Identifying and Characterizing Alternative Molecular Markers for the Symbiotic and Free-Living Dinoflagellate Genus Symbiodinium
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{"title"=>"Identifying and characterizing alternative molecular markers for the symbiotic and free-living dinoflagellate genus symbiodinium", "type"=>"journal", "authors"=>[{"first_name"=>"Xavier", "last_name"=>"Pochon", "scopus_author_id"=>"6508177987"}, {"first_name"=>"Hollie M.", "last_name"=>"Putnam", "scopus_author_id"=>"25621868600"}, {"first_name"=>"Fabien", "last_name"=>"Burki", "scopus_author_id"=>"57191566814"}, {"first_name"=>"Ruth D.", "last_name"=>"Gates", "scopus_author_id"=>"7102178009"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84855406723", "sgr"=>"84855406723", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22238660", "doi"=>"10.1371/journal.pone.0029816", "pui"=>"364037787"}, "id"=>"fc676b43-d304-3604-b0f5-46a7e4d4fc80", "abstract"=>"Dinoflagellates in the genus Symbiodinium are best known as endosymbionts of corals and other invertebrate as well as protist hosts, but also exist free-living in coastal environments. Despite their importance in marine ecosystems, less than 10 loci have been used to explore phylogenetic relationships in this group, and only the multi-copy nuclear ribosomal Internal Transcribed Spacer (ITS) regions 1 and 2 have been used to characterize fine-scale genetic diversity within the nine clades (A-I) that comprise the genus. Here, we describe a three-step molecular approach focused on 1) identifying new candidate genes for phylogenetic analysis of Symbiodinium spp., 2) characterizing the phylogenetic relationship of these candidate genes from DNA samples spanning eight Symbiodinium clades (A-H), and 3) conducting in-depth phylogenetic analyses of candidate genes displaying genetic divergences equal or higher than those within the ITS-2 of Symbiodinium clade C. To this end, we used bioinformatics tools and reciprocal comparisons to identify homologous genes from 55,551 cDNA sequences representing two Symbiodinium and six additional dinoflagellate EST libraries. Of the 84 candidate genes identified, 7 Symbiodinium genes (elf2, coI, coIII, cob, calmodulin, rad24, and actin) were characterized by sequencing 23 DNA samples spanning eight Symbiodinium clades (A-H). Four genes displaying higher rates of genetic divergences than ITS-2 within clade C were selected for in-depth phylogenetic analyses, which revealed that calmodulin has limited taxonomic utility but that coI, rad24, and actin behave predictably with respect to Symbiodinium lineage C and are potential candidates as new markers for this group. The approach for targeting candidate genes described here can serve as a model for future studies aimed at identifying and testing new phylogenetically informative genes for taxa where transcriptomic and genomics data are available.", "link"=>"http://www.mendeley.com/research/identifying-characterizing-alternative-molecular-markers-symbiotic-freeliving-dinoflagellate-genus-s", "reader_count"=>136, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>5, "Researcher"=>24, "Student > Ph. D. Student"=>49, "Student > Postgraduate"=>7, "Student > Master"=>25, "Other"=>3, "Student > Bachelor"=>13, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>3, "Student > Doctoral Student"=>5, "Researcher"=>24, "Student > Ph. D. Student"=>49, "Student > Postgraduate"=>7, "Student > Master"=>25, "Other"=>3, "Student > Bachelor"=>13, "Lecturer"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>9, "Environmental Science"=>13, "Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>97, "Neuroscience"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>97}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Unspecified"=>{"Unspecified"=>9}, "Environmental Science"=>{"Environmental Science"=>13}}, "reader_count_by_country"=>{"United States"=>4, "Japan"=>2, "United Kingdom"=>1, "Russia"=>1, "New Zealand"=>2, "Guadeloupe"=>1, "Ireland"=>1, "Taiwan"=>2, "Finland"=>1, "Brazil"=>3, "Mexico"=>1, "France"=>1, "Australia"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/354041", "https://ndownloader.figshare.com/files/354125", "https://ndownloader.figshare.com/files/354214", "https://ndownloader.figshare.com/files/354304", "https://ndownloader.figshare.com/files/354427", "https://ndownloader.figshare.com/files/354596", "https://ndownloader.figshare.com/files/354661", "https://ndownloader.figshare.com/files/354704"], "description"=>"<div><p>Dinoflagellates