0152-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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21
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Genetic relationships in the natural population of Pholiota nameko from Japan based on DNA polymorphisms. MYCOSCIENCE 2002. [DOI: 10.1007/s102670200067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Genetic diversity and strain-typing in cultivated strains of Lentinula edodes (the shii-take mushroom) in Japan by AFLP analysis. ACTA ACUST UNITED AC 2002. [DOI: 10.1017/s0953756201005007] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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23
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Muthumeenakshi S, Goldstein AL, Stewart A, Whipps JM. Molecular studies on intraspecific diversity and phylogenetic position of Coniothyrium minitans. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0953-7562(08)61968-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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24
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RAPD characterisation of heterogeneity in spore progenies and sexuality in the genus Agaricus. ACTA ACUST UNITED AC 2001. [DOI: 10.1017/s0953756201003641] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Chiu SW, Law SC, Ching ML, Cheung KW, Chen MJ. Themes for mushroom exploitation in the 21st century: Sustainability, waste management, and conservation. J GEN APPL MICROBIOL 2000; 46:269-282. [PMID: 12483569 DOI: 10.2323/jgam.46.269] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Because many natural resources are limited, sustainability becomes an important concept in maintaining the human population, health, and environment. Mushrooms are a group of saprotrophic fungi. Mushroom cultivation is a direct utilization of their ecological role in the bioconversion of solid wastes generated from industry and agriculture into edible biomass, which could also be regarded as a functional food or as a source of drugs and pharmaceuticals. To make the mushroom cultivation an environmentally friendly industry, the basic biology of mushrooms and the cultivation technology must be researched and developed. This is very true for Lentinula edodes, Volvariella volvacea, and Ganoderma lucidum, which are commonly consumed in Asian communities but are now gaining popularity worldwide. Besides the conventional method, strain improvement can also be exploited by protoplast fusion and transformation. Biodiversity is the key contribution to the genetic resource for breeding programs to fulfill different consumer demands. The conservation of these mushrooms becomes essential and is in immediate need not only because of the massive habitat loss as a result of human inhabitation and deforestation, but also because of the introduced competition by a cultivar with the wild germ plasm. Spent mushroom compost, a bulky solid waste generated from the mushroom industry, however, can be exploited as a soil fertilizer and as a prospective bioremediating agent.
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Affiliation(s)
- Siu Wai Chiu
- Department of Biology and Environmental Science Programme, The Chinese University of Hong Kong, Shatin, N. T., Hong Kong, China
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Segregation of genotypically diverse progeny from self-fertilized haploids of the Chinese straw mushroom, Volvariella volvacea. ACTA ACUST UNITED AC 1999. [DOI: 10.1017/s0953756299001422] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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An integrated study of individualism in Lentinula edodes in nature and its implication for cultivation strategy. ACTA ACUST UNITED AC 1999. [DOI: 10.1017/s095375629900859x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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