Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood
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{"title"=>"Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood", "type"=>"journal", "authors"=>[{"first_name"=>"Chiaki", "last_name"=>"Hori", "scopus_author_id"=>"25027341600"}, {"first_name"=>"Takuya", "last_name"=>"Ishida", "scopus_author_id"=>"7403961709"}, {"first_name"=>"Kiyohiko", "last_name"=>"Igarashi", "scopus_author_id"=>"7402350297"}, {"first_name"=>"Masahiro", "last_name"=>"Samejima", "scopus_author_id"=>"7006742999"}, {"first_name"=>"Hitoshi", "last_name"=>"Suzuki", "scopus_author_id"=>"56922377000"}, {"first_name"=>"Emma", "last_name"=>"Master", "scopus_author_id"=>"6506791831"}, {"first_name"=>"Patricia", "last_name"=>"Ferreira", "scopus_author_id"=>"36890069100"}, {"first_name"=>"Francisco J.", "last_name"=>"Ruiz-Dueñas", "scopus_author_id"=>"6602611442"}, {"first_name"=>"Benjamin", "last_name"=>"Held", "scopus_author_id"=>"7006004501"}, {"first_name"=>"Paulo", "last_name"=>"Canessa", "scopus_author_id"=>"16642213100"}, {"first_name"=>"Luis F.", "last_name"=>"Larrondo", "scopus_author_id"=>"6603826074"}, {"first_name"=>"Monika", "last_name"=>"Schmoll", "scopus_author_id"=>"6603571822"}, {"first_name"=>"Irina S.", "last_name"=>"Druzhinina", "scopus_author_id"=>"6603711142"}, {"first_name"=>"Christian P.", "last_name"=>"Kubicek", "scopus_author_id"=>"7007106343"}, {"first_name"=>"Jill A.", "last_name"=>"Gaskell", "scopus_author_id"=>"7003336912"}, {"first_name"=>"Phil", "last_name"=>"Kersten", "scopus_author_id"=>"7007160118"}, {"first_name"=>"Franz", "last_name"=>"St. John", "scopus_author_id"=>"25654094600"}, {"first_name"=>"Jeremy", "last_name"=>"Glasner", "scopus_author_id"=>"6603386759"}, {"first_name"=>"Grzegorz", "last_name"=>"Sabat", "scopus_author_id"=>"6507306356"}, {"first_name"=>"Sandra", "last_name"=>"Splinter BonDurant", "scopus_author_id"=>"35485802600"}, {"first_name"=>"Khajamohiddin", "last_name"=>"Syed", "scopus_author_id"=>"35729820500"}, {"first_name"=>"Jagjit", "last_name"=>"Yadav", "scopus_author_id"=>"55830656400"}, {"first_name"=>"Anthony C.", "last_name"=>"Mgbeahuruike", "scopus_author_id"=>"36971041400"}, {"first_name"=>"Andriy", "last_name"=>"Kovalchuk", "scopus_author_id"=>"24597960000"}, {"first_name"=>"Fred O.", "last_name"=>"Asiegbu", "scopus_author_id"=>"6701591434"}, {"first_name"=>"Gerald", "last_name"=>"Lackner", "scopus_author_id"=>"18434673700"}, {"first_name"=>"Dirk", "last_name"=>"Hoffmeister", "scopus_author_id"=>"7004681675"}, {"first_name"=>"Jorge", "last_name"=>"Rencoret", "scopus_author_id"=>"35272974100"}, {"first_name"=>"Ana", "last_name"=>"Gutiérrez", "scopus_author_id"=>"7202028857"}, {"first_name"=>"Hui", "last_name"=>"Sun", "scopus_author_id"=>"56258040400"}, {"first_name"=>"Erika", "last_name"=>"Lindquist", "scopus_author_id"=>"34571433600"}, {"first_name"=>"Kerrie", "last_name"=>"Barry", "scopus_author_id"=>"12791813200"}, {"first_name"=>"Robert", "last_name"=>"Riley", "scopus_author_id"=>"36524070500"}, {"first_name"=>"Igor V.", "last_name"=>"Grigoriev", "scopus_author_id"=>"25027225800"}, {"first_name"=>"Bernard", "last_name"=>"Henrissat", "scopus_author_id"=>"7005911606"}, {"first_name"=>"Ursula", "last_name"=>"Kües", "scopus_author_id"=>"56247644100"}, {"first_name"=>"Randy M.", "last_name"=>"Berka", "scopus_author_id"=>"7003766471"}, {"first_name"=>"Angel T.", "last_name"=>"Martínez", "scopus_author_id"=>"55622506400"}, {"first_name"=>"Sarah F.", "last_name"=>"Covert", "scopus_author_id"=>"7003836360"}, {"first_name"=>"Robert A.", "last_name"=>"Blanchette", "scopus_author_id"=>"7004254875"}, {"first_name"=>"Daniel", "last_name"=>"Cullen", "scopus_author_id"=>"7202109135"}], "year"=>2014, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"84919682712", "doi"=>"10.1371/journal.pgen.1004759", "scopus"=>"2-s2.0-84919682712", "pmid"=>"25474575", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "issn"=>"15537404", "pui"=>"601033607"}, "id"=>"04f724a8-dccb-3c97-be76-1b131577c2ac", "abstract"=>"Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea's extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes.", "link"=>"http://www.mendeley.com/research/analysis-phlebiopsis-gigantea-genome-transcriptome-secretome-provides-insight-pioneer-colonization-s", "reader_count"=>74, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Librarian"=>1, "Researcher"=>21, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>6, "Lecturer"=>2, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Librarian"=>1, "Researcher"=>21, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>23, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>1, "Student > Bachelor"=>6, "Lecturer"=>2, "Professor"=>3}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>60, "Chemical Engineering"=>1, "Chemistry"=>1, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>60}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>3}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "United States"=>3, "Taiwan"=>1, "Switzerland"=>1, "Germany"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1821782"], "description"=>"<p>CROs were distinguished as previously described <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759-VandenWymelenberg4\" target=\"_blank\">[76]</a>. Lytic polysaccharide monooxygenases were formerly classified as GH61 within the CAZy system (<a href=\"http://www.cazy.org/\" target=\"_blank\">http://www.cazy.org/</a>; <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759-Cantarel1\" target=\"_blank\">[16]</a>). Glycoside hydrolase family GH5 was subdivided as described <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759-Aspeborg1\" target=\"_blank\">[77]</a> (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s022\" target=\"_blank\">Figure S22</a>).</p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260323, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.g004", "stats"=>{"downloads"=>1, "page_views"=>38, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_genes_identified_in_white_rot_fungi_P_gigantea_Phlgi_P_chrysosporium_Phach_27_C_subvermispora_Cersu_22_and_H_annosum_Hetan_75_and_the_brown_rot_fungus_P_placenta_Pospl_45_/1260323", "title"=>"Number of genes identified in white rot fungi <i>P. gigantea</i> (Phlgi), <i>P. chrysosporium</i> (Phach)[27], <i>C. subvermispora</i> (Cersu)[22], and <i>H. annosum</i> (Hetan)[75], and the brown rot fungus <i>P. placenta</i> (Pospl)[45].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:08:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821819"], "description"=>"<p>Enzymes encoded by upregulated genes are black highlighted and associated with thickened arrows. Abbreviations: ABC-G1, ABC transporter associated with monoterpene tolerance; ADH/AO, Acyl-CoA dehydrogenase/oxidase; AH, Aconitate hydratase; CoA ligase, long fatty acid-CoA ligase; DLAT, Dihydrolipoyllysine-residue acetyltransferase; DLST, Dihydrolipoyllysine-residue succinyltransferase; EH, Enoyl-CoA hydratase; FDH, Formate dehydrogenase; FH, Fumarate hydratase; KT, Ketothiolase (acetyl-CoA C-acyltransferase); HAD, 3-Hydroxyacyl-CoA dehydrogenase; ICL, Isocitrate lyase; IDH, Isocitrate dehydrogenase; MDH, Malate dehydrogenase; MS, Malate synthase; ODH, Oxoglutarate dehydrogenase; OXA, Oxaloacetase; OXDC, Oxalate decarboxylase; OXO, Oxalate oxidase; PC, Pyruvate carboxylase; PDH, Pyruvate dehydrogenase; PEP, Phosphoenolpyruvate; PEPCK, Phosphoenolpyruvate carboxykinase; PEPK, Phosphoenolpyruvate kinase; SDH, succinate dehydrogenase. See <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s059\" target=\"_blank\">Dataset S2</a> for detailed gene expression data.</p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260358, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.g009", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Glyoxalate_shunt_and_proposed_relationship_to_lipid_oxidation_when_P_gigantea_is_cultivated_on_wood_containing_media_ELP_or_NELP_relative_to_Glc_medium_/1260358", "title"=>"Glyoxalate shunt and proposed relationship to lipid oxidation when <i>P. gigantea</i> is cultivated on wood-containing media (ELP or NELP) relative to Glc medium.