in the genus <em>Symbiodinium</em> are best known as endosymbionts of corals and other invertebrate as well as protist hosts, but also exist free-living in coastal environments. Despite their importance in marine ecosystems, less than 10 loci have been used to explore phylogenetic relationships in this group, and only the multi-copy nuclear ribosomal Internal Transcribed Spacer (<em>ITS</em>) regions 1 and 2 have been used to characterize fine-scale genetic diversity within the nine clades (A–I) that comprise the genus. Here, we describe a three-step molecular approach focused on <em>1</em>) identifying new candidate genes for phylogenetic analysis of <em>Symbiodinium</em> spp., <em>2</em>) characterizing the phylogenetic relationship of these candidate genes from DNA samples spanning eight <em>Symbiodinium</em> clades (A–H), and <em>3</em>) conducting in-depth phylogenetic analyses of candidate genes displaying genetic divergences equal or higher than those within the <em>ITS-2</em> of <em>Symbiodinium</em> clade C. To this end, we used bioinformatics tools and reciprocal comparisons to identify homologous genes from 55,551 cDNA sequences representing two <em>Symbiodinium</em> and six additional dinoflagellate EST libraries. Of the 84 candidate genes identified, 7 <em>Symbiodinium</em> genes (<em>elf2</em>, <em>coI</em>, <em>coIII</em>, <em>cob</em>, <em>calmodulin</em>, <em>rad24</em>, and <em>actin</em>) were characterized by sequencing 23 DNA samples spanning eight <em>Symbiodinium</em> clades (A–H). Four genes displaying higher rates of genetic divergences than <em>ITS-2</em> within clade C were selected for in-depth phylogenetic analyses, which revealed that <em>calmodulin</em> has limited taxonomic utility but that <em>coI</em>, <em>rad24</em>, and <em>actin</em> behave predictably with respect to <em>Symbiodinium</em> lineage C and are potential candidates as new markers for this group. The approach for targeting candidate genes described here can serve as a model for future studies aimed at identifying and testing new phylogenetically informative genes for taxa where transcriptomic and genomics data are available.</p> </div>", "links"=>[], "tags"=>["identifying", "characterizing", "molecular", "markers", "symbiotic", "free-living", "dinoflagellate", "genus"], "article_id"=>129965, "categories"=>["Inorganic Chemistry", "Information And Computing Sciences", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Xavier Pochon", "Hollie M. Putnam", "Fabien Burki", "Ruth D. Gates"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0029816.s001", "https://dx.doi.org/10.1371/journal.pone.0029816.s002", "https://dx.doi.org/10.1371/journal.pone.0029816.s003", "https://dx.doi.org/10.1371/journal.pone.0029816.s004", "https://dx.doi.org/10.1371/journal.pone.0029816.s005", "https://dx.doi.org/10.1371/journal.pone.0029816.s006", "https://dx.doi.org/10.1371/journal.pone.0029816.s007", "https://dx.doi.org/10.1371/journal.pone.0029816.s008"], "stats"=>{"downloads"=>33, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Identifying_and_Characterizing_Alternative_Molecular_Markers_for_the_Symbiotic_and_Free_Living_Dinoflagellate_Genus_Symbiodinium_/129965", "title"=>"Identifying and Characterizing Alternative Molecular Markers for the Symbiotic and Free-Living Dinoflagellate Genus <em>Symbiodinium</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-01-04 02:46:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/695917"], "description"=>"a<p>Letters A to H correspond to the <i>Symbiodinium</i> clades. Species names of outgroup samples are indicated: <i>Gymnodinium simplex</i>, <i>Pelagodinium beii</i>, and <i>Polarella glacialis</i>.</p>b<p>Alpha-numeric names correspond to <i>Symbiodinium ITS-2</i> rDNA molecular taxonomy sensu <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816-Pochon3\" target=\"_blank\">[71]</a>. Letters correspond to the <i>Symbiodinium</i> clades, and numbers correspond to a specific <i>ITS-2</i> sequence. All samples are genetically distinct, except for <i>Symbiodinium</i> A2, which was found in two distinct cultures and referred here to as A2_1 and A2_2. Sample D1.2 corresponds to the PSP1-05 sample originally isolated from the sponge <i>Haliclona koremella</i> (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816-Pochon3\" target=\"_blank\">[71]</a> for details).