Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with Chlorella-Like Species (Chlorophyta)
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{"title"=>"Combining and comparing coalescent, distance and character-based approaches for barcoding microalgaes: A test with Chlorella-like species (Chlorophyta)", "type"=>"journal", "authors"=>[{"first_name"=>"Shanmei", "last_name"=>"Zou", "scopus_author_id"=>"56506341900"}, {"first_name"=>"Cong", "last_name"=>"Fei", "scopus_author_id"=>"57000051200"}, {"first_name"=>"Jiameng", "last_name"=>"Song", "scopus_author_id"=>"57189214903"}, {"first_name"=>"Yachao", "last_name"=>"Bao", "scopus_author_id"=>"57189219050"}, {"first_name"=>"Meilin", "last_name"=>"He", "scopus_author_id"=>"54793018500"}, {"first_name"=>"Changhai", "last_name"=>"Wang", "scopus_author_id"=>"56005082700"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84966440050", "doi"=>"10.1371/journal.pone.0153833", "isbn"=>"1932-6203", "pmid"=>"WOS:000374541200048", "issn"=>"19326203", "scopus"=>"2-s2.0-84966440050", "pui"=>"609983119"}, "id"=>"41b79015-ed64-36ba-bb76-f466559f80b5", "abstract"=>"Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. Chlorella is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of Chlorella-like organisms is easily confused. Here we report a comprehensive barcoding analysis of Chlorella-like species from Chlorella, Chloroidium, Dictyosphaerium and Actinastrum based on rbcL, ITS, tufA and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of Chlorella-like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in C. sorokiniana, D. ehrenbergianum and C. Vulgaris. The tufA proved to be the most efficient barcoding locus, which thus could be as potential \"specific barcode\" for Chlorella-like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among rbcL, ITS and tuf A genes. The best resolution for species differentiation appeared in tuf A analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of rbcL, ITS and tufA sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.", "link"=>"http://www.mendeley.com/research/combining-comparing-coalescent-distance-characterbased-approaches-barcoding-microalgaes-test-chlorel", "reader_count"=>19, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Student > Doctoral Student"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Student > Doctoral Student"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>2, "Other"=>2, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>8, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/4973461"], "description"=>"<p>Vertical bars on the right indicate the clades detected by the coalescent-based GMYC, PID, PTP, the distance-based ABGD approach, the character-based CAOS and the final assignment. Posterior probabilities and NJ bootstrap values were included.</p>", "links"=>[], "tags"=>["ABGD", "DNA", "16 S sequences", "barcoding", "GMYC", "Chlorella", "P ID", "method", "PTP", "tufA", "species discrimination"], "article_id"=>3186880, "categories"=>["Biophysics", "Genetics", "Molecular Biology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry", "Plant Biology"], "users"=>["Shanmei Zou", "Cong Fei", "Jiameng Song", "Yachao Bao", "Meilin He", "Changhai Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0153833.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Bayesian_phylogenetic_tree_for_the_ITS_gene_/3186880", "title"=>"Bayesian phylogenetic tree for the ITS gene.", "pos_in_sequence"=>3, "defined_type"=>1, "published_date"=>"2016-04-19 05:34:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4973497"], "description"=>"<p>Nucleotide numbers refer to 30 selected positions on the <i>tufA</i> sequences (positions 19–673).