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Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation
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...
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| Published in: | PloS one 2016-08, Vol.11 (8), p.e0160336-e0160336 |
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| creator | Chen, Lianfu Gong, Yuhua Cai, Yingli Liu, Wei Zhou, Yan Xiao, Yang Xu, Zhangyi Liu, Yin Lei, Xiaoyu Wang, Gangzheng Guo, Mengpei Ma, Xiaolong Bian, Yinbing |
| description | 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. |
| doi_str_mv | 10.1371/journal.pone.0160336 |
| format | article |
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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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0160336</identifier><identifier>PMID: 27500531</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acids ; Agricultural resources ; Agricultural wastes ; Agriculture ; Analysis ; Aroma ; Biodegradation ; Bioinformatics ; Biological evolution ; Biology and Life Sciences ; Carbohydrates ; Cellulose ; Cladistic analysis ; Cultivation ; Degradation ; Divergence ; Enzymes ; Evolution ; Evolution (Biology) ; Food science ; Fungal Proteins - genetics ; Fungi ; Gene expression ; Genes ; Genetic aspects ; Genetic research ; Genome, Fungal ; Genomes ; Genomics ; Glucose ; Gymnopus ; High-Throughput Nucleotide Sequencing ; Laboratories ; Lentinula edodes ; Lignin ; Lignin - genetics ; Lignin - metabolism ; Lignocellulose ; Molecular biology ; Mushrooms ; Mycelia ; Nucleotide sequence ; Phylogenetics ; Phylogeny ; Physical Sciences ; Plant sciences ; Polysaccharides ; Proteins ; Research and Analysis Methods ; Saccharides ; Sawdust ; Shiitake Mushrooms - genetics ; Shiitake Mushrooms - growth & development ; Shiitake Mushrooms - metabolism ; Species ; Straw ; Transcription (Genetics) ; White rot ; White rot fungi ; Wood ; Wood waste ; Wood wastes</subject><ispartof>PloS one, 2016-08, Vol.11 (8), p.e0160336-e0160336</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Chen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2016 Chen et al 2016 Chen et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c626t-86395a5f1da2aeedfddbd6c62939c81f49a708fee0509f000ebef73a25801b6f3</citedby><cites>FETCH-LOGICAL-c626t-86395a5f1da2aeedfddbd6c62939c81f49a708fee0509f000ebef73a25801b6f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/1812534505/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/1812534505?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,315,733,786,790,891,25783,27957,27958,37047,37048,44625,53827,53829,75483</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27500531$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Cullen, Daniel</contributor><creatorcontrib>Chen, Lianfu</creatorcontrib><creatorcontrib>Gong, Yuhua</creatorcontrib><creatorcontrib>Cai, Yingli</creatorcontrib><creatorcontrib>Liu, Wei</creatorcontrib><creatorcontrib>Zhou, Yan</creatorcontrib><creatorcontrib>Xiao, Yang</creatorcontrib><creatorcontrib>Xu, Zhangyi</creatorcontrib><creatorcontrib>Liu, Yin</creatorcontrib><creatorcontrib>Lei, Xiaoyu</creatorcontrib><creatorcontrib>Wang, Gangzheng</creatorcontrib><creatorcontrib>Guo, Mengpei</creatorcontrib><creatorcontrib>Ma, Xiaolong</creatorcontrib><creatorcontrib>Bian, Yinbing</creatorcontrib><title>Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>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.</description><subject>Acids</subject><subject>Agricultural resources</subject><subject>Agricultural wastes</subject><subject>Agriculture</subject><subject>Analysis</subject><subject>Aroma</subject><subject>Biodegradation</subject><subject>Bioinformatics</subject><subject>Biological evolution</subject><subject>Biology and Life Sciences</subject><subject>Carbohydrates</subject><subject>Cellulose</subject><subject>Cladistic analysis</subject><subject>Cultivation</subject><subject>Degradation</subject><subject>Divergence</subject><subject>Enzymes</subject><subject>Evolution</subject><subject>Evolution (Biology)</subject><subject>Food science</subject><subject>Fungal Proteins - genetics</subject><subject>Fungi</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic research</subject><subject>Genome, Fungal</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Glucose</subject><subject>Gymnopus</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Laboratories</subject><subject>Lentinula edodes</subject><subject>Lignin</subject><subject>Lignin - genetics</subject><subject>Lignin - metabolism</subject><subject>Lignocellulose</subject><subject>Molecular biology</subject><subject>Mushrooms</subject><subject>Mycelia</subject><subject>Nucleotide