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{"title"=>"PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution", "type"=>"journal", "authors"=>[{"first_name"=>"Stéphane", "last_name"=>"Mahé", "scopus_author_id"=>"23028026300"}, {"first_name"=>"Marie", "last_name"=>"Duhamel", "scopus_author_id"=>"49861202800"}, {"first_name"=>"Thomas", "last_name"=>"Le Calvez", "scopus_author_id"=>"26642630900"}, {"first_name"=>"Laetitia", "last_name"=>"Guillot", "scopus_author_id"=>"57197883295"}, {"first_name"=>"Ludmila", "last_name"=>"Sarbu", "scopus_author_id"=>"55360500600"}, {"first_name"=>"Anthony", "last_name"=>"Bretaudeau", "scopus_author_id"=>"54789485300"}, {"first_name"=>"Olivier", "last_name"=>"Collin", "scopus_author_id"=>"55325352600"}, {"first_name"=>"Alexis", "last_name"=>"Dufresne", "scopus_author_id"=>"7007123282"}, {"first_name"=>"E. Toby", "last_name"=>"Kiers", "scopus_author_id"=>"6507537220"}, {"first_name"=>"Philippe", "last_name"=>"Vandenkoornhuyse", "scopus_author_id"=>"6603438618"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"365666328", "doi"=>"10.1371/journal.pone.0043117", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"23028445", "issn"=>"19326203", "scopus"=>"2-s2.0-84866389483", "sgr"=>"84866389483"}, "id"=>"71239eee-f442-3d3a-b93a-26bf5f592c3c", "abstract"=>"BACKGROUND: In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation.\n\nMETHODS AND PRINCIPAL FINDINGS: To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ~20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples.\n\nCONCLUSION: PHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as 'reference alignments', (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available. The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org/.", "link"=>"http://www.mendeley.com/research/phymycodb-curated-database-analyses-fungal-diversity-evolution", "reader_count"=>66, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>25, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>3, "Student > Master"=>9, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>25, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>3, "Student > Master"=>9, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>8, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>46, "Medicine and Dentistry"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>46}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>8}}, "reader_count_by_country"=>{"Canada"=>3, "Netherlands"=>1, "Sweden"=>1, "United States"=>4, "Philippines"=>1, "Brazil"=>1, "United Kingdom"=>1, "Italy"=>1, "Australia"=>1, "France"=>2, "Chile"=>1, "Switzerland"=>1}, "group_count"=>1}

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• http://doi.org/10.1111/mec.13655
• http://doi.org/10.1371/journal.pone.0094088
• http://doi.org/10.1016/j.scitotenv.2014.05.073
• http://doi.org/10.7717/peerj.7463
• http://doi.org/10.1038/srep32467
• http://doi.org/10.1016/j.margen.2017.09.007
• http://doi.org/10.1111/nph.13340
• http://doi.org/10.1093/database/bau061
• http://doi.org/10.1093/femsec/fiw004
• http://doi.org/10.3389/fmicb.2017.00180
• http://doi.org/10.1186/s40168-016-0192-z
• http://doi.org/10.1111/1365-2745.13279

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• {"id"=>"246522956795228160", "text"=>"This could be useful as GenBank is full of fungal junk: Curated Database for Analyses of Fungal Diversity and Evolution http://t.co/TY1RbbfN", "created_at"=>"2012-09-14T08:17:07Z", "user"=>"gedankenstuecke", "user_name"=>"Bastian Greshake", "user_profile_image"=>"http://a0.twimg.com/profile_images/2466316198/7D66C55E-2643-4F71-8115-B524A7B8E72F_normal"}
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• {"id"=>"249538713028276224", "text"=>"RT @fungalgenomes: PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution http://t.co/hUVQKes5", "created_at"=>"2012-09-22T16:00:40Z", "user"=>"VaillancourtLab", "user_name"=>"Vaillancourt Lab", "user_profile_image"=>"http://a0.twimg.com/profile_images/2346355571/4esowvxx5wsxb4jvbdu2_normal.jpeg"}
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• {"files"=>["https://ndownloader.figshare.com/files/577350"], "description"=>"<p>The sequences highlighted in blue illustrate examples of sequences removed from PHYMYCO-DB. The compromised nature can stem from erroneous sequencing (e.g. repeated gaps), wrong annotation (e.g. sequence corresponding to another clade), high numbers of undetermined nucleotides, homopolymers insertions, erroneous alignment or reverse complementary sequences and presence of long insertions and introns or presence of deletions.</p>", "links"=>[], "tags"=>["sequences", "deleted", "curation", "alignment"], "article_id"=>247830, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Microbiology", "Evolutionary Biology"], "users"=>["Stéphane Mahé", "Marie Duhamel", "Thomas Le Calvez", "Laetitia Guillot", "Ludmila Sarbu", "Anthony Bretaudeau", "Olivier Collin", "Alexis Dufresne", "E. Toby Kiers", "Philippe Vandenkoornhuyse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043117.g002", "stats"=>{"downloads"=>0, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Visualisation_of_sequences_deleted_by_the_manual_curation_after_alignment_ClustalX_2_1_/247830", "title"=>"Visualisation of sequences deleted by the manual curation after alignment (ClustalX 2.1).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-13 02:10:30"}