</p>c<p>Culture names of DNAs extracted from <i>Symbiodinium</i> cultures. N/A = Not Available.</p><p>*Indicates new sequences.</p>", "links"=>[], "tags"=>["genomic", "dnas"], "article_id"=>366339, "categories"=>["Inorganic Chemistry", "Information And Computing Sciences", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Xavier Pochon", "Hollie M. Putnam", "Fabien Burki", "Ruth D. Gates"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029816.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Description_of_the_genomic_DNAs_used_in_this_study_/366339", "title"=>"Description of the genomic DNAs used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-04 01:45:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/695855"], "description"=>"<p>Characteristics of the four genes (<i>coI</i>, <i>calmodulin</i>, <i>rad24</i>, and <i>actin</i>) selected for in-depth phylogenetic analyses.</p>", "links"=>[], "tags"=>["genes", "in-depth", "phylogenetic"], "article_id"=>366275, "categories"=>["Inorganic Chemistry", "Information And Computing Sciences", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Xavier Pochon", "Hollie M. Putnam", "Fabien Burki", "Ruth D. Gates"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029816.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_the_four_genes_coI_calmodulin_rad24_and_actin_selected_for_in_depth_phylogenetic_analyses_/366275", "title"=>"Characteristics of the four genes (<i>coI</i>, <i>calmodulin</i>, <i>rad24</i>, and <i>actin</i>) selected for in-depth phylogenetic analyses.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-04 01:44:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/695757"], "description"=>"<p>(<b>A</b>) 71 nuclear large subunit (<i>nr28S</i>) sequences (alignment size: 915 bp) (<b>B</b>) 26 cytochrome oxidase subunit 1 (<i>coI</i>) sequences (1057 bp), (<b>C</b>) 92 <i>calmodulin</i> sequences (154 bp), (<b>D</b>) 73 <i>rad24</i> sequences (580 bp), and (<b>E</b>) 71 <i>actin</i> sequences (925 bp). The <i>nr28S</i> topology is used here as the benchmark marker, with colors corresponding to clades A (red), B (pink), C (green), D (brown), E (orange), F (dark blue), G (yellow), and H (light blue). Phylogenies are rooted using the dinoflagellates <i>Gymnodinium simplex</i>, <i>Pelagodinium beii</i>, and <i>Polarella glacialis</i>. Detailed phylogenetic reconstructions, including node support values from the ML bootstrap analyses and Bayesian posterior probabilities, as well as the GenBank accession numbers, are shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s001\" target=\"_blank\">Figures S1</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s002\" target=\"_blank\">S2</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s003\" target=\"_blank\">S3</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s004\" target=\"_blank\">S4</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s005\" target=\"_blank\">S5</a>.</p>", "links"=>[], "tags"=>["benchmark"], "article_id"=>366178, "categories"=>["Inorganic Chemistry", "Information And Computing Sciences", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Xavier Pochon", "Hollie M. Putnam", "Fabien Burki", "Ruth D. Gates"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029816.g003", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Topological_comparison_of_benchmark_nr28S_and_four_selected_candidate_genes_/366178", "title"=>"Topological comparison of benchmark <i>nr28S</i> and four selected candidate genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-04 01:42:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/695450"], "description"=>"<p>Flow diagram of the step-wise procedure for molecular marker identification.</p>", "links"=>[], "tags"=>["diagram", "step-wise", "molecular"], "article_id"=>365872, "categories"=>["Inorganic Chemistry", "Information And Computing Sciences", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Xavier Pochon", "Hollie M. Putnam", "Fabien Burki", "Ruth D. Gates"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029816.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flow_diagram_of_the_step_wise_procedure_for_molecular_marker_identification_/365872", "title"=>"Flow diagram of the step-wise procedure for molecular marker identification.