Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well
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{"title"=>"Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well", "type"=>"journal", "authors"=>[{"first_name"=>"Aron J.", "last_name"=>"Fazekas", "scopus_author_id"=>"14029660900"}, {"first_name"=>"Kevin S.", "last_name"=>"Burgess", "scopus_author_id"=>"23007643100"}, {"first_name"=>"Prasad R.", "last_name"=>"Kesanakurti", "scopus_author_id"=>"24765476000"}, {"first_name"=>"Sean W.", "last_name"=>"Graham", "scopus_author_id"=>"7401977993"}, {"first_name"=>"Steven G.", "last_name"=>"Newmaster", "scopus_author_id"=>"6507138540"}, {"first_name"=>"Brian C.", "last_name"=>"Husband", "scopus_author_id"=>"7003473709"}, {"first_name"=>"Diana M.", "last_name"=>"Percy", "scopus_author_id"=>"7006754700"}, {"first_name"=>"Mehrdad", "last_name"=>"Hajibabaei", "scopus_author_id"=>"12240029000"}, {"first_name"=>"Spencer C.H.", "last_name"=>"Barrett", "scopus_author_id"=>"7201982686"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"18665273", "doi"=>"10.1371/journal.pone.0002802", "sgr"=>"50949125486", "isbn"=>"1932-6203 (Electronic)", "scopus"=>"2-s2.0-50949125486", "issn"=>"19326203", "pui"=>"352269662"}, "id"=>"db6c2ef7-2220-384f-964f-60400569f398", "abstract"=>"A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s). We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples). The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA) and three non-coding (trnH-psbA, atpF-atpH, and psbK-psbI) loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA) to 59% (trnH-psbA) of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85-100% for plastid loci), with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs). Several loci (matK, psbK-psbI, trnH-psbA) were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69-71%; values that were approached by several two- and three-region combinations). This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the contentious debate on plant barcoding should therefore involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barcoding systems.", "link"=>"http://www.mendeley.com/research/multiple-multilocus-dna-barcodes-plastid-genome-discriminate-plant-species-equally", "reader_count"=>373, "reader_count_by_academic_status"=>{"Unspecified"=>8, "Professor > Associate Professor"=>23, "Researcher"=>93, "Student > Doctoral Student"=>11, "Student > Ph. D. Student"=>93, "Student > Postgraduate"=>19, "Student > Master"=>51, "Other"=>7, "Student > Bachelor"=>43, "Lecturer"=>7, "Lecturer > Senior Lecturer"=>1, "Professor"=>17}, "reader_count_by_user_role"=>{"Unspecified"=>8, "Professor > Associate Professor"=>23, "Researcher"=>93, "Student > Doctoral Student"=>11, "Student > Ph. D. Student"=>93, "Student > Postgraduate"=>19, "Student > Master"=>51, "Other"=>7, "Student > Bachelor"=>43, "Lecturer"=>7, "Lecturer > Senior Lecturer"=>1, "Professor"=>17}, "reader_count_by_subject_area"=>{"Unspecified"=>16, "Engineering"=>1, "Environmental Science"=>21, "Biochemistry, Genetics and Molecular Biology"=>29, "Agricultural and Biological Sciences"=>291, "Medicine and Dentistry"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>3, "Chemistry"=>2, "Social Sciences"=>1, "Computer Science"=>3, "Earth and Planetary Sciences"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Chemistry"=>{"Chemistry"=>2}, "Social Sciences"=>{"Social Sciences"=>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"=>291}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>29}, "Unspecified"=>{"Unspecified"=>16}, "Environmental Science"=>{"Environmental Science"=>21}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>3}}, "reader_count_by_country"=>{"Argentina"=>1, "United States"=>8, "Uruguay"=>1, "Philippines"=>1, "United Kingdom"=>3, "Kenya"=>1, "Iceland"=>1, "Spain"=>4, "India"=>2, "Russia"=>1, "Canada"=>4, "Netherlands"=>2, "Sweden"=>1, "Pakistan"=>2, "Belgium"=>1, "Ireland"=>1, "Brazil"=>8, "Italy"=>5, "Nigeria"=>1, "Australia"=>1, "France"=>1, "Germany"=>6}, "group_count"=>10}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/926251"], "description"=>"<p>The number of regions used per combination is indicated by different symbols and colors (see legend). The specific regions used in each combination are noted in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002802#pone.0002802.s002\" target=\"_blank\">Table S2</a> (note that the combinations exclude <i>cox1</i> and 23S rDNA). Circled symbols correspond to combinations proposed in the recent plant barcoding literature (see text): 1) <i>rbcL</i>+<i>trnH-psbA</i>; 2) <i>matK</i>+<i>rpoC1</i>+<i>rpoB</i>; 3) <i>matK</i>+<i>rpoC1</i>+<i>trnH-psbA</i>; 4) <i>matK</i>+<i>atpF–atpH</i>+<i>psbK–psbI</i>; 5) <i>matK</i>+<i>atpF–atpH</i>+<i>trnH-psbA</i>. All regions are from the plastid genome (except <i>cox1</i>; mitochondrial genome).