• {"files"=>["https://ndownloader.figshare.com/files/306253"], "description"=>"<div><h3>Background</h3><p>In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept.</p> <p>Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation.</p> <h3>Methods and Principal Findings</h3><p>To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ∼20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples.</p> <h3>Conclusion</h3><p>PHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as ‘reference alignments’, (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available.</p> <p>The PHYMYCO-DB is accessible through the URL <a href=\"http://phymycodb.genouest.org/\">http://phymycodb.genouest.org/</a>.</p> </div>", "links"=>[], "tags"=>["curated", "analyses", "fungal"], "article_id"=>120420, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Microbiology", "Evolutionary Biology"], "users"=>["Stéphane Mahé", "Marie Duhamel", "Thomas Le Calvez", "Laetitia Guillot", "Ludmila Sarbu", "Anthony Bretaudeau", "Olivier Collin", "Alexis Dufresne", "E. Toby Kiers", "Philippe Vandenkoornhuyse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043117", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/PHYMYCO_DB_A_Curated_Database_for_Analyses_of_Fungal_Diversity_and_Evolution/120420", "title"=>"PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-13 00:07:00"}
• {"files"=>["https://ndownloader.figshare.com/files/577218"], "description"=>"<p>The arrows indicate the flow of gene sequences extracted from the GenBank database, through the automated and manual curation steps. All the sequences made available to users has passed the 2 curation processes. After each upgrade of the database (i.e. 4 times per year), expert manual curation is performed.</p>", "links"=>[], "tags"=>["microbiology", "Computational biology", "computer science", "Evolutionary biology"], "article_id"=>247698, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Microbiology", "Evolutionary Biology"], "users"=>["Stéphane Mahé", "Marie Duhamel", "Thomas Le Calvez", "Laetitia Guillot", "Ludmila Sarbu", "Anthony Bretaudeau", "Olivier Collin", "Alexis Dufresne", "E. Toby Kiers", "Philippe Vandenkoornhuyse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043117.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flowchart_of_the_data_in_the_PHYMYCO_DB_/247698", "title"=>"Flowchart of the data in the PHYMYCO-DB.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-13 02:08:18"}
• {"files"=>["https://ndownloader.figshare.com/files/577491"], "description"=>"<p>Topology was built using MrBayes v.3.1.2 (Scale bar: 0.1 estimated substitutions per site, 3000000 generations sampled every 100 generations and an average standart deviation of split frequencies of 0.004140) from a ClustalW 2.1 alignment. The model GTR+I+G was designated by jModelTest 0.1. Node support values are given in the following order: Maximum Parsimony/Maximum Likelihood (both calculated with PAUP 4.0β10 version, 500 bootstraps)/MrBayes. <i>Corallochytrium limacisporum</i> (L42528), a putative choanoflagellate, was used as outgroup. <i>Maunachytrium keaense</i> (it is not part of PHYMYCO-DB) was also used to help build the tree. All sequences are listed with their GenBank accession numbers. The topologies were congruent apart from doted lines indicated in the figure. Thin lines show bootstrap values >50% and BPP >0.5 (MP/ML/MrBayes) and thick lines: bootstrap values >70% and BPP >0.7 (MP/ML/MrBayes). The sequences belonging to the <i>Lobulomycetaceae</i> family are indicated with their BLASTn percentage of maximum identity compared to the three deep-sea Chytridiomycota OTUs.</p>", "links"=>[], "tags"=>["rrna", "phylogenetic", "positions", "deep-sea", "chytridiomycota", "ssu", "fungal"], "article_id"=>247967, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Microbiology", "Evolutionary Biology"], "users"=>["Stéphane Mahé", "Marie Duhamel", "Thomas Le Calvez", "Laetitia Guillot", "Ludmila Sarbu", "Anthony Bretaudeau", "Olivier Collin", "Alexis Dufresne", "E. Toby Kiers", "Philippe Vandenkoornhuyse"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0043117.g003", "stats"=>{"downloads"=>3, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SSU_rRNA_phylogenetic_positions_of_deep_sea_Chytridiomycota_colored_terminals_along_with_the_closest_known_related_SSU_rRNA_fungal_sequences_/247967", "title"=>"SSU rRNA phylogenetic positions of deep-sea Chytridiomycota (colored terminals) along with the closest known related SSU rRNA fungal sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-13 02:12:47"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime