Fungi in Thailand: A Case Study of the Efficacy of an ITS Barcode for Automatically Identifying Species within the Annulohypoxylon and Hypoxylon Genera
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{"title"=>"Fungi in Thailand: A Case Study of the Efficacy of an ITS Barcode for Automatically Identifying Species within the Annulohypoxylon and Hypoxylon Genera", "type"=>"journal", "authors"=>[{"first_name"=>"Nuttika", "last_name"=>"Suwannasai", "scopus_author_id"=>"36995621600"}, {"first_name"=>"María P.", "last_name"=>"Martín", "scopus_author_id"=>"7406971964"}, {"first_name"=>"Cherdchai", "last_name"=>"Phosri", "scopus_author_id"=>"16175996600"}, {"first_name"=>"Prakitsin", "last_name"=>"Sihanonth", "scopus_author_id"=>"6507489659"}, {"first_name"=>"Anthony J.S.", "last_name"=>"Whalley", "scopus_author_id"=>"7003990029"}, {"first_name"=>"John L.", "last_name"=>"Spouge", "scopus_author_id"=>"7005453937"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84873500605", "doi"=>"10.1371/journal.pone.0054529", "issn"=>"19326203", "pui"=>"368294399", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"23390499", "scopus"=>"2-s2.0-84873500605"}, "id"=>"e1120076-9634-35a4-8cd4-b23a09e1d753", "abstract"=>"Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera Annulohypoxylon and Hypoxylon, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI), we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of Annulohypoxylon and Hypoxylon. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1) Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2) Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3) Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many Annulohypoxylon and Hypoxylon species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in Annulohypoxylon and Hypoxylon, however. The URL http://tinyurl.com/spouge-barcode contains computer programs and other supplementary material relevant to this article.", "link"=>"http://www.mendeley.com/research/fungi-thailand-case-study-efficacy-barcode-automatically-identifying-species-within-annulohypoxylon", "reader_count"=>36, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>5, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>5, "Student > Master"=>8, "Other"=>3, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>23, "Medicine and Dentistry"=>1, "Social Sciences"=>1, "Computer Science"=>3, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>23}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"Philippines"=>1, "Brazil"=>1, "Thailand"=>1, "India"=>1}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/495046"], "description"=>"<p>Stromata (a–p); perithecial structure (q–s); ascospore shapes (t–z); perispore dehiscence (v, y, z). (a) <i>Annulohypoxylon stygium</i> SUT058, (b) <i>A. purpureonitens</i> H125, (c) <i>A. nitens</i> H154, (d) <i>A.</i> aff. <i>nitens</i> H099, (e) <i>Annulohypoxylon</i> sp. H213, (f) <i>Annulohypoxylon</i> sp. H255, (g) <i>Hypoxylon monticulosum</i> H188, (h) <i>H</i>. <i>lenormandii</i> H212, (i) <i>H. investiens</i> H259, (j) <i>H. perforatum</i> SUT218, (k) <i>H. duranii</i> H250, (l) <i>H. haematostroma</i> H114, (m) <i>H. crocopeplum</i> H119, (n) <i>H. pelliculosum</i> H227, (o) <i>H. diatrypeoides</i> H226, (p) <i>H. rubiginosum</i> SUT082, (q) <i>H. fendleri</i> SUT061, (r) <i>H. investiens</i> H259, (s) <i>H. haematostroma</i> H114, (t) <i>H. haematostroma</i> SUT293, (u) <i>A. stygium</i> SUT010, (v) <i>H. duranii</i> SUT284, (w) <i>H. investiens</i> SUT041, (x) <i>A. nitens</i> SUT249, (y) <i>H. monticulosum</i> SUT185 and (z) <i>A. nitens</i> SUT025.</p>", "links"=>[], "tags"=>["characteristics"], "article_id"=>165568, "categories"=>["Microbiology", "Biological Sciences", "Plant Biology", "Evolutionary Biology"], "users"=>["Nuttika Suwannasai", "María P. Martín", "Cherdchai Phosri", "Prakitsin Sihanonth", "Anthony J. S. Whalley", "John L. Spouge"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054529.g001", "stats"=>{"downloads"=>2, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Morphological_characteristics_of_Annulohypoxylon_and_Hypoxylon_species_found_in_Thailand_/165568", "title"=>"Morphological characteristics of <i>Annulohypoxylon</i> and <i>Hypoxylon</i> species found in Thailand.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-04 01:32:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/482221", "https://ndownloader.figshare.com/files/482222", "https://ndownloader.figshare.com/files/482227"], "description"=>"<div><p>Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera <em>Annulohypoxylon</em> and <em>Hypoxylon</em>, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI), we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of <em>Annulohypoxylon</em> and <em>Hypoxylon</em>. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1) Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2) Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3) Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many <em>Annulohypoxylon</em> and <em>Hypoxylon</em> species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in <em>Annulohypoxylon</em> and <em>Hypoxylon</em>, however. The URL <a href=\"http://tinyurl.com/spouge-barcode\">http://tinyurl.com/spouge-barcode</a> contains computer programs and other supplementary material relevant to this article.</p> </div>", "links"=>[], "tags"=>["fungi", "efficacy", "barcode", "identifying", "annulohypoxylon", "hypoxylon", "genera"], "article_id"=>155740, "categories"=>["Microbiology", "Biological Sciences", "Plant Biology", "Evolutionary Biology"], "users"=>["Nuttika Suwannasai", "María P. Martín", "Cherdchai Phosri", "Prakitsin Sihanonth", "Anthony J. S. Whalley", "John L. Spouge"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0054529.s001", "https://dx.doi.org/10.1371/journal.pone.0054529.s002", "https://dx.doi.org/10.1371/journal.pone.0054529.s003"], "stats"=>{"downloads"=>9, "page_views"=>42, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Fungi_in_Thailand_A_Case_Study_of_the_Efficacy_of_an_ITS_Barcode_for_Automatically_Identifying_Species_within_the_Annulohypoxylon_and_Hypoxylon_Genera__/155740", "title"=>"Fungi in Thailand: A Case Study of the Efficacy of an ITS Barcode for Automatically Identifying Species within the Annulohypoxylon and Hypoxylon Genera", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-02-04 01:35:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/495259"], "description"=>"<p>The error bars indicate 95% confidence intervals, as calculated by the Wilson score interval <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054529#pone.0054529-Wilson1\" target=\"_blank\">[46]</a>. The four alignment types used (indicated by different colors at the bottom) were multiple sequence alignment (which imposes an implicit pairwise global alignment on each pair of sequences), and global, semi-global, and local pairwise alignment. The two types of sequence distance used for each alignment method were alignment distance and evolutionary distance. (In fact, for a fixed alignment type and dataset, all evolutionary distances produced the same PCI as p-distance.) The green bars give the value of the barcode gap PCI.</p>", "links"=>[], "tags"=>["alignment", "types"], "article_id"=>165783, "categories"=>["Microbiology", "Biological Sciences", "Plant Biology", "Evolutionary Biology"], "users"=>["Nuttika Suwannasai", "María P. Martín", "Cherdchai Phosri", "Prakitsin Sihanonth", "Anthony J. S. Whalley", "John L. Spouge"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0054529.g002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCIs_for_each_of_four_alignment_types_and_two_types_of_sequence_distance_/165783", "title"=>"PCIs for each of four alignment types and two types of sequence distance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-04 01:36:23"}

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[295, 511, 651, 775, 882, 992, 1100, 1201, 1304, 1400, 1486, 1570, 1650]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}]}
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