</p>", "links"=>[], "tags"=>["characters", "summed", "genus-level", "supported", "monophyletic", "genera", "bootstrap", "multilocus"], "article_id"=>596681, "categories"=>["Ecology", "Genetics", "Evolutionary Biology", "Plant Biology"], "users"=>["Aron J. Fazekas", "Kevin S. Burgess", "Prasad R. Kesanakurti", "Sean W. Graham", "Steven G. Newmaster", "Brian C. Husband", "Diana M. Percy", "Mehrdad Hajibabaei", "Spencer C. H. Barrett"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002802.g001", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relation_between_sequence_variation_PICs_8202_8202_parsimony_informative_characters_summed_across_genus_level_comparisons_and_percentage_species_resolution_species_supported_as_monophyletic_within_genera_with_at_least_70_bootstrap_support_for_a_selection/596681", "title"=>"Relation between sequence variation (PICs = parsimony-informative characters summed across genus-level comparisons) and percentage species resolution (species supported as monophyletic within genera with at least 70% bootstrap support) for a selection of single and multilocus combinations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-30 01:51:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/926496"], "description"=>"<p>Values indicate the number of species for each genus identified as monophyletic with at least 70% bootstrap support for each multi-locus combination; ‘M’ indicates that none of the species in that genus had more than one sample, or that only one species was amplified and sequenced.</p>", "links"=>[], "tags"=>["genus", "resolved", "monophyletic", "multilocus", "barcoding"], "article_id"=>596938, "categories"=>["Ecology", "Genetics", "Evolutionary Biology", "Plant Biology"], "users"=>["Aron J. Fazekas", "Kevin S. Burgess", "Prasad R. Kesanakurti", "Sean W. Graham", "Steven G. Newmaster", "Brian C. Husband", "Diana M. Percy", "Mehrdad Hajibabaei", "Spencer C. H. Barrett"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002802.t003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_species_per_genus_resolved_as_monophyletic_for_each_of_five_proposed_multilocus_barcoding_combinations_/596938", "title"=>"Number of species per genus resolved as monophyletic for each of five proposed multilocus barcoding combinations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-07-30 01:55:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/457424", "https://ndownloader.figshare.com/files/457496", "https://ndownloader.figshare.com/files/457554"], "description"=>"<div><p>A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s). We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (<em>N</em> = 251 samples). The plastid markers comprise portions of five coding (<em>rpoB</em>, <em>rpoC1</em>, <em>rbcL</em>, <em>matK</em> and 23S rDNA) and three non-coding (<em>trnH-psbA</em>, <em>atpF–atpH</em>, and <em>psbK–psbI</em>) loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA) to 59% (<em>trnH-psbA</em>) of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85–100% for plastid loci), with <em>mat</em>K requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs). Several loci (<em>matK</em>, <em>psbK–psbI</em>, <em>trnH-psbA</em>) were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69–71%; values that were approached by several two- and three-region combinations). This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the contentious debate on plant barcoding should therefore involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barcoding systems.</p></div>", "links"=>[], "tags"=>["multilocus", "dna", "barcodes", "plastid", "genome", "discriminate"], "article_id"=>150104, "categories"=>["Ecology", "Genetics", "Evolutionary Biology", "Cell Biology"], "users"=>["Aron J. Fazekas", "Kevin S. Burgess", "Prasad R. Kesanakurti", "Sean W. Graham", "Steven G. Newmaster", "Brian C. Husband", "Diana M. Percy", "Mehrdad Hajibabaei", "Spencer C. H. Barrett"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0002802.s001", "https://dx.doi.org/10.1371/journal.pone.0002802.s002", "https://dx.doi.org/10.1371/journal.pone.0002802.s003"], "stats"=>{"downloads"=>19, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Multiple_Multilocus_DNA_Barcodes_from_the_Plastid_Genome_Discriminate_Plant_Species_Equally_Well/150104", "title"=>"Multiple Multilocus DNA Barcodes from the Plastid Genome Discriminate Plant Species Equally Well", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-07-30 00:01:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/926461"], "description"=>"<p>Values indicate the number of species for each genus identified as monophyletic with at least 70% bootstrap support. ‘M’ indicates that none of the species in that genus had more than one sample, or that only one species was amplified; ‘NA’: amplifications not attempted in all species for this genus.