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:08:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821785"], "description"=>"<p>Scatterplots show the distribution of RNA-seq RPKM values (log<sub>2</sub>) for 11,376 <i>P. gigantea</i> genes when grown on basal salts containing A, acetone-extracted loblolly pine wood (ELP) or B, non-extracted loblolly pine wood (NELP) relative to glucose (Glc). Plot lines define 2-fold borders and best fit regression. Darkened points represent 164 (A) and 145 (B) transcripts accumulating>4-fold at p<0.01. Venn diagram (C) illustrates genes with RPKM signals>10 and upregulated>4-fold in NELP or ELP relative to Glc.</p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260326, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.g005", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_P_gigantea_transcriptome_/1260326", "title"=>"<i>P. gigantea</i> transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:08:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821787"], "description"=>"<p>The number of genes encoding mass spectrometry-identified proteins was limited to those matching≥2 unique peptides after 5–9 days growth in media containing NELP or ELP. RPKM values>100 for RNA derived from these cultures were arbitrarily selected as the threshold for high transcript levels. Genes designated as ‘regulated’ showed significant accumulation (p<0.05;>2-fold) in NELP or ELP relative to glucose containing media. Methods and complete data are presented in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s057\" target=\"_blank\">Text S1</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s059\" target=\"_blank\">Dataset S2</a>.</p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260328, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.g006", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_and_expression_of_genes_likely_involved_in_lignocellulose_degradation_/1260328", "title"=>"Number and expression of genes likely involved in lignocellulose degradation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:08:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821821"], "description"=>"<p>Differentially regulated genes in media containing non-extracted loblolly pine wood (NELP), solvent extracted loblolly pine wood (ELP), or glucose (Glc) as sole carbon source.</p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260361, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.t001", "stats"=>{"downloads"=>3, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differentially_regulated_genes_in_media_containing_non_extracted_loblolly_pine_wood_NELP_solvent_extracted_loblolly_pine_wood_ELP_or_glucose_Glc_as_sole_carbon_source_/1260361", "title"=>"Differentially regulated genes in media containing non-extracted loblolly pine wood (NELP), solvent extracted loblolly pine wood (ELP), or glucose (Glc) as sole carbon source.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-04 03:08:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821822"], "description"=>"<p>Transcripts accumulating>4-fold in non-extracted loblolly pine wood (NELP) relative to extracted loblolly pine wood (ELP).<sup><a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#nt105\" target=\"_blank\">1</a></sup></p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260362, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.t002", "stats"=>{"downloads"=>7, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcripts_accumulating_4_fold_in_non_extracted_loblolly_pine_wood_NELP_relative_to_extracted_loblolly_pine_wood_ELP_1_/1260362", "title"=>"Transcripts accumulating>4-fold in non-extracted loblolly pine wood (NELP) relative to extracted loblolly pine wood (ELP).<sup>1</sup>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-04 03:08:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821825"], "description"=>"<p>Genes encoding LC-MS/MS detected proteins and exhibiting>2-fold regulation in comparisons of NELP and ELP cultures.