Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data
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{"title"=>"Tasting soil fungal diversity with earth tongues: Phylogenetic test of SATé alignments for environmental ITS data", "type"=>"journal", "authors"=>[{"first_name"=>"Zheng", "last_name"=>"Wang", "scopus_author_id"=>"57192974403"}, {"first_name"=>"R. Henrik", "last_name"=>"Nilsson", "scopus_author_id"=>"26647760100"}, {"first_name"=>"Francesc", "last_name"=>"Lopez-Giraldez", "scopus_author_id"=>"8730232400"}, {"first_name"=>"Wen ying", "last_name"=>"Zhuang", "scopus_author_id"=>"55665799600"}, {"first_name"=>"Yu cheng", "last_name"=>"Dai", "scopus_author_id"=>"56010602400"}, {"first_name"=>"Peter R.", "last_name"=>"Johnston", "scopus_author_id"=>"57201399362"}, {"first_name"=>"Jeffrey P.", "last_name"=>"Townsend", "scopus_author_id"=>"7202641882"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-79955456045", "doi"=>"10.1371/journal.pone.0019039", "sgr"=>"79955456045", "isbn"=>"1932-6203", "pmid"=>"21533038", "issn"=>"19326203", "pui"=>"361676529"}, "id"=>"18f6bc4d-5bec-38bf-bc8b-2bf101ee4309", "abstract"=>"An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes), a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficiently identified ITS sequences from the public sequence databases were assigned to the Geoglossomycetes. The association between earth tongues and plants has been hypothesized for a long time, but hard evidence is yet to be collected. The ITS phylogeny showed that four ectomycorrhizal isolates shared a clade with Geoglossum but not with Trichoglossum earth tongues, pointing to the significant potential inherent to ecological data mining of environmental samples. Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit.", "link"=>"http://www.mendeley.com/research/tasting-soil-fungal-diversity-earth-tongues-phylogenetic-test-sat%C3%A9-alignments-environmental-data", "reader_count"=>75, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>9, "Librarian"=>1, "Researcher"=>19, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>5, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>3, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>9, "Librarian"=>1, "Researcher"=>19, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>5, "Student > Master"=>6, "Other"=>1, "Student > Bachelor"=>3, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>58, "Arts and Humanities"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Social Sciences"=>{"Social Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>58}, "Computer Science"=>{"Computer Science"=>1}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>5}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Sweden"=>2, "United States"=>5, "Italy"=>1, "Mexico"=>2, "South Africa"=>1, "France"=>1, "Spain"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/781332"], "description"=>"<p>Bayesian posterior probabilities higher than 0.94 are indicated with bold branches. Taxonomic groups were coded with colors and initials of the classes. Examples of ascoma morphology and habits of the earth tongues; photo credits and courtesy of: Clive Shirley (<i>Geoglossum glutinosum</i>), Thomas Læssøe (<i>Sarcoleotia globosa</i>), Andrus Votik (<i>Thuemenidium arenarium</i>), and Mark Steinmetz (<i>Trichoglossum hirsutum</i>). Environmental ITS sequences grouped in the earth tongue clades are marked with one or more annotations indicating whether the isolate would be designated an earth tongue by other approaches. Affinity of marked isolates to the earth tongues was suggested by: * the sequence search suite <i>emerencia</i>; & BLAST of known earth-tongue ITS sequence against INSD; and by # annotation in INSD as unclassified Pezizomycotina environmental samples. Newly generated sequences for this study are presented as taxa without INSD accession numbers while download sequences are listed with their INSD accession numbers.</p>", "links"=>[], "tags"=>["generated", "mrbayes", "clustal"], "article_id"=>451700, "categories"=>["Biological Sciences", "Ecology", "Microbiology"], "users"=>["Zheng Wang", "R. Henrik Nilsson", "Francesc López-Giráldez", "Wen-Ying Zhuang", "Yu-cheng Dai", "Peter R. Johnston", "Jeffrey P. Townsend"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019039.