sequence</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Physical Sciences</subject><subject>Plant sciences</subject><subject>Polysaccharides</subject><subject>Proteins</subject><subject>Research and Analysis Methods</subject><subject>Saccharides</subject><subject>Sawdust</subject><subject>Shiitake Mushrooms - genetics</subject><subject>Shiitake Mushrooms - growth & development</subject><subject>Shiitake Mushrooms - metabolism</subject><subject>Species</subject><subject>Straw</subject><subject>Transcription (Genetics)</subject><subject>White rot</subject><subject>White rot fungi</subject><subject>Wood</subject><subject>Wood waste</subject><subject>Wood 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Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation</title><author>Chen, Lianfu ; Gong, Yuhua ; Cai, Yingli ; Liu, Wei ; Zhou, Yan ; Xiao, Yang ; Xu, Zhangyi ; Liu, Yin ; Lei, Xiaoyu ; Wang, Gangzheng ; Guo, Mengpei ; Ma, Xiaolong ; Bian, Yinbing</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c626t-86395a5f1da2aeedfddbd6c62939c81f49a708fee0509f000ebef73a25801b6f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Acids</topic><topic>Agricultural resources</topic><topic>Agricultural wastes</topic><topic>Agriculture</topic><topic>Analysis</topic><topic>Aroma</topic><topic>Biodegradation</topic><topic>Bioinformatics</topic><topic>Biological evolution</topic><topic>Biology and Life Sciences</topic><topic>Carbohydrates</topic><topic>Cellulose</topic><topic>Cladistic 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Gangzheng</au><au>Guo, Mengpei</au><au>Ma, Xiaolong</au><au>Bian, Yinbing</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2016-08-08</date><risdate>2016</risdate><volume>11</volume><issue>8</issue><spage>e0160336</spage><epage>e0160336</epage><pages>e0160336-e0160336</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><notes>ObjectType-Article-1</notes><notes>SourceType-Scholarly Journals-1</notes><notes>ObjectType-Feature-2</notes><notes>content type line 23</notes><notes>Conceived and designed the experiments: YBB LFC YHG YLC.Performed the experiments: LFC YHG YLC.Analyzed the data: LFC.Contributed reagents/materials/analysis tools: LFC YHG YLC.Wrote the paper: YBB LFC YHG YLC WL YZ YX ZYX YL XYL GZW MPG XLM.Collected the strains: YX.</notes><notes>Competing Interests: The authors have declared that no competing interests exist.</notes><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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>27500531</pmid><doi>10.1371/journal.pone.0160336</doi><oa>free_for_read</oa></addata></record> |
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| recordid | cdi_plos_journals_1812534505 |
| source | Publicly Available Content Database; PubMed Central |
| subjects | Acids Agricultural resources Agricultural wastes Agriculture Analysis Aroma Biodegradation Bioinformatics Biological evolution Biology and Life Sciences Carbohydrates Cellulose Cladistic analysis Cultivation Degradation Divergence Enzymes Evolution Evolution (Biology) Food science Fungal Proteins - genetics Fungi Gene expression Genes Genetic aspects Genetic research Genome, Fungal Genomes Genomics Glucose Gymnopus High-Throughput Nucleotide Sequencing Laboratories Lentinula edodes Lignin Lignin - genetics Lignin - metabolism Lignocellulose Molecular biology Mushrooms Mycelia Nucleotide sequence Phylogenetics Phylogeny Physical Sciences Plant sciences Polysaccharides Proteins Research and Analysis Methods Saccharides Sawdust Shiitake Mushrooms - genetics Shiitake Mushrooms - growth & development Shiitake Mushrooms - metabolism Species Straw Transcription (Genetics) White rot White rot fungi Wood Wood waste Wood wastes |
| title | Genome Sequence of the Edible Cultivated Mushroom Lentinula edodes (Shiitake) Reveals Insights into Lignocellulose Degradation |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-09-21T17%3A14%3A04IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome%20Sequence%20of%20the%20Edible%20Cultivated%20Mushroom%20Lentinula%20edodes%20(Shiitake)%20Reveals%20Insights%20into%20Lignocellulose%20Degradation&rft.jtitle=PloS%20one&rft.au=Chen,%20Lianfu&rft.date=2016-08-08&rft.volume=11&rft.issue=8&rft.spage=e0160336&rft.epage=e0160336&rft.pages=e0160336-e0160336&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0160336&rft_dat=%3Cgale_plos_%3EA470631511%3C/gale_plos_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c626t-86395a5f1da2aeedfddbd6c62939c81f49a708fee0509f000ebef73a25801b6f3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=1812534505&rft_id=info:pmid/27500531&rft_galeid=A470631511&rfr_iscdi=true |