<sup><a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#nt108\" target=\"_blank\">1</a></sup></p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260365, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.t003", "stats"=>{"downloads"=>4, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_encoding_LC_MS_MS_detected_proteins_and_exhibiting_2_fold_regulation_in_comparisons_of_NELP_and_ELP_cultures_1_/1260365", "title"=>"Genes encoding LC-MS/MS detected proteins and exhibiting>2-fold regulation in comparisons of NELP and ELP cultures.<sup>1</sup>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-04 03:08:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821792"], "description"=>"<p>Scatterplot (A) shows the distribution of RNA-seq RPKM values (log<sub>2</sub>) for 11,376 <i>P. gigantea</i> genes when grown on basal salts containing acetone-extracted loblolly pine wood (ELP) or non-extracted loblolly pine wood (NELP). Lines define 2-fold borders and best fit regression. Darkened points represent 44 transcripts accumulating>4-fold at p<0.01. Venn diagram (B) illustrates genes with RPKM signals>10 and upregulated>4-fold in NELP relative to ELP. Twenty-two genes showed significant transcript accumulation in NELP relative to ELP suggesting potential response to resin and pitch content. Under these stringent thresholds (p<0.01;>4-fold), only one gene, a MCO model Phlgi1_129839, showed significant transcript accumulation in ELP relative to NELP. Additional detail appears in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen-1004759-t001\" target=\"_blank\">Tables 1</a>-<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen-1004759-t003\" target=\"_blank\">3</a>. Detailed methods and complete data are presented in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s057\" target=\"_blank\">Text S1</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s059\" target=\"_blank\">Dataset S2</a>.</p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260333, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.g007", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_P_gigantea_transcriptome_/1260333", "title"=>"<i>P. gigantea</i> transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:08:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821765"], "description"=>"<p>(A) Principal component analysis (PCA) of 21 fungi using 73 CAZy and 12 AA families (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s058\" target=\"_blank\">Dataset S1</a>). GMC oxidoreductases methanol oxidase, glucose oxidase and aryl alcohol oxidase were excluded because confident functional assignments could not be made and/or their inclusion did not contribute to separation of white- and brown-rot species. (B) PCA of 21 fungi using genes encoding 14 enzymes involved in lipid metabolism (KEGG reference pathway 00071, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s058\" target=\"_blank\">Dataset S1</a>). There is no significant segregation of white-rot and brown-rot fungi although <i>P. gigantea</i> was positioned in the third quadrant with <i>B. adusta</i> and <i>P. carnosa</i>. Symbols for white rot and brown rot fungi appear in blue and red, respectively. <i>Tremella mesenterica</i> is a mycoparasite. For raw data and contributions of the top 20 families see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s058\" target=\"_blank\">Dataset S1</a>, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s057\" target=\"_blank\">Text S1</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s002\" target=\"_blank\">Figures S2</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s003\" target=\"_blank\">S3</a>.