Choosing and Using a Plant DNA Barcode
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{"title"=>"Choosing and using a plant DNA barcode", "type"=>"journal", "authors"=>[{"first_name"=>"Peter M.", "last_name"=>"Hollingsworth", "scopus_author_id"=>"7004779636"}, {"first_name"=>"Sean W.", "last_name"=>"Graham", "scopus_author_id"=>"7401977993"}, {"first_name"=>"Damon P.", "last_name"=>"Little", "scopus_author_id"=>"7202966342"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"361828974", "sgr"=>"79957554546", "issn"=>"19326203", "pmid"=>"21637336", "scopus"=>"2-s2.0-79957554546", "doi"=>"10.1371/journal.pone.0019254", "isbn"=>"10.1371/journal.pone.0019254"}, "id"=>"ce7202bb-b330-3b61-ae6d-159b8d78b4a2", "abstract"=>"The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.", "link"=>"http://www.mendeley.com/research/choosing-using-plant-dna-barcode-4", "reader_count"=>686, "reader_count_by_academic_status"=>{"Unspecified"=>17, "Professor > Associate Professor"=>24, "Librarian"=>1, "Researcher"=>131, "Student > Doctoral Student"=>24, "Student > Ph. D. Student"=>152, "Student > Postgraduate"=>48, "Student > Master"=>117, "Other"=>22, "Student > Bachelor"=>104, "Lecturer"=>12, "Lecturer > Senior Lecturer"=>2, "Professor"=>32}, "reader_count_by_user_role"=>{"Unspecified"=>17, "Professor > Associate Professor"=>24, "Librarian"=>1, "Researcher"=>131, "Student > Doctoral Student"=>24, "Student > Ph. D. Student"=>152, "Student > Postgraduate"=>48, "Student > Master"=>117, "Other"=>22, "Student > Bachelor"=>104, "Lecturer"=>12, "Lecturer > Senior Lecturer"=>2, "Professor"=>32}, "reader_count_by_subject_area"=>{"Unspecified"=>26, "Agricultural and Biological Sciences"=>457, "Arts and Humanities"=>3, "Veterinary Science and Veterinary Medicine"=>1, "Business, Management and Accounting"=>2, "Chemical Engineering"=>1, "Chemistry"=>9, "Computer Science"=>3, "Earth and Planetary Sciences"=>6, "Engineering"=>8, "Environmental Science"=>48, "Biochemistry, Genetics and Molecular Biology"=>79, "Nursing and Health Professions"=>1, "Medicine and Dentistry"=>31, "Pharmacology, Toxicology and Pharmaceutical Science"=>4, "Social Sciences"=>5, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>31}, "Social Sciences"=>{"Social Sciences"=>5}, "Unspecified"=>{"Unspecified"=>26}, "Environmental Science"=>{"Environmental Science"=>48}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>4}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>3}, "Engineering"=>{"Engineering"=>8}, "Chemistry"=>{"Chemistry"=>9}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>6}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>457}, "Computer Science"=>{"Computer Science"=>3}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>2}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>79}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Republic of Singapore"=>1, "United States"=>11, "Malaysia"=>1, "Portugal"=>1, "Iceland"=>1, "Russia"=>2, "Greece"=>1, "Netherlands"=>2, "Sweden"=>1, "Pakistan"=>1, "China"=>1, "Brazil"=>4, "Guatemala"=>1, "Poland"=>1, "Chile"=>1, "Nigeria"=>1, "France"=>1, "Colombia"=>3, "Japan"=>1, "Tanzania"=>1, "United Kingdom"=>3, "Kenya"=>1, "Spain"=>3, "India"=>3, "New Zealand"=>2, "Canada"=>3, "Czech Republic"=>1, "South Africa"=>3, "Mexico"=>2, "Italy"=>3, "Australia"=>1, "Germany"=>4, "Indonesia"=>1}, "group_count"=>28}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/770908"], "description"=>"<p>Colours (red = warm; blue = cool) represent an informal measure of enthusiasm among DNA barcoding researchers in the systematics community for CBOL and iBOL adoption of different markers. The different shading of <i>trnL</i> (P6) reflects the parallel use of the P6 loop for DNA profiling of degraded DNAs in ecological studies (see text). * = the two markers that form the core-barcode for land plants. <i>rbcL</i><u>a</u> is used in this figure to distinguish this shorter barcode region of the gene proposed by Kress and Erikson <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Kress2\" target=\"_blank\">[7]</a> and the full length (ca. 1400 bp) gene sequence of <i>rbcL</i>. Elsewhere in the text, when we refer to <i>rbcL</i> we are referring to the short barcode region. The dashed lines indicate the timing of three international barcoding conferences in London (2005), Taipei (2007) and Mexico City (2009). The consideration of the different markers as barcodes are from the following sources: Kress et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Kress1\" target=\"_blank\">[5]</a>, Chase et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Chase2\" target=\"_blank\">[102]</a>, Chen et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Chen1\" target=\"_blank\">[54]</a>, Kew consortium <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Ford1\" target=\"_blank\">[4]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Chase1\" target=\"_blank\">[6]</a>, Kim et al. see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Pennisi1\" target=\"_blank\">[103]</a>, Lahaye et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Lahaye1\" target=\"_blank\">[8]</a>, Newmaster et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Newmaster1\" target=\"_blank\">[104]</a>, Kress and Erickson <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Kress2\" target=\"_blank\">[7]</a>, Taberlet et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Taberlet2\" target=\"_blank\">[44]</a>, Presting et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Presting1\" target=\"_blank\">[105]</a>.</p>", "links"=>[], "tags"=>["timeline", "markers"], "article_id"=>441280, "categories"=>["Plant Biology", "Evolutionary Biology"], "users"=>["Peter M. Hollingsworth", "Sean W. Graham", "Damon P. Little"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019254.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_timeline_of_the_consideration_of_different_markers_as_plant_barcodes_/441280", "title"=>"Schematic timeline of the consideration of different markers as plant barcodes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-26 00:21:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/387044"], "description"=>"<div><p>The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the <em>cytochrome oxidase 1</em> (<em>CO1</em>) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.