Filling Gaps in Biodiversity Knowledge for Macrofungi: Contributions and Assessment of an Herbarium Collection DNA Barcode Sequencing Project
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{"title"=>"Filling Gaps in Biodiversity Knowledge for Macrofungi: Contributions and Assessment of an Herbarium Collection DNA Barcode Sequencing Project", "type"=>"journal", "authors"=>[{"first_name"=>"Todd W.", "last_name"=>"Osmundson", "scopus_author_id"=>"12768757000"}, {"first_name"=>"Vincent A.", "last_name"=>"Robert", "scopus_author_id"=>"8834684300"}, {"first_name"=>"Conrad L.", "last_name"=>"Schoch", "scopus_author_id"=>"55668341100"}, {"first_name"=>"Lydia J.", "last_name"=>"Baker", "scopus_author_id"=>"57191166009"}, {"first_name"=>"Amy", "last_name"=>"Smith", "scopus_author_id"=>"35396358500"}, {"first_name"=>"Giovanni", "last_name"=>"Robich", "scopus_author_id"=>"57199572430"}, {"first_name"=>"Luca", "last_name"=>"Mizzan", "scopus_author_id"=>"42161886300"}, {"first_name"=>"Matteo M.", "last_name"=>"Garbelotto", "scopus_author_id"=>"6701803969"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"368837375", "sgr"=>"84876976654", "pmid"=>"23638077", "scopus"=>"2-s2.0-84876976654", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0062419", "issn"=>"19326203"}, "id"=>"03c4c776-5f51-3022-b072-84239db76939", "abstract"=>"Despite recent advances spearheaded by molecular approaches and novel technologies, species description and DNA sequence information are significantly lagging for fungi compared to many other groups of organisms. Large scale sequencing of vouchered herbarium material can aid in closing this gap. Here, we describe an effort to obtain broad ITS sequence coverage of the approximately 6000 macrofungal-species-rich herbarium of the Museum of Natural History in Venice, Italy. Our goals were to investigate issues related to large sequencing projects, develop heuristic methods for assessing the overall performance of such a project, and evaluate the prospects of such efforts to reduce the current gap in fungal biodiversity knowledge. The effort generated 1107 sequences submitted to GenBank, including 416 previously unrepresented taxa and 398 sequences exhibiting a best BLAST match to an unidentified environmental sequence. Specimen age and taxon affected sequencing success, and subsequent work on failed specimens showed that an ITS1 mini-barcode greatly increased sequencing success without greatly reducing the discriminating power of the barcode. Similarity comparisons and nonmetric multidimensional scaling ordinations based on pairwise distance matrices proved to be useful heuristic tools for validating the overall accuracy of specimen identifications, flagging potential misidentifications, and identifying taxa in need of additional species-level revision. Comparison of within- and among-species nucleotide variation showed a strong increase in species discriminating power at 1-2% dissimilarity, and identified potential barcoding issues (same sequence for different species and vice-versa). All sequences are linked to a vouchered specimen, and results from this study have already prompted revisions of species-sequence assignments in several taxa.", "link"=>"http://www.mendeley.com/research/filling-gaps-biodiversity-knowledge-macrofungi-contributions-assessment-herbarium-collection-dna-bar", "reader_count"=>83, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>4, "Researcher"=>20, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>4, "Student > Master"=>13, "Other"=>6, "Student > Bachelor"=>7, "Lecturer"=>5, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>4, "Researcher"=>20, "Student > Ph. D. Student"=>14, "Student > Postgraduate"=>4, "Student > Master"=>13, "Other"=>6, "Student > Bachelor"=>7, "Lecturer"=>5, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>7, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>56, "Medicine and Dentistry"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Computer Science"=>2, "Earth and Planetary Sciences"=>4}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>56}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>7}, "Environmental Science"=>{"Environmental Science"=>4}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "United States"=>2, "Philippines"=>1, "Brazil"=>1, "Italy"=>3, "Switzerland"=>1, "Iceland"=>1, "Indonesia"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1048633"], "description"=>"<p>NMDS ordination of genetic distances based on ITS1 sequences, with symbols colored by genus. Table inset shows Pearson correlation coefficients between pairwise genetic distance matrices generated for the two spacer regions (ITS1 and ITS2) separately and the full-length sequences from the 1107-sequence dataset.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "microbial ecology", "Evolutionary biology", "Evolutionary systematics", "taxonomy", "Microbial taxonomy", "genomics", "Genome databases", "Sequence databases", "metagenomics", "microbiology", "Mycology", "Fungal classification", "fungi", "Plant science", "Botany"], "article_id"=>693984, "categories"=>["Biological Sciences"], "users"=>["Todd W. Osmundson", "Vincent A. Robert", "Conrad L. Schoch", "Lydia J. Baker", "Amy Smith", "Giovanni Robich", "Luca Mizzan", "Matteo M. Garbelotto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0062419.g004", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Classification_potential_of_ITS_mini_barcodes_/693984", "title"=>"Classification potential of ITS mini-barcodes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-30 01:06:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/1048631"], "description"=>"<p>a. Data symbols coded by genus. b. Data symbols coded by family.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "microbial ecology", "Evolutionary biology", "Evolutionary systematics", "taxonomy", "Microbial taxonomy", "genomics", "Genome databases", "Sequence databases", "metagenomics", "microbiology", "Mycology", "Fungal classification", "fungi", "Plant science", "Botany", "concordance", "taxonomic", "dna", "nonmetric", "multidimensional", "scaling", "ordination", "pairwise"], "article_id"=>693982, "categories"=>["Biological Sciences"], "users"=>["Todd W. Osmundson", "Vincent A. Robert", "Conrad L. Schoch", "Lydia J. Baker", "Amy Smith", "Giovanni Robich", "Luca Mizzan", "Matteo M. Garbelotto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0062419.g003", "stats"=>{"downloads"=>3, "page_views"=>65, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Assessment_of_concordance_between_taxonomic_herbarium_determination_and_DNA_similarity_assignment_using_nonmetric_multidimensional_scaling_NMDS_ordination_of_the_pairwise_genetic_distance_matrix_/693982", "title"=>"Assessment of concordance between taxonomic (herbarium determination) and DNA similarity assignment using nonmetric multidimensional scaling (NMDS) ordination of the pairwise genetic distance matrix.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-30 01:06:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/1048636"], "description"=>"<p>PCR and sequencing success rates are shown for 30 randomly-selected samples from 3 macrofungal genera; samples were previously negative for full-length ITS1+5.8S+ITS2 amplification.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "microbial ecology", "Evolutionary biology", "Evolutionary systematics", "taxonomy", "Microbial taxonomy", "genomics", "Genome databases", "Sequence databases", "metagenomics", "microbiology", "Mycology", "Fungal classification", "fungi", "Plant science", "Botany", "pcr", "sequencing", "rates", "its1"], "article_id"=>693987, "categories"=>["Biological Sciences"], "users"=>["Todd W. Osmundson", "Vincent A. Robert", "Conrad L. Schoch", "Lydia J. Baker", "Amy Smith", "Giovanni Robich", "Luca Mizzan", "Matteo M. Garbelotto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0062419.t001", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Improvement_of_PCR_and_sequencing_success_rates_using_ITS1_mini_barcodes_/693987", "title"=>"Improvement of PCR and sequencing success rates using ITS1 mini-barcodes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-30 01:06:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/1048635"], "description"=>"<p>Plot of within- and between-species nucleotide divergence (bp).</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "microbial ecology", "Evolutionary biology", "Evolutionary systematics", "taxonomy", "Microbial taxonomy", "genomics", "Genome databases", "Sequence databases", "metagenomics", "microbiology", "Mycology", "Fungal classification", "fungi", "Plant science", "Botany", "within-", "between-species", "nucleotide", "divergence"], "article_id"=>693986, "categories"=>["Biological Sciences"], "users"=>["Todd W. Osmundson", "Vincent A. Robert", "Conrad L. Schoch", "Lydia J. Baker", "Amy Smith", "Giovanni Robich", "Luca Mizzan", "Matteo M. Garbelotto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0062419.g005", "stats"=>{"downloads"=>3, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Plot_of_within_and_between_species_nucleotide_divergence_bp_/693986", "title"=>"Plot of within- and between-species nucleotide divergence (bp).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-30 01:06:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1048630"], "description"=>"<p>Pearson Chi-square test of independence: p<0.0001. Asterisks denote categories with standardized adjusted residuals significant α = 0.05. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062419#pone.0062419.s005\" target=\"_blank\">Table S3</a> for data and post hoc test results.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "microbial ecology", "Evolutionary biology", "Evolutionary systematics", "taxonomy", "Microbial taxonomy", "genomics", "Genome databases", "Sequence databases", "metagenomics", "microbiology", "Mycology", "Fungal classification", "fungi", "Plant science", "Botany", "taxon", "specimen", "pcr", "amplification", "primers", "its1f"], "article_id"=>693981, "categories"=>["Biological Sciences"], "users"=>["Todd W. Osmundson", "Vincent A. Robert", "Conrad L. Schoch", "Lydia J. Baker", "Amy Smith", "Giovanni Robich", "Luca Mizzan", "Matteo M. Garbelotto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0062419.g002", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Association_between_taxon_controlled_for_specimen_age_and_PCR_amplification_success_using_primers_ITS1F_and_ITS4_/693981", "title"=>"Association between taxon (controlled for specimen age) and PCR amplification success using primers ITS1F and ITS4.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-30 01:06:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/1048629"], "description"=>"<p>Pearson Chi-square test of independence (N = 2763, d.f. = 2) significant at p<0.0001. Asterisks denote categories with standardized adjusted residuals significant at a Bonferroni-corrected α = 0.00833. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062419#pone.0062419.s004\" target=\"_blank\">Table S2</a> for data and post hoc test results.</p>", "links"=>[], "tags"=>["ecology", "biodiversity", "microbial ecology", "Evolutionary biology", "Evolutionary systematics", "taxonomy", "Microbial taxonomy", "genomics", "Genome databases", "Sequence databases", "metagenomics", "microbiology", "Mycology", "Fungal classification", "fungi", "Plant science", "Botany", "specimen", "pcr", "amplification", "primers", "its1f"], "article_id"=>693980, "categories"=>["Biological Sciences"], "users"=>["Todd W. Osmundson", "Vincent A. Robert", "Conrad L. Schoch", "Lydia J. Baker", "Amy Smith", "Giovanni Robich", "Luca Mizzan", "Matteo M. Garbelotto"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0062419.g001", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Association_between_specimen_age_and_PCR_amplification_success_using_primers_ITS1F_and_ITS4_/693980", "title"=>"Association between specimen age and PCR amplification success using primers ITS1F and ITS4.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-30 01:06:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1048640", "https://ndownloader.figshare.com/files/1048642", "https://ndownloader.figshare.com/files/1048643", "https://ndownloader.figshare.com/files/1048644", "https://ndownloader.figshare.com/files/1048645"], "description"=>"<div><p>Despite recent advances spearheaded by molecular approaches and novel technologies, species description and DNA sequence information are significantly lagging for fungi compared to many other groups of organisms. Large scale sequencing of vouchered herbarium material can aid in closing this gap. Here, we describe an effort to obtain broad ITS sequence coverage of the approximately 6000 macrofungal-species-rich herbarium of the Museum of Natural History in Venice, Italy. Our goals were to investigate issues related to large sequencing projects, develop heuristic methods for assessing the overall performance of such a project, and evaluate the prospects of such efforts to reduce the current gap in fungal biodiversity knowledge. The effort generated 1107 sequences submitted to GenBank, including 416 previously unrepresented taxa and 398 sequences exhibiting a best BLAST match to an unidentified environmental sequence. Specimen age and taxon affected sequencing success, and subsequent work on failed specimens showed that an ITS1 mini-barcode greatly increased sequencing success without greatly reducing the discriminating power of the barcode. Similarity comparisons and nonmetric multidimensional scaling ordinations based on pairwise distance matrices proved to be useful heuristic tools for validating the overall accuracy of specimen identifications, flagging potential misidentifications, and identifying taxa in need of additional species-level revision. Comparison of within- and among-species nucleotide variation showed a strong increase in species discriminating power at 1–2% dissimilarity, and identified potential barcoding issues (same sequence for different species and vice-versa). All sequences are linked to a vouchered specimen, and results from this study have already prompted revisions of species-sequence assignments in several taxa.</p></div>", "links"=>[], "tags"=>["ecology", "biodiversity", "microbial ecology", "Evolutionary biology", "Evolutionary systematics", "taxonomy", "Microbial taxonomy", "genomics", "Genome databases", "Sequence databases", "metagenomics", "microbiology", "Mycology", "Fungal classification", "fungi", "Plant science", "Botany", "gaps", "contributions", "herbarium", "dna", "barcode", "sequencing"], "article_id"=>693989, "categories"=>["Biological Sciences"], "users"=>["Todd W. Osmundson", "Vincent A. Robert", "Conrad L. Schoch", "Lydia J. Baker", "Amy Smith", "Giovanni Robich", "Luca Mizzan", "Matteo M. Garbelotto"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0062419.s001", "https://dx.doi.org/10.1371/journal.pone.0062419.s002", "https://dx.doi.org/10.1371/journal.pone.0062419.s003", "https://dx.doi.org/10.1371/journal.pone.0062419.s004", "https://dx.doi.org/10.1371/journal.pone.0062419.s005"], "stats"=>{"downloads"=>18, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Filling_Gaps_in_Biodiversity_Knowledge_for_Macrofungi_Contributions_and_Assessment_of_an_Herbarium_Collection_DNA_Barcode_Sequencing_Project_/693989", "title"=>"Filling Gaps in Biodiversity Knowledge for Macrofungi: Contributions and Assessment of an Herbarium Collection DNA Barcode Sequencing Project", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-04-30 01:06:29"}

PMC Usage Stats | Further Information

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Relative Metric

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