</p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260306, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.g003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_analysis_of_gene_repertoires_associated_with_degradation_of_plant_cell_wall_polymers_and_extractives_in_21_fungal_genomes_/1260306", "title"=>"Comparative analysis of gene repertoires associated with degradation of plant cell wall polymers and extractives in 21 fungal genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:08:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821799"], "description"=>"<p>Proteins (upper panel) and transcripts (lower panel) were identified by LC-MS/MS and RNA-seq, respectively. Protein identification was limited to those with>2 unique peptides after five days incubation. Transcript upregulation was limited to significant accumulation (p<0.05;>2-fold) on NELP or ELP relative to glucose-containing medium. Secretome and transcriptome experimental details and complete data are presented in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s057\" target=\"_blank\">Text S1</a> and <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s059\" target=\"_blank\">Dataset S2</a>.</p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260340, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.g008", "stats"=>{"downloads"=>3, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Glycoside_hydrolase_encoding_genes_show_similar_patterns_of_expression_in_media_containing_freshly_ground_and_non_extracted_loblolly_pine_wood_NELP_relative_to_the_same_substrate_but_extracted_with_acetone_ELP_to_remove_pitch_and_resins_/1260340", "title"=>"Glycoside hydrolase encoding genes show similar patterns of expression in media containing freshly ground and non-extracted loblolly pine wood (NELP) relative to the same substrate but extracted with acetone (ELP) to remove pitch and resins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:08:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1824660", "https://ndownloader.figshare.com/files/1824661", "https://ndownloader.figshare.com/files/1824662", "https://ndownloader.figshare.com/files/1824663", "https://ndownloader.figshare.com/files/1824664", "https://ndownloader.figshare.com/files/1824665", "https://ndownloader.figshare.com/files/1824666", "https://ndownloader.figshare.com/files/1824667", "https://ndownloader.figshare.com/files/1824668", "https://ndownloader.figshare.com/files/1824669", "https://ndownloader.figshare.com/files/1824670", "https://ndownloader.figshare.com/files/1824671", "https://ndownloader.figshare.com/files/1824672", "https://ndownloader.figshare.com/files/1824673", "https://ndownloader.figshare.com/files/1824674", "https://ndownloader.figshare.com/files/1824675", "https://ndownloader.figshare.com/files/1824676", "https://ndownloader.figshare.com/files/1824677", "https://ndownloader.figshare.com/files/1824678", "https://ndownloader.figshare.com/files/1824679", "https://ndownloader.figshare.com/files/1824680", "https://ndownloader.figshare.com/files/1824681", "https://ndownloader.figshare.com/files/1824682", "https://ndownloader.figshare.com/files/1824683", "https://ndownloader.figshare.com/files/1824684", "https://ndownloader.figshare.com/files/1824685", "https://ndownloader.figshare.com/files/1824686", "https://ndownloader.figshare.com/files/1824687", "https://ndownloader.figshare.com/files/1824688", "https://ndownloader.figshare.com/files/1824689", "https://ndownloader.figshare.com/files/1824690", "https://ndownloader.figshare.com/files/1824691", "https://ndownloader.figshare.com/files/1824692", "https://ndownloader.figshare.com/files/1824693", "https://ndownloader.figshare.com/files/1824694", "https://ndownloader.figshare.com/files/1824695", "https://ndownloader.figshare.com/files/1824696", "https://ndownloader.figshare.com/files/1824697", "https://ndownloader.figshare.com/files/1824698", "https://ndownloader.figshare.com/files/1824699", "https://ndownloader.figshare.com/files/1824700", "https://ndownloader.figshare.com/files/1824701", "https://ndownloader.figshare.com/files/1824702", "https://ndownloader.figshare.com/files/1824703", "https://ndownloader.figshare.com/files/1824704", "https://ndownloader.figshare.com/files/1824705", "https://ndownloader.figshare.com/files/1824706", "https://ndownloader.