</p> </div>", "links"=>[], "tags"=>["choosing", "dna", "barcode"], "article_id"=>136410, "categories"=>["Cell Biology", "Evolutionary Biology"], "users"=>["Peter M. Hollingsworth", "Sean W. Graham", "Damon P. Little"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019254", "stats"=>{"downloads"=>17, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Choosing_and_Using_a_Plant_DNA_Barcode/136410", "title"=>"Choosing and Using a Plant DNA Barcode", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-26 01:46:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/770997"], "description"=>"<p>Parts (A) and (B) each represent two species (one shades of red, one shades of blue), each consisting of three populations. The black line between the species indicates a barrier to gene flow, with the thickness of the line indicating the strength of the barrier. In (A) intra-specific gene flow among populations is high (indicated by the vertical arrows). Thus, where gene flow occurs between species (wavy arrow), there is a barrier to extensive neutral introgression because establishment of immigrant alleles is prevented by a regular influx of conspecific alleles from other populations. In (B) intra-specific gene flow among populations is low. Thus populations are more differentiated from one another and are less likely to show taxon-specific barcode markers. In addition, the flux preventing establishment of introgressed alleles is lower because it involves only alleles in the (middle) recipient population and not the other populations of the ‘blue’ species.</p>", "links"=>[], "tags"=>["impacts", "intra-specific"], "article_id"=>441372, "categories"=>["Plant Biology", "Evolutionary Biology"], "users"=>["Peter M. Hollingsworth", "Sean W. Graham", "Damon P. Little"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019254.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_the_impacts_of_intra_specific_gene_flow_on_species_discrimination_success_/441372", "title"=>"Schematic representation of the impacts of intra-specific gene flow on species discrimination success.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-26 00:22:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/771107"], "description"=>"<p>The table includes studies using a range of barcoding markers (beyond the <i>rbcL</i>+<i>matK</i> core barcode) to capture the broad spectrum of current applications.</p>", "links"=>[], "tags"=>["dna", "barcoding"], "article_id"=>441482, "categories"=>["Plant Biology", "Evolutionary Biology"], "users"=>["Peter M. Hollingsworth", "Sean W. Graham", "Damon P. Little"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019254.t003", "stats"=>{"downloads"=>7, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Applications_of_DNA_barcoding_in_plants_/441482", "title"=>"Applications of DNA barcoding in plants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-26 00:24:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/771156"], "description"=>"<p>Examples of plant DNA barcoding projects underway or in the planning stage in 2011.</p>", "links"=>[], "tags"=>["dna", "barcoding", "projects", "underway"], "article_id"=>441527, "categories"=>["Plant Biology", "Evolutionary Biology"], "users"=>["Peter M. Hollingsworth", "Sean W. Graham", "Damon P. Little"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019254.t004", "stats"=>{"downloads"=>4, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_plant_DNA_barcoding_projects_underway_or_in_the_planning_stage_in_2011_/441527", "title"=>"Examples of plant DNA barcoding projects underway or in the planning stage in 2011.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-26 00:25:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/771074"], "description"=>"<p>The number of sequences deposited in GenBank for each marker was estimated from sequence annotations and should be considered only as an approximation. Estimates of amplicon size (including priming sites) and frequencies of mononucleotide repeats were made from all annotated land plant whole plastid genomes deposited in GenBank and for nrITS from a curated set of nrITS sequences. Mononucleotide repeats less than 10 bp in length were excluded because these generally do not affect sequence quality <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Fazekas3\" target=\"_blank\">[36]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019254#pone.0019254-Fazekas4\" target=\"_blank\">[37]</a>.</p>", "links"=>[], "tags"=>["markers", "been", "included", "barcoding"], "article_id"=>441445, "categories"=>["Plant Biology", "Evolutionary Biology"], "users"=>["Peter M. Hollingsworth", "Sean W. Graham", "Damon P. Little"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019254.t001", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_different_markers_that_have_routinely_been_included_in_plant_barcoding_studies_/441445", "title"=>"Characteristics of different markers that have routinely been included in plant barcoding studies.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-26 00:24:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/771137"], "description"=>"<p>Key factors likely to lead to lower levels of success in species discrimination in DNA barcoding studies.</p>", "links"=>[], "tags"=>["factors", "levels", "dna", "barcoding"], "article_id"=>441505, "categories"=>["Plant Biology", "Evolutionary Biology"], "users"=>["Peter M. Hollingsworth", "Sean W. Graham", "Damon P. Little"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0019254.t002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Key_factors_likely_to_lead_to_lower_levels_of_success_in_species_discrimination_in_DNA_barcoding_studies_/441505", "title"=>"Key factors likely to lead to lower levels of success in species discrimination in DNA barcoding studies.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-26 00:25:05"}

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Relative Metric

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