Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective
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{"title"=>"Taxonomic reliability of DNA sequences in public sequences databases: A fungal perspective", "type"=>"journal", "authors"=>[{"first_name"=>"R. Henrik", "last_name"=>"Nilsson", "scopus_author_id"=>"26647760100"}, {"first_name"=>"Martin", "last_name"=>"Ryberg", "scopus_author_id"=>"24176455300"}, {"first_name"=>"Erik", "last_name"=>"Kristiansson", "scopus_author_id"=>"8986273500"}, {"first_name"=>"Kessy", "last_name"=>"Abarenkov", "scopus_author_id"=>"8599680200"}, {"first_name"=>"Karl Henrik", "last_name"=>"Larsson", "scopus_author_id"=>"7202534021"}, {"first_name"=>"Urmas", "last_name"=>"Köljalg", "scopus_author_id"=>"6603238587"}], "year"=>2006, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"36049004436", "pmid"=>"17183689", "doi"=>"10.1371/journal.pone.0000059", "pui"=>"352571193", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203", "scopus"=>"2-s2.0-36049004436"}, "id"=>"214d461a-ea86-38ab-b8bb-0af67decf54c", "abstract"=>"BACKGROUND DNA sequences are increasingly seen as one of the primary information sources for species identification in many organism groups. Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries. METHODOLOGY/PRINCIPAL FINDINGS The present study uses a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database to show that the taxon sampling of fungi is far from complete, that about 20% of the entries may be incorrectly identified to species level, and that the majority of entries lack descriptive and up-to-date annotations. CONCLUSIONS The problems with taxonomic reliability and insufficient annotations in public DNA repositories form a tangible obstacle to sequence-based species identification, and it is manifest that the greatest challenges to biological barcoding will be of taxonomical, rather than technical, nature.", "link"=>"http://www.mendeley.com/research/taxonomic-reliability-dna-sequences-public-sequences-databases-fungal-perspective", "reader_count"=>295, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>15, "Researcher"=>79, "Student > Doctoral Student"=>18, "Student > Ph. D. Student"=>81, "Student > Postgraduate"=>8, "Student > Master"=>34, "Other"=>13, "Student > Bachelor"=>24, "Lecturer"=>2, "Professor"=>17}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>15, "Researcher"=>79, "Student > Doctoral Student"=>18, "Student > Ph. D. Student"=>81, "Student > Postgraduate"=>8, "Student > Master"=>34, "Other"=>13, "Student > Bachelor"=>24, "Lecturer"=>2, "Professor"=>17}, "reader_count_by_subject_area"=>{"Unspecified"=>13, "Agricultural and Biological Sciences"=>216, "Arts and Humanities"=>1, "Veterinary Science and Veterinary Medicine"=>1, "Chemistry"=>3, "Computer Science"=>6, "Earth and Planetary Sciences"=>3, "Environmental Science"=>19, "Biochemistry, Genetics and Molecular Biology"=>20, "Medicine and Dentistry"=>5, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>5}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Social Sciences"=>{"Social Sciences"=>1}, "Unspecified"=>{"Unspecified"=>13}, "Environmental Science"=>{"Environmental Science"=>19}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Chemistry"=>{"Chemistry"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>5}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>216}, "Computer Science"=>{"Computer Science"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>20}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Ecuador"=>1, "United States"=>14, "United Kingdom"=>4, "Portugal"=>2, "New Caledonia"=>1, "India"=>1, "Spain"=>2, "Canada"=>4, "Netherlands"=>1, "Sweden"=>2, "China"=>1, "Denmark"=>1, "Brazil"=>2, "South Africa"=>1, "Italy"=>4, "Algeria"=>1, "Australia"=>1, "Germany"=>7, "Indonesia"=>1}, "group_count"=>13}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/470108"], "description"=>"<div><h3>Background</h3><p>DNA sequences are increasingly seen as one of the primary information sources for species identification in many organism groups. Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries.</p> <h3>Methodology/Principal Findings</h3><p>The present study uses a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database to show that the taxon sampling of fungi is far from complete, that about 20% of the entries may be incorrectly identified to species level, and that the majority of entries lack descriptive and up-to-date annotations.</p> <h3>Conclusions</h3><p>The problems with taxonomic reliability and insufficient annotations in public DNA repositories form a tangible obstacle to sequence-based species identification, and it is manifest that the greatest challenges to biological barcoding will be of taxonomical, rather than technical, nature.</p> </div>", "links"=>[], "tags"=>["taxonomic", "dna", "sequences", "fungal"], "article_id"=>152647, "categories"=>["Biological Sciences", "Cell Biology"], "users"=>["R. Henrik Nilsson", "Martin Ryberg", "Erik Kristiansson", "Kessy Abarenkov", "Karl-Henrik Larsson", "Urmas Kõljalg"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000059", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Taxonomic_Reliability_of_DNA_Sequences_in_Public_Sequence_Databases_A_Fungal_Perspective/152647", "title"=>"Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2006-12-20 00:44:07"}

PMC Usage Stats | Further Information

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