Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies
Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We...
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| Veröffentlicht in: | Genome biology and evolution 2018-12, Vol.10 (12), p.3250-3261 |
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| creator | Wu, Baojun Xu, Zhangyi Knudson, Alicia Carlson, Alexis Chen, Naiyao Kovaka, Sam LaButti, Kurt Lipzen, Anna Pennachio, Christa Riley, Robert Schakwitz, Wendy Umezawa, Kiwamu Ohm, Robin A Grigoriev, Igor V Nagy, László G Gibbons, John Hibbett, David |
| description | Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53-39.88 Mb, with 15,581-15,380 genes, respectively). We mated the Sec and Aga monokaryons, genotyped the progeny, and performed bulked segregant analysis (BSA). We also fruited three Sec/Sec and three Aga/Aga dikaryons, and sampled transcriptomes at four developmental stages. Using BSA, we identified 105 top candidate genes with nonsynonymous SNPs that cosegregate with fruiting body phenotype. Transcriptome analyses of Sec/Sec versus Aga/Aga dikaryons identified 907 differentially expressed genes (DEGs) along four developmental stages. On the basis of BSA and DEGs, the top 25 candidate genes related to fruiting body development span 1.5 Mb (4% of the genome), possibly on a single chromosome, although the precise locus that controls the secotioid phenotype is unresolved. The top candidates include genes encoding a cytochrome P450 and an ATP-dependent RNA helicase, which may play a role in development, based on studies in other fungi. |
| doi_str_mv | 10.1093/gbe/evy246 |
| format | Article |
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Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53-39.88 Mb, with 15,581-15,380 genes, respectively). We mated the Sec and Aga monokaryons, genotyped the progeny, and performed bulked segregant analysis (BSA). We also fruited three Sec/Sec and three Aga/Aga dikaryons, and sampled transcriptomes at four developmental stages. Using BSA, we identified 105 top candidate genes with nonsynonymous SNPs that cosegregate with fruiting body phenotype. Transcriptome analyses of Sec/Sec versus Aga/Aga dikaryons identified 907 differentially expressed genes (DEGs) along four developmental stages. On the basis of BSA and DEGs, the top 25 candidate genes related to fruiting body development span 1.5 Mb (4% of the genome), possibly on a single chromosome, although the precise locus that controls the secotioid phenotype is unresolved. The top candidates include genes encoding a cytochrome P450 and an ATP-dependent RNA helicase, which may play a role in development, based on studies in other fungi.</description><identifier>ISSN: 1759-6653</identifier><identifier>EISSN: 1759-6653</identifier><identifier>DOI: 10.1093/gbe/evy246</identifier><identifier>PMID: 30398645</identifier><language>eng</language><publisher>England: Society for Molecular Biology and Evolution</publisher><subject>BASIC BIOLOGICAL SCIENCES ; basidiomycetes ; Biological Evolution ; bulked segregant analysis ; development ; Fruiting Bodies, Fungal - genetics ; Fruiting Bodies, Fungal - growth & development ; Fruiting Bodies, Fungal - metabolism ; fungi ; gasteromycetes ; Gene Expression ; Gene Expression Profiling ; Genome Report ; Genome, Fungal ; Lentinula - genetics ; Lentinula - growth & development ; Lentinula - metabolism ; Phenotype ; Polymorphism, Single Nucleotide ; transcriptome ; Whole Genome Sequencing</subject><ispartof>Genome biology and evolution, 2018-12, Vol.10 (12), p.3250-3261</ispartof><rights>The Author(s) 2018. 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The top candidates include genes encoding a cytochrome P450 and an ATP-dependent RNA helicase, which may play a role in development, based on studies in other fungi.</description><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>basidiomycetes</subject><subject>Biological Evolution</subject><subject>bulked segregant analysis</subject><subject>development</subject><subject>Fruiting Bodies, Fungal - genetics</subject><subject>Fruiting Bodies, Fungal - growth & development</subject><subject>Fruiting Bodies, Fungal - metabolism</subject><subject>fungi</subject><subject>gasteromycetes</subject><subject>Gene Expression</subject><subject>Gene Expression Profiling</subject><subject>Genome Report</subject><subject>Genome, Fungal</subject><subject>Lentinula - genetics</subject><subject>Lentinula - growth & development</subject><subject>Lentinula - metabolism</subject><subject>Phenotype</subject><subject>Polymorphism, Single Nucleotide</subject><subject>transcriptome</subject><subject>Whole Genome Sequencing</subject><issn>1759-6653</issn><issn>1759-6653</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpVkU2LFDEQhoMo7ode_AESPInQbtLpTiYehHXHXYURQZQ9hnRSPR3pTtokPTL_fjPMuqyXqoJ6eOvjRegVJe8pkexi28EF7PZ1w5-gUypaWXHesqeP6hN0ltJvQjhvOHuOThhhcsWb9hTNN-DD5EzC2lu8hh2MYZ7AZxx6vCnZ-SXh7LbxUHzAl_h2cBmqHyHj2xBstQaj985v8bclDTGECf91ecBrN4U4D87g67i4fAA-BesgvUDPej0meHmfz9Gv688_r75Um-83X68uN5VhXOYSa2mEFsJaKqSwVBPKNe9XFKy1KyIN01xS0HVHpeZGsK6nRJhOQM1XPbBz9PGoOy_dBNaUU6Ie1RzdpONeBe3U_x3vBrUNO8UZaetGFIE3R4GQslPJlKvNYIL3YLKibcN5LQv09n5KDH8WSFlNLhkYR-0hLEnVtLyaNIwf9N4dURNDShH6h10oUQcfVfFRHX0s8OvH2z-g_4xjd2mSnE0</recordid><startdate>20181201</startdate><enddate>20181201</enddate><creator>Wu, Baojun</creator><creator>Xu, Zhangyi</creator><creator>Knudson, Alicia</creator><creator>Carlson, Alexis</creator><creator>Chen, Naiyao</creator><creator>Kovaka, Sam</creator><creator>LaButti, Kurt</creator><creator>Lipzen, Anna</creator><creator>Pennachio, Christa</creator><creator>Riley, Robert</creator><creator>Schakwitz, Wendy</creator><creator>Umezawa, Kiwamu</creator><creator>Ohm, Robin A</creator><creator>Grigoriev, Igor V</creator><creator>Nagy, László G</creator><creator>Gibbons, John</creator><creator>Hibbett, David</creator><general>Society for Molecular Biology and Evolution</general><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>OIOZB</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>20181201</creationdate><title>Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies</title><author>Wu, Baojun ; Xu, Zhangyi ; Knudson, Alicia ; Carlson, Alexis ; Chen, Naiyao ; Kovaka, Sam ; LaButti, Kurt ; Lipzen, Anna ; Pennachio, Christa ; Riley, Robert ; Schakwitz, Wendy ; Umezawa, Kiwamu ; Ohm, Robin A ; Grigoriev, Igor V ; Nagy, László G ; Gibbons, John ; Hibbett, David</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c369t-c329c7a77dd1797d1a016a6f81eddd809c3a691ea2b19a6c73bf107cb7e268fe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>basidiomycetes</topic><topic>Biological Evolution</topic><topic>bulked segregant analysis</topic><topic>development</topic><topic>Fruiting Bodies, Fungal - genetics</topic><topic>Fruiting Bodies, Fungal - growth & development</topic><topic>Fruiting Bodies, Fungal - metabolism</topic><topic>fungi</topic><topic>gasteromycetes</topic><topic>Gene Expression</topic><topic>Gene Expression Profiling</topic><topic>Genome Report</topic><topic>Genome, Fungal</topic><topic>Lentinula - genetics</topic><topic>Lentinula - growth & development</topic><topic>Lentinula - metabolism</topic><topic>Phenotype</topic><topic>Polymorphism, Single Nucleotide</topic><topic>transcriptome</topic><topic>Whole Genome Sequencing</topic><toplevel>online_resources</toplevel><creatorcontrib>Wu, Baojun</creatorcontrib><creatorcontrib>Xu, Zhangyi</creatorcontrib><creatorcontrib>Knudson, Alicia</creatorcontrib><creatorcontrib>Carlson, Alexis</creatorcontrib><creatorcontrib>Chen, Naiyao</creatorcontrib><creatorcontrib>Kovaka, Sam</creatorcontrib><creatorcontrib>LaButti, Kurt</creatorcontrib><creatorcontrib>Lipzen, Anna</creatorcontrib><creatorcontrib>Pennachio, Christa</creatorcontrib><creatorcontrib>Riley, Robert</creatorcontrib><creatorcontrib>Schakwitz, Wendy</creatorcontrib><creatorcontrib>Umezawa, Kiwamu</creatorcontrib><creatorcontrib>Ohm, Robin A</creatorcontrib><creatorcontrib>Grigoriev, Igor V</creatorcontrib><creatorcontrib>Nagy, László G</creatorcontrib><creatorcontrib>Gibbons, John</creatorcontrib><creatorcontrib>Hibbett, David</creatorcontrib><creatorcontrib>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genome biology and evolution</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wu, Baojun</au><au>Xu, Zhangyi</au><au>Knudson, Alicia</au><au>Carlson, Alexis</au><au>Chen, Naiyao</au><au>Kovaka, Sam</au><au>LaButti, Kurt</au><au>Lipzen, Anna</au><au>Pennachio, Christa</au><au>Riley, Robert</au><au>Schakwitz, Wendy</au><au>Umezawa, Kiwamu</au><au>Ohm, Robin A</au><au>Grigoriev, Igor V</au><au>Nagy, László G</au><au>Gibbons, John</au><au>Hibbett, David</au><au>Katz, Laura</au><aucorp>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies</atitle><jtitle>Genome biology and evolution</jtitle><addtitle>Genome Biol Evol</addtitle><date>2018-12-01</date><risdate>2018</risdate><volume>10</volume><issue>12</issue><spage>3250</spage><epage>3261</epage><pages>3250-3261</pages><issn>1759-6653</issn><eissn>1759-6653</eissn><abstract>Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53-39.88 Mb, with 15,581-15,380 genes, respectively). We mated the Sec and Aga monokaryons, genotyped the progeny, and performed bulked segregant analysis (BSA). We also fruited three Sec/Sec and three Aga/Aga dikaryons, and sampled transcriptomes at four developmental stages. Using BSA, we identified 105 top candidate genes with nonsynonymous SNPs that cosegregate with fruiting body phenotype. Transcriptome analyses of Sec/Sec versus Aga/Aga dikaryons identified 907 differentially expressed genes (DEGs) along four developmental stages. On the basis of BSA and DEGs, the top 25 candidate genes related to fruiting body development span 1.5 Mb (4% of the genome), possibly on a single chromosome, although the precise locus that controls the secotioid phenotype is unresolved. The top candidates include genes encoding a cytochrome P450 and an ATP-dependent RNA helicase, which may play a role in development, based on studies in other fungi.</abstract><cop>England</cop><pub>Society for Molecular Biology and Evolution</pub><pmid>30398645</pmid><doi>10.1093/gbe/evy246</doi><tpages>12</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | BASIC BIOLOGICAL SCIENCES basidiomycetes Biological Evolution bulked segregant analysis development Fruiting Bodies, Fungal - genetics Fruiting Bodies, Fungal - growth & development Fruiting Bodies, Fungal - metabolism fungi gasteromycetes Gene Expression Gene Expression Profiling Genome Report Genome, Fungal Lentinula - genetics Lentinula - growth & development Lentinula - metabolism Phenotype Polymorphism, Single Nucleotide transcriptome Whole Genome Sequencing |
| title | Genomics and Development of Lentinus tigrinus: A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies |
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