figshare.com/files/1824708", "https://ndownloader.figshare.com/files/1824709", "https://ndownloader.figshare.com/files/1824710", "https://ndownloader.figshare.com/files/1824711", "https://ndownloader.figshare.com/files/1824712", "https://ndownloader.figshare.com/files/1824714", "https://ndownloader.figshare.com/files/1824715", "https://ndownloader.figshare.com/files/1824716", "https://ndownloader.figshare.com/files/1824717", "https://ndownloader.figshare.com/files/1824718", "https://ndownloader.figshare.com/files/1824719", "https://ndownloader.figshare.com/files/1824720"], "description"=>"<div><p>Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by <i>Phlebiopsis gigantea</i>, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which <i>P. gigantea</i> tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated <i>P. gigantea</i> genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The <i>P. gigantea</i> genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in <i>P. gigantea</i>'s extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes.</p></div>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1261590, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004759.s001", "https://dx.doi.org/10.1371/journal.pgen.1004759.s002", "https://dx.doi.org/10.1371/journal.pgen.1004759.s003", "https://dx.doi.org/10.1371/journal.pgen.1004759.s004", "https://dx.doi.org/10.1371/journal.pgen.1004759.s005", "https://dx.doi.org/10.1371/journal.pgen.1004759.s006", "https://dx.doi.org/10.1371/journal.pgen.1004759.s007", "https://dx.doi.org/10.1371/journal.pgen.1004759.s008", "https://dx.doi.org/10.1371/journal.pgen.1004759.s009", "https://dx.doi.org/10.1371/journal.pgen.1004759.s010", "https://dx.doi.org/10.1371/journal.pgen.1004759.s011", "https://dx.doi.org/10.1371/journal.pgen.1004759.s012", "https://dx.doi.org/10.1371/journal.pgen.1004759.s013", "https://dx.doi.org/10.1371/journal.pgen.1004759.s014", "https://dx.doi.org/10.1371/journal.pgen.1004759.s015", "https://dx.doi.org/10.1371/journal.pgen.1004759.s016", "https://dx.doi.org/10.1371/journal.pgen.1004759.s017", "https://dx.doi.org/10.1371/journal.pgen.1004759.s018", "https://dx.doi.org/10.1371/journal.pgen.1004759.s019", "https://dx.doi.org/10.1371/journal.pgen.1004759.s020", "https://dx.doi.org/10.1371/journal.pgen.1004759.s021", "https://dx.doi.org/10.1371/journal.pgen.1004759.s022", "https://dx.doi.org/10.1371/journal.pgen.1004759.s023", "https://dx.doi.org/10.1371/journal.pgen.1004759.s024", "https://dx.doi.org/10.1371/journal.pgen.1004759.s025", "https://dx.doi.org/10.1371/journal.pgen.1004759.s026", "https://dx.doi.org/10.1371/journal.pgen.1004759.s027", "https://dx.doi.org/10.1371/journal.pgen.1004759.s028", "https://dx.doi.org/10.1371/journal.pgen.1004759.s029", "https://dx.doi.org/10.1371/journal.pgen.1004759.s030", "https://dx.doi.org/10.1371/journal.pgen.1004759.s031", "https://dx.doi.org/10.1371/journal.pgen.1004759.s032", "https://dx.doi.org/10.1371/journal.pgen.1004759.s033", "https://dx.doi.org/10.1371/journal.pgen.1004759.s034", "https://dx.doi.org/10.1371/journal.pgen.1004759.s035", "https://dx.doi.org/10.1371/journal.pgen.1004759.s036", "https://dx.doi.org/10.1371/journal.pgen.1004759.s037", "https://dx.doi.org/10.1371/journal.pgen.1004759.s038", "https://dx.doi.org/10.1371/journal.pgen.1004759.s039", "https://dx.doi.org/10.1371/journal.pgen.1004759.s040", "https://dx.doi.org/10.1371/journal.pgen.1004759.s041", "https://dx.doi.org/10.1371/journal.pgen.1004759.s042", "https://dx.doi.org/10.1371/journal.pgen.1004759.s043", "https://dx.doi.org/10.1371/journal.pgen.1004759.s044", "https://dx.doi.org/10.1371/journal.pgen.1004759.s045", "https://dx.doi.org/10.1371/journal.pgen.1004759.s046", "https://dx.doi.org/10.1371/journal.pgen.1004759.s047", "https://dx.doi.org/10.1371/journal.pgen.1004759.s048", "https://dx.doi.org/10.1371/journal.pgen.1004759.s049", "https://dx.doi.org/10.1371/journal.pgen.1004759.s050", "https://dx.doi.org/10.1371/journal.pgen.1004759.s051", "https://dx.doi.org/10.1371/journal.pgen.1004