</p>", "links"=>[], "tags"=>["ABGD", "DNA", "16 S sequences", "barcoding", "GMYC", "Chlorella", "P ID", "method", "PTP", "tufA", "species discrimination"], "article_id"=>3186913, "categories"=>["Biophysics", "Genetics", "Molecular Biology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry", "Plant Biology"], "users"=>["Shanmei Zou", "Cong Fei", "Jiameng Song", "Yachao Bao", "Meilin He", "Changhai Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0153833.g008", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Combinations_of_diagnostic_nucleotides_for_each_of_the_14_i_Chlorella_i_like_taxa_recovered_in_Fig_3_/3186913", "title"=>"Combinations of diagnostic nucleotides for each of the 14 <i>Chlorella</i>-like taxa recovered in Fig 3.", "pos_in_sequence"=>9, "defined_type"=>1, "published_date"=>"2016-04-19 05:34:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4973467"], "description"=>"<p><i>Vertical bars on the right</i> indicate the clades detected by the coalescent-based GMYC, PID, PTP, the distance-based ABGD approach, the character-based CAOS and the final assignment. Posterior probabilities and NJ bootstrap values were included.</p>", "links"=>[], "tags"=>["ABGD", "DNA", "16 S sequences", "barcoding", "GMYC", "Chlorella", "P ID", "method", "PTP", "tufA", "species discrimination"], "article_id"=>3186883, "categories"=>["Biophysics", "Genetics", "Molecular Biology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry", "Plant Biology"], "users"=>["Shanmei Zou", "Cong Fei", "Jiameng Song", "Yachao Bao", "Meilin He", "Changhai Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0153833.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Bayesian_phylogenetic_tree_for_the_i_tufA_i_gene_/3186883", "title"=>"Bayesian phylogenetic tree for the <i>tufA</i> gene.", "pos_in_sequence"=>4, "defined_type"=>1, "published_date"=>"2016-04-19 05:34:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4973473"], "description"=>"<p><b>A</b> (a): Histograms of intra- (in blue) and inter-specific (in red) average distances between <i>rbcL</i> sequences; (b): Histograms of intra- (in blue) and inter-specific (in red) pairwise distances between <i>rbcL</i> sequences. <b>B</b> (a): Histograms of intra- (in blue) and inter-specific (in red) average distances between ITS sequences; (b) Histograms of intra- (in blue) and inter-specific (in red) pairwise distances between ITS sequences.</p>", "links"=>[], "tags"=>["ABGD", "DNA", "16 S sequences", "barcoding", "GMYC", "Chlorella", "P ID", "method", "PTP", "tufA", "species discrimination"], "article_id"=>3186889, "categories"=>["Biophysics", "Genetics", "Molecular Biology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry", "Plant Biology"], "users"=>["Shanmei Zou", "Cong Fei", "Jiameng Song", "Yachao Bao", "Meilin He", "Changhai Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0153833.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Combining_and_Comparing_Coalescent_Distance_and_Character_Based_Approaches_for_Barcoding_Microalgaes_A_Test_with_i_Chlorella_i_Like_Species_Chlorophyta_Fig_4/3186889", "title"=>"Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with <i>Chlorella</i>-Like Species (Chlorophyta) - Fig 4", "pos_in_sequence"=>5, "defined_type"=>1, "published_date"=>"2016-04-19 05:34:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4973374", "https://ndownloader.figshare.com/files/4973434", "https://ndownloader.figshare.com/files/4973431", "https://ndownloader.figshare.com/files/4973428", "https://ndownloader.figshare.com/files/4973425", "https://ndownloader.figshare.com/files/4973422", "https://ndownloader.figshare.com/files/4973419", "https://ndownloader.figshare.com/files/4973416", "https://ndownloader.figshare.com/files/4973413", "https://ndownloader.figshare.com/files/4973407", "https://ndownloader.figshare.com/files/4973404", "https://ndownloader.figshare.com/files/4973398", "https://ndownloader.figshare.com/files/4973395", "https://ndownloader.figshare.com/files/4973392", "https://ndownloader.figshare.com/files/4973389", "https://ndownloader.figshare.com/files/4973386", "https://ndownloader.figshare.com/files/4973383", "https://ndownloader.figshare.com/files/4973377", "https://ndownloader.figshare.com/files/4973437"], "description"=>"<div><p>Several different barcoding methods of distinguishing species have been advanced, but which method is the best is still controversial. <i>Chlorella</i> is becoming particularly promising in the development