</p>†<p>Low resolution (1 of 3 species) attributed to partial amplification success in this genus, rather than failure to form a monophyletic group.</p>", "links"=>[], "tags"=>["genus", "resolved", "monophyletic", "barcoding"], "article_id"=>596901, "categories"=>["Ecology", "Genetics", "Evolutionary Biology", "Plant Biology"], "users"=>["Aron J. Fazekas", "Kevin S. Burgess", "Prasad R. Kesanakurti", "Sean W. Graham", "Steven G. Newmaster", "Brian C. Husband", "Diana M. Percy", "Mehrdad Hajibabaei", "Spencer C. H. Barrett"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002802.t002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_species_per_genus_resolved_as_monophyletic_for_each_of_nine_candidate_barcoding_regions_/596901", "title"=>"Number of species per genus resolved as monophyletic for each of nine candidate barcoding regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-07-30 01:55:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/926361"], "description"=>"<p>Means (±SD) for two to six regions are based on the relatively arbitrarily chosen combinations of regions considered here (note that the plastid 23S rDNA locus and the mitochondrial locus <i>cox1</i> were not considered in these combinations). Least square regression: <i>R</i><sup>2</sup> = 0.73; y = 0.52+0.11 ln x = 0.05 (ln x−1.1)<sup>2</sup>; <i>F</i><sub>1,43</sub> = 56.8, <i>P</i><0.0001. Note: cpDNA = plastid DNA.</p>", "links"=>[], "tags"=>["plastid", "regions", "supported", "monophyletic", "genera", "bootstrap"], "article_id"=>596804, "categories"=>["Ecology", "Genetics", "Evolutionary Biology", "Plant Biology"], "users"=>["Aron J. Fazekas", "Kevin S. Burgess", "Prasad R. Kesanakurti", "Sean W. Graham", "Steven G. Newmaster", "Brian C. Husband", "Diana M. Percy", "Mehrdad Hajibabaei", "Spencer C. H. Barrett"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002802.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relation_between_the_number_of_plastid_regions_used_and_mean_percentage_species_resolution_species_supported_as_monophyletic_within_genera_with_at_least_70_bootstrap_support_/596804", "title"=>"Relation between the number of plastid regions used and mean percentage species resolution (species supported as monophyletic within genera with at least 70% bootstrap support).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-07-30 01:53:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/926421"], "description"=>"<p>Sequences from the first seven regions were sought for 251 samples representing 92 species. <i>Cox1</i> and 23S rDNA were attempted for 236 samples and 90 species. The sequence ranges used in the analysis are provided in reference to the complete plastid and mitochondrial genomes of <i>Arabidopsis thaliana</i> (Genbank accessions NC 000932, NC 001284).</p>†<p>Aligned across angiosperms and gymnosperms only.</p>††<p>Aligned across individual genera only.</p>‡<p>Based on trimmed alignments for coding regions.</p>*<p>92 species attempted, except 23S rDNA and <i>cox1</i> (90 species).</p>**<p>251 individuals attempted for all genes except 23S rDNA and <i>cox1</i> (236 individuals);</p>***<p>Percentage sequencing success (i.e., number of individuals successfully sequenced/number of individuals attempted);</p>¶<p>The number of reads represents the mean number of unidirectional sequences from successful amplifications that are required to establish a reliable sequence for each sample;</p>§<p>Sequences with less than 80% bidirectional coverage are primarily due to the presence of homopolymer runs.</p>", "links"=>[], "tags"=>["efficacy", "coding", "non-coding"], "article_id"=>596863, "categories"=>["Ecology", "Genetics", "Evolutionary Biology", "Plant Biology"], "users"=>["Aron J. Fazekas", "Kevin S. Burgess", "Prasad R. Kesanakurti", "Sean W. Graham", "Steven G. Newmaster", "Brian C. Husband", "Diana M. Percy", "Mehrdad Hajibabaei", "Spencer C. H. Barrett"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002802.t001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequencing_success_and_efficacy_for_six_coding_and_three_non_coding_regions_/596863", "title"=>"Sequencing success and efficacy for six coding and three non-coding regions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-07-30 01:54:23"}

PMC Usage Stats | Further Information

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Relative Metric

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