759.s052", "https://dx.doi.org/10.1371/journal.pgen.1004759.s053", "https://dx.doi.org/10.1371/journal.pgen.1004759.s054", "https://dx.doi.org/10.1371/journal.pgen.1004759.s055", "https://dx.doi.org/10.1371/journal.pgen.1004759.s056", "https://dx.doi.org/10.1371/journal.pgen.1004759.s057", "https://dx.doi.org/10.1371/journal.pgen.1004759.s058", "https://dx.doi.org/10.1371/journal.pgen.1004759.s059"], "stats"=>{"downloads"=>265, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Analysis_of_the_Phlebiopsis_gigantea_Genome_Transcriptome_and_Secretome_Provides_Insight_into_Its_Pioneer_Colonization_Strategies_of_Wood/1261590", "title"=>"Analysis of the <i>Phlebiopsis gigantea</i> Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-12-04 14:57:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821753"], "description"=>"<p>Comparative weight loss of parental strain 11061 and single basidiospore derivatives on colonized loblolly pine wood (<i>Pinus taeda</i>) wood wafers were determined after 4, 8 and 12 weeks incubation (bottom left panel) as described in Methods. Single basidiospore strain 5–6 also aggressively decayed birch and spruce (<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759.s057\" target=\"_blank\">Text S1</a>) and was selected for sequencing. Upper panels show scanning electron microscopy <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004759#pgen.1004759-Blanchette2\" target=\"_blank\">[68]</a> of radial (left) and transverse (right) sections of pine wood tracheids that were substantially eroded or completely degraded by <i>P. gigantea</i> strain 5–6 by week twelve. Transverse section of sound wood (bottom photo) provides comparison. (Bar  = 40 µm).</p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260297, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Wood_decay_characteristics_/1260297", "title"=>"Wood decay characteristics.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:08:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821713"], "description"=>"<p>Panel A: The extractives (long chain fatty acids, triglycerides, resin acids and terpenes) are found primarily in the resin ducts, but damage to pine wood causes the release of these compounds across wounded areas. Panel B: In tracheid cell walls, the amorphous, phenylpropanoid polymer lignin (brown) form a matrix around the more structured carbohydrate polymers, hemicellulose (yellow and green) and cellulose (blue).</p>", "links"=>[], "tags"=>["Phlebiopsis gigantea Genome", "wood cell walls", "gigantea genome", "gene", "carbon cycling processes", "extractive", "Secretome Provides Insight", "abc", "metabolizes resinous compounds", "Pioneer Colonization Strategies"], "article_id"=>1260280, "categories"=>["Biological Sciences"], "users"=>["Chiaki Hori", "Takuya Ishida", "Kiyohiko Igarashi", "Masahiro Samejima", "Hitoshi Suzuki", "Emma Master", "Patricia Ferreira", "Francisco J. Ruiz-Dueñas", "Benjamin Held", "Paulo Canessa", "Luis F. Larrondo", "Monika Schmoll", "Irina S. Druzhinina", "Christian P. Kubicek", "Jill A. Gaskell", "Phil Kersten", "Franz St. John", "Jeremy Glasner", "Grzegorz Sabat", "Sandra Splinter BonDurant", "Khajamohiddin Syed", "Jagjit Yadav", "Anthony C. Mgbeahuruike", "Andriy Kovalchuk", "Fred O. Asiegbu", "Gerald Lackner", "Dirk Hoffmeister", "Jorge Rencoret", "Ana Gutierrez", "Hui Sun", "Erika Lindquist", "Kerrie Barry", "Robert Riley", "Igor V. Grigoriev", "Bernard Henrissat", "Ursula Kües", "Randy M. Berka", "Angel T. Martínez", "Sarah F. Covert", "Robert A. Blanchette", "Daniel Cullen"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004759.g001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representations_of_lignocellulose_components_in_cell_walls_of_pine_wood_/1260280", "title"=>"Schematic representations of lignocellulose components in cell walls of pine wood.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:08:44"}

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Relative Metric

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