of second-generation biofuels. However, the taxonomy of <i>Chlorella–</i>like organisms is easily confused. Here we report a comprehensive barcoding analysis of <i>Chlorella-</i>like species from <i>Chlorella</i>, <i>Chloroidium</i>, <i>Dictyosphaerium</i> and <i>Actinastrum</i> based on <i>rbcL</i>, ITS, <i>tufA</i> and 16S sequences to test the efficiency of traditional barcoding, GMYC, ABGD, PTP, P ID and character-based barcoding methods. First of all, the barcoding results gave new insights into the taxonomic assessment of <i>Chlorella-</i>like organisms studied, including the clear species discrimination and resolution of potentially cryptic species complexes in <i>C</i>. <i>sorokiniana</i>, <i>D</i>. <i>ehrenbergianum</i> and <i>C</i>. <i>Vulgaris</i>. The <i>tufA</i> proved to be the most efficient barcoding locus, which thus could be as potential “specific barcode” for <i>Chlorella-</i>like species. The 16S failed in discriminating most closely related species. The resolution of GMYC, PTP, P ID, ABGD and character-based barcoding methods were variable among <i>rbcL</i>, ITS and <i>tufA</i> genes. The best resolution for species differentiation appeared in <i>tufA</i> analysis where GMYC, PTP, ABGD and character-based approaches produced consistent groups while the PTP method over-split the taxa. The character analysis of <i>rbcL</i>, ITS and <i>tufA</i> sequences could clearly distinguish all taxonomic groups respectively, including the potentially cryptic lineages, with many character attributes. Thus, the character-based barcoding provides an attractive complement to coalescent and distance-based barcoding. Our study represents the test that proves the efficiency of multiple DNA barcoding in species discrimination of microalgaes.</p></div>", "links"=>[], "tags"=>["ABGD", "DNA", "16 S sequences", "barcoding", "GMYC", "Chlorella", "P ID", "method", "PTP", "tufA", "species discrimination"], "article_id"=>3186862, "categories"=>["Biophysics", "Genetics", "Molecular Biology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry", "Plant Biology"], "users"=>["Shanmei Zou", "Cong Fei", "Jiameng Song", "Yachao Bao", "Meilin He", "Changhai Wang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0153833.s001", "https://dx.doi.org/10.1371/journal.pone.0153833.s018", "https://dx.doi.org/10.1371/journal.pone.0153833.s017", "https://dx.doi.org/10.1371/journal.pone.0153833.s016", "https://dx.doi.org/10.1371/journal.pone.0153833.s015", "https://dx.doi.org/10.1371/journal.pone.0153833.s014", "https://dx.doi.org/10.1371/journal.pone.0153833.s013", "https://dx.doi.org/10.1371/journal.pone.0153833.s012", "https://dx.doi.org/10.1371/journal.pone.0153833.s011", "https://dx.doi.org/10.1371/journal.pone.0153833.s010", "https://dx.doi.org/10.1371/journal.pone.0153833.s009", "https://dx.doi.org/10.1371/journal.pone.0153833.s008", "https://dx.doi.org/10.1371/journal.pone.0153833.s007", "https://dx.doi.org/10.1371/journal.pone.0153833.s006", "https://dx.doi.org/10.1371/journal.pone.0153833.s005", "https://dx.doi.org/10.1371/journal.pone.0153833.s004", "https://dx.doi.org/10.1371/journal.pone.0153833.s003", "https://dx.doi.org/10.1371/journal.pone.0153833.s002", "https://dx.doi.org/10.1371/journal.pone.0153833.s019"], "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Combining_and_Comparing_Coalescent_Distance_and_Character_Based_Approaches_for_Barcoding_Microalgaes_A_Test_with_i_Chlorella_i_Like_Species_Chlorophyta_/3186862", "title"=>"Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with <i>Chlorella</i>-Like Species (Chlorophyta)", "pos_in_sequence"=>1, "defined_type"=>4, "published_date"=>"2016-04-19 05:34:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4973479"], "description"=>"<p>(a) Histograms of intra- (in blue) and inter-specific (in red) average distances between <i>tufA</i> sequences; (b) Histograms of intra- (in blue) and inter-specific (in red) pairwise distances between <i>tufA</i> sequences.