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_best_tree_generated_by_MrBayes_for_the_whole_ITS_Clustal_W_alignment_/451700", "title"=>"The best tree generated by MrBayes for the whole ITS Clustal W alignment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-21 00:28:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/781735"], "description"=>"<p>BPP higher than 0.94 are indicated with bold branches. Taxonomic groups were coded with colors and initials of the classes. Environmental ITS sequences grouped in the earth tongue clades are marked with one or more annotations indicating whether the isolate would be designated an earth tongue by other approaches. Affinity of marked isolates to the earth tongues was suggested by: * the sequence search suite <i>emerencia</i>; & BLAST of known earth-tongue ITS sequence against INSD; and by # annotation in INSD as unclassified Pezizomycotina environmental samples. Newly generated sequences for this study are presented as taxa without INSD accession numbers while download sequences are listed with their INSD accession numbers.</p>", "links"=>[], "tags"=>["generated", "mrbayes", "re-included", "alignment"], "article_id"=>452101, "categories"=>["Biological Sciences", "Ecology", "Microbiology"], "users"=>["Zheng Wang", "R. Henrik Nilsson", "Francesc López-Giráldez", "Wen-Ying Zhuang", "Yu-cheng Dai", "Peter R. Johnston", "Jeffrey P. Townsend"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019039.g005", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_best_tree_generated_by_MrBayes_for_the_5_8S_re_included_SAT_233_alignment_of_the_large_data_set_/452101", "title"=>"The best tree generated by MrBayes for the 5.8S re-included SATé alignment of the large data set.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-21 00:35:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/392205", "https://ndownloader.figshare.com/files/392249", "https://ndownloader.figshare.com/files/392292", "https://ndownloader.figshare.com/files/392350", "https://ndownloader.figshare.com/files/392512", "https://ndownloader.figshare.com/files/392668", "https://ndownloader.figshare.com/files/392876", "https://ndownloader.figshare.com/files/393090"], "description"=>"<div><p>An abundance of novel fungal lineages have been indicated by DNA sequencing of the nuclear ribosomal ITS region from environmental samples such as soil and wood. Although phylogenetic analysis of these novel lineages is a key component of unveiling the structure and diversity of complex communities, such analyses are rare for environmental ITS data due to the difficulties of aligning this locus across significantly divergent taxa. One potential approach to this issue is simultaneous alignment and tree estimation. We targeted divergent ITS sequences of the earth tongue fungi (Geoglossomycetes), a basal class in the Ascomycota, to assess the performance of SATé, recent software that combines progressive alignment and tree building. We found that SATé performed well in generating high-quality alignments and in accurately estimating the phylogeny of earth tongue fungi. Drawing from a data set of 300 sequences of earth tongues and progressively more distant fungal lineages, 30 insufficiently identified ITS sequences from the public sequence databases were assigned to the Geoglossomycetes. The association between earth tongues and plants has been hypothesized for a long time, but hard evidence is yet to be collected. The ITS phylogeny showed that four ectomycorrhizal isolates shared a clade with <em>Geoglossum</em> but not with <em>Trichoglossum</em> earth tongues, pointing to the significant potential inherent to ecological data mining of environmental samples. Environmental sampling holds the key to many focal questions in mycology, and simultaneous alignment and tree estimation, as performed by SATé, can be a highly efficient companion in that pursuit.</p> </div>", "links"=>[], "tags"=>["tasting", "fungal", "phylogenetic", "alignments"], "article_id"=>137467, "categories"=>["Biological Sciences", "Ecology", "Microbiology"], "users"=>["Zheng Wang", "R. Henrik Nilsson", "Francesc López-Giráldez", "Wen-Ying Zhuang", "Yu-cheng Dai", "Peter R. Johnston", "Jeffrey P. Townsend"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0019039.s001", "https://dx.doi.org/10.1371/journal.pone.0019039.s002", "https://dx.doi.org/10.1371/journal.pone.0019039.s003", "https://dx.doi.org/10.1371/journal.pone.0019039.s004", "https://dx.doi.org/10.1371/journal.pone.0019039.s005", "https://dx.doi.org/10.1371/journal.pone.0019039.s006", "https://dx.doi.org/10.1371/journal.pone.0019039.s007", "https://dx.doi.org/10.1371/journal.pone.0019039.s008"], "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Tasting_Soil_Fungal_Diversity_with_Earth_Tongues_Phylogenetic_Test_of_SAT_Alignments_for_Environmental_ITS_Data/137467", "title"=>"Tasting Soil Fungal Diversity with Earth Tongues: Phylogenetic Test of SATé Alignments for Environmental ITS Data", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-04-21 02:04:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/781231"], "description"=>"<p>Flowchart depicting how the four different alignments were prepared using Clustal W and SATé, and how they were analyzed using MrBayes.</p>", "links"=>[], "tags"=>["depicting", "alignments", "prepared", "clustal"], "article_id"=>451596, "categories"=>["Biological Sciences", "Ecology", "Microbiology"], "users"=>["Zheng Wang", "R. Henrik Nilsson", "Francesc López-Giráldez", "Wen-Ying Zhuang", "Yu-cheng Dai", "Peter R. Johnston", "Jeffrey P. Townsend"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019039.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flowchart_depicting_how_the_four_different_alignments_were_prepared_using_Clustal_W_and_SAT_233_and_how_they_were_analyzed_using_MrBayes_/451596", "title"=>"Flowchart depicting how the four different alignments were prepared using Clustal W and SATé, and how they were analyzed using MrBayes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-21 00:26:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/781583"], "description"=>"<p>Bayesian posterior probabilities higher than 0.94 are indicated with bold branches. Taxonomic groups were coded with colors and initials of the classes. Environmental ITS sequences grouped in the earth tongue clades are marked with one or more annotations indicating whether the isolate would be designated an earth tongue by other approaches. Affinity of marked isolates to the earth tongues was suggested by: * the sequence search suite <i>emerencia</i>; & BLAST of known earth-tongue ITS sequence against INSD; and by # annotation in INSD as unclassified Pezizomycotina environmental samples. Newly generated sequences for this study are presented as taxa without INSD accession numbers while download sequences are listed with their INSD accession numbers.</p>", "links"=>[], "tags"=>["generated", "mrbayes", "anchored", "alignment"], "article_id"=>451950, "categories"=>["Biological Sciences", "Ecology", "Microbiology"], "users"=>["Zheng Wang", "R. Henrik Nilsson", "Francesc López-Giráldez", "Wen-Ying Zhuang", "Yu-cheng Dai", "Peter R. Johnston", "Jeffrey P. Townsend"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019039.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_best_tree_generated_by_MrBayes_for_the_anchored_ITS_SAT_233_alignment_of_the_large_data_set_/451950", "title"=>"The best tree generated by MrBayes for the anchored ITS SATé alignment of the large data set.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-21 00:32:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/781473"], "description"=>"<p>Bayesian posterior probabilities higher than 0.94 are indicated with bold branches. Taxonomic groups were coded with colors and initials of the classes. Environmental ITS sequences grouped in the earth tongue clades are marked with one or more annotations indicating whether the isolate would be designated an earth tongue by other approaches. Affinity of marked isolates to the earth tongues was suggested by: * the sequence search suite <i>emerencia</i>; & BLAST of known earth-tongue ITS sequence against INSD; and by # annotation in INSD as unclassified Pezizomycotina environmental samples. Newly generated sequences for this study are presented as taxa without INSD accession numbers while download sequences are listed with their INSD accession numbers.</p>", "links"=>[], "tags"=>["generated", "mrbayes", "best-scored"], "article_id"=>451839, "categories"=>["Biological Sciences", "Ecology", "Microbiology"], "users"=>["Zheng Wang", "R. Henrik Nilsson", "Francesc López-Giráldez", "Wen-Ying Zhuang", "Yu-cheng Dai", "Peter R. Johnston", "Jeffrey P. Townsend"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019039.g003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_best_tree_generated_by_MrBayes_for_the_best_scored_whole_ITS_SAT_233_alignment_/451839", "title"=>"The best tree generated by MrBayes for the best-scored whole ITS SATé alignment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-21 00:30:39"}

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