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-04 01:37:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/695948"], "description"=>"<p>The minimum, maximum and averaged uncorrected genetic distances among clade C <i>Symbiodinium</i> types are indicated for each marker investigated. Calculations for <i>calmodulin</i>, <i>rad24</i>, and <i>actin</i> were made on sequence alignments excluding (−) and including (+) introns.</p>a<p>No sequences were obtained for <i>Symbiodinium</i> C90 and C91 so only two types were compared.</p>b<p>No sequences were obtained for <i>Symbiodinium</i> C90, so only three types were compared.</p>", "links"=>[], "tags"=>["divergence", "rates", "markers", "types"], "article_id"=>366363, "categories"=>["Inorganic Chemistry", "Information And Computing Sciences", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Xavier Pochon", "Hollie M. Putnam", "Fabien Burki", "Ruth D. Gates"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029816.t003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimation_of_divergence_rates_between_markers_for_Symbiodinium_types_C1_C15_C90_and_C91_/366363", "title"=>"Estimation of divergence rates between markers for <i>Symbiodinium</i> types C1, C15, C90, and C91.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-04 01:46:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/695624"], "description"=>"<p>Positions and numbers of coding (exons [E]; shown in green) and non-coding regions (introns [I]; shown in red) in the genes <i>calmodulin</i> (<b>A</b>), <i>rad24</i> (<b>B</b>), and <i>actin</i> (<b>C</b>). The sizes of the non-coding regions indicated here depict the maximum intron size recorded in genomic samples in each <i>Symbiodinium</i> clade. DNA alignments ranged from 1,107 bp to 3,087 bp in length and letters A to H correspond to the eight <i>Symbiodinium</i> clades.</p>", "links"=>[], "tags"=>["intron-containing"], "article_id"=>366044, "categories"=>["Inorganic Chemistry", "Information And Computing Sciences", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Xavier Pochon", "Hollie M. Putnam", "Fabien Burki", "Ruth D. Gates"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029816.g002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Intron_position_mapping_of_three_intron_containing_genes_/366044", "title"=>"Intron position mapping of three intron-containing genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-04 01:40:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/695897"], "description"=>"<p>Genes are sorted by decreasing level of transcript abundance in the two <i>Symbiodinium</i> EST libraries combined. Details of the EST libraries displaying hits in BLASTn are indicated for each gene by letters A, C, Ac, At, Ht, Kb, Km, and Lp, which correspond to EST libraries <i>Symbiodinium</i> A, <i>Symbiodinium</i> C, <i>Amphidinium carterae</i>, <i>Alexandrium tamarense</i>, <i>Heterocapsa triquetra</i>, <i>Karenia brevis</i>, <i>Karlodinium micrum</i>, and <i>Lingulodinium polyedrum</i>, respectively. Protein descriptions were obtained using BLASTx. The complete list of candidate genes (n = 84) identified after BLASTn comparisons of eight dinoflagellate EST libraries is presented in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s006\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["eighty-four", "genes", "downstream"], "article_id"=>366314, "categories"=>["Inorganic Chemistry", "Information And Computing Sciences", "Genetics", "Biological Sciences", "Ecology", "Evolutionary Biology"], "users"=>["Xavier Pochon", "Hollie M. Putnam", "Fabien Burki", "Ruth D. Gates"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0029816.t001", "stats"=>{"downloads"=>3, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Seven_out_of_eighty_four_candidate_genes_selected_for_downstream_analyses_/366314", "title"=>"Seven out of eighty-four candidate genes selected for downstream analyses.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-04 01:45:14"}

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[366, 574, 695, 795, 885, 973, 1063, 1148, 1233, 1319, 1389, 1459, 1533, 1611, 1685, 1754, 1820, 1882, 1937, 2001, 2071, 2129, 2219, 2273, 2335]}, {"subject_area"=>"/Computer and information sciences", "average_usage"=>[352, 587, 696, 809, 901, 989, 1072, 1156, 1257, 1334, 1422, 1486, 1555, 1647, 1714, 1780, 1844, 1919, 1997, 2051, 2138, 2198, 2267, 2324, 2391]}]}
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