</p>", "links"=>[], "tags"=>["ABGD", "DNA", "16 S sequences", "barcoding", "GMYC", "Chlorella", "P ID", "method", "PTP", "tufA", "species discrimination"], "article_id"=>3186895, "categories"=>["Biophysics", "Genetics", "Molecular Biology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry", "Plant Biology"], "users"=>["Shanmei Zou", "Cong Fei", "Jiameng Song", "Yachao Bao", "Meilin He", "Changhai Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0153833.g005", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Combining_and_Comparing_Coalescent_Distance_and_Character_Based_Approaches_for_Barcoding_Microalgaes_A_Test_with_i_Chlorella_i_Like_Species_Chlorophyta_Fig_5/3186895", "title"=>"Combining and Comparing Coalescent, Distance and Character-Based Approaches for Barcoding Microalgaes: A Test with <i>Chlorella</i>-Like Species (Chlorophyta) - Fig 5", "pos_in_sequence"=>6, "defined_type"=>1, "published_date"=>"2016-04-19 05:34:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4973485"], "description"=>"<p>Nucleotide numbers refer to 45 selected positions on the <i>rbcL</i> sequences (positions 151 to 998).</p>", "links"=>[], "tags"=>["ABGD", "DNA", "16 S sequences", "barcoding", "GMYC", "Chlorella", "P ID", "method", "PTP", "tufA", "species discrimination"], "article_id"=>3186901, "categories"=>["Biophysics", "Genetics", "Molecular Biology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry", "Plant Biology"], "users"=>["Shanmei Zou", "Cong Fei", "Jiameng Song", "Yachao Bao", "Meilin He", "Changhai Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0153833.g006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Combinations_of_diagnostic_nucleotides_for_each_of_the_31_i_Chlorella_i_like_taxa_recovered_in_Fig_1_/3186901", "title"=>"Combinations of diagnostic nucleotides for each of the 31 <i>Chlorella</i>-like taxa recovered in Fig 1.", "pos_in_sequence"=>7, "defined_type"=>1, "published_date"=>"2016-04-19 05:34:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4973491"], "description"=>"<p>Nucleotide numbers refer to 44 selected positions on the ITS sequences (positions 229–1069).</p>", "links"=>[], "tags"=>["ABGD", "DNA", "16 S sequences", "barcoding", "GMYC", "Chlorella", "P ID", "method", "PTP", "tufA", "species discrimination"], "article_id"=>3186907, "categories"=>["Biophysics", "Genetics", "Molecular Biology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry", "Plant Biology"], "users"=>["Shanmei Zou", "Cong Fei", "Jiameng Song", "Yachao Bao", "Meilin He", "Changhai Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0153833.g007", "stats"=>{"downloads"=>4, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Combinations_of_diagnostic_nucleotides_for_each_of_the_20_i_Chlorella_i_like_taxa_recovered_in_Fig_2_/3186907", "title"=>"Combinations of diagnostic nucleotides for each of the 20 <i>Chlorella</i>-like taxa recovered in Fig 2.", "pos_in_sequence"=>8, "defined_type"=>1, "published_date"=>"2016-04-19 05:34:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/4973452"], "description"=>"<p><i>Vertical bars on the right</i> indicate the clades detected by the coalescent-based GMYC, PID, PTP, the distance-based ABGD approach, the character-based CAOS and the final assignment. Posterior probabilities and NJ bootstrap values were included.</p>", "links"=>[], "tags"=>["ABGD", "DNA", "16 S sequences", "barcoding", "GMYC", "Chlorella", "P ID", "method", "PTP", "tufA", "species discrimination"], "article_id"=>3186877, "categories"=>["Biophysics", "Genetics", "Molecular Biology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Chemical Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Inorganic Chemistry", "Plant Biology"], "users"=>["Shanmei Zou", "Cong Fei", "Jiameng Song", "Yachao Bao", "Meilin He", "Changhai Wang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0153833.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Bayesian_phylogenetic_tree_for_the_i_rbcL_i_gene_/3186877", "title"=>"Bayesian phylogenetic tree for the <i>rbcL</i> gene.", "pos_in_sequence"=>2, "defined_type"=>1, "published_date"=>"2016-04-19 05:34:41"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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