LTR-Retrotransposons in R. exoculata and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements
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{"title"=>"LTR-Retrotransposons in R. exoculata and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements", "type"=>"journal", "authors"=>[{"first_name"=>"Mathieu", "last_name"=>"Piednoël", "scopus_author_id"=>"25825411600"}, {"first_name"=>"Tifenn", "last_name"=>"Donnart", "scopus_author_id"=>"37018111800"}, {"first_name"=>"Caroline", "last_name"=>"Esnault", "scopus_author_id"=>"24340619400"}, {"first_name"=>"Paula", "last_name"=>"Graça", "scopus_author_id"=>"6602386229"}, {"first_name"=>"Dominique", "last_name"=>"Higuet", "scopus_author_id"=>"6602475976"}, {"first_name"=>"Eric", "last_name"=>"Bonnivard", "scopus_author_id"=>"6602796805"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"368465164", "sgr"=>"84874618441", "pmid"=>"23469217", "scopus"=>"2-s2.0-84874618441", "isbn"=>"1932-6203", "doi"=>"10.1371/journal.pone.0057675", "issn"=>"19326203"}, "id"=>"59161f6b-96df-3c4c-8b2c-e0c375a311a2", "abstract"=>"Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. They can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. LTR-retrotransposons have been reported in many diverse eukaryote species, describing a ubiquitous distribution. Given their abundance, diversity and their extended ranges in C-values, environment and life styles, crustaceans are a great taxon to investigate the genomic component of adaptation and its possible relationships with TEs. However, crustaceans have been greatly underrepresented in transposable element studies. Using both degenerate PCR and approaches, we have identified 35 Copia and 46 Gypsy families in 15 and 18 crustacean species, respectively. In particular, we characterized several full-length elements from the shrimp that is listed as a model organism from hydrothermal vents. Phylogenic analyses show that Copia and Gypsy retrotransposons likely present two opposite dynamics within crustaceans. The Gypsy elements appear relatively frequent and diverse whereas Copia are much more homogeneous, as 29 of them belong to the single GalEa clade, and species- or lineage-dependent. Our results also support the hypothesis of the Copia retrotransposon scarcity in metazoans compared to Gypsy elements. In such a context, the GalEa-like elements present an outstanding wide distribution among eukaryotes, from fishes to red algae, and can be even highly predominant within a large taxon, such as Malacostraca. Their distribution among crustaceans suggests a dynamics that follows a \"domino days spreading\" branching process in which successive amplifications may interact positively.", "link"=>"http://www.mendeley.com/research/ltrretrotransposons-r-exoculata-other-crustaceans-outstanding-success-galealike-copia-elements", "reader_count"=>22, "reader_count_by_academic_status"=>{"Librarian"=>1, "Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>1, "Student > Master"=>6, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Librarian"=>1, "Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Postgraduate"=>1, "Student > Master"=>6, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>15, "Veterinary Science and Veterinary Medicine"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Environmental Science"=>{"Environmental Science"=>2}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Canada"=>2, "Brazil"=>2}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/977072"], "description"=>"<p>Genetic relationships between crustacean classes and orders are represented by a tree topology reconstructed from previous studies (Regier <i>et al.</i> 2010, Giribet and Edgecombe, 2011; Ahyong and O’Meally, 2004). <b>M</b>: Malacostraca, <b>D</b>: Decapoda. For Copia retrotransposons, GalEa and non-GalEa elements are distinguished. Only a few representatives of the Copia elements described <i>in D. pulex</i> were studied. nt: not tested; -: no element detected; <sup>a</sup> species screened using degenerate PCRs.</p>", "links"=>[], "tags"=>["copia", "gypsy", "elements", "studied"], "article_id"=>644400, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Mathieu Piednoël", "Tifenn Donnart", "Caroline Esnault", "Paula Graça", "Dominique Higuet", "Eric Bonnivard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057675.g002", "stats"=>{"downloads"=>2, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_Copia_and_Gypsy_elements_studied_in_crustaceans_/644400", "title"=>"Number of Copia and Gypsy elements studied in crustaceans.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-05 10:54:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/977079", "https://ndownloader.figshare.com/files/977080", "https://ndownloader.figshare.com/files/977084", "https://ndownloader.figshare.com/files/977085", "https://ndownloader.figshare.com/files/977086"], "description"=>"<div><p>Transposable elements are major constituents of eukaryote genomes and have a great impact on genome structure and stability. They can contribute to the genetic diversity and evolution of organisms. Knowledge of their distribution among several genomes is an essential condition to study their dynamics and to better understand their role in species evolution. LTR-retrotransposons have been reported in many diverse eukaryote species, describing a ubiquitous distribution. Given their abundance, diversity and their extended ranges in C-values, environment and life styles, crustaceans are a great taxon to investigate the genomic component of adaptation and its possible relationships with TEs. However, crustaceans have been greatly underrepresented in transposable element studies. Using both degenerate PCR and <i>in silico</i> approaches, we have identified 35 Copia and 46 Gypsy families in 15 and 18 crustacean species, respectively. In particular, we characterized several full-length elements from the shrimp <i>Rimicaris exoculata</i> that is listed as a model organism from hydrothermal vents. Phylogenic analyses show that Copia and Gypsy retrotransposons likely present two opposite dynamics within crustaceans. The Gypsy elements appear relatively frequent and diverse whereas Copia are much more homogeneous, as 29 of them belong to the single GalEa clade, and species- or lineage-dependent. Our results also support the hypothesis of the Copia retrotransposon scarcity in metazoans compared to Gypsy elements. In such a context, the GalEa-like elements present an outstanding wide distribution among eukaryotes, from fishes to red algae, and can be even highly predominant within a large taxon, such as Malacostraca. Their distribution among crustaceans suggests a dynamics that follows a “domino days spreading” branching process in which successive amplifications may interact positively.</p> </div>", "links"=>[], "tags"=>["ltr-retrotransposons", "galea-like", "copia", "elements"], "article_id"=>644405, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Mathieu Piednoël", "Tifenn Donnart", "Caroline Esnault", "Paula Graça", "Dominique Higuet", "Eric Bonnivard"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057675.s001", "https://dx.doi.org/10.1371/journal.pone.0057675.s002", "https://dx.doi.org/10.1371/journal.pone.0057675.s003", "https://dx.doi.org/10.1371/journal.pone.0057675.s004", "https://dx.doi.org/10.1371/journal.pone.0057675.s005"], "stats"=>{"downloads"=>7, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/LTR_Retrotransposons_in_R_exoculata_and_Other_Crustaceans_The_Outstanding_Success_of_GalEa_Like_Copia_Elements__/644405", "title"=>"LTR-Retrotransposons in <em>R. exoculata</em> and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-05 10:55:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/977070"], "description"=>"<p>When an element is described in full-length, its size (in bp), the size of its LTRs and its bordering nucleotides are given. The <i>gag</i> and <i>pol</i> regions are represented using grey blocks and their conserved domains are indicated by black triangles. Light grey blocks show putative altered <i>gag</i> regions. Positions of the Primer Binding Site (PBS) and the PolyPurine Tract (PPT) are indicated by white triangles.</p>", "links"=>[], "tags"=>["gyrex", "retrotransposons"], "article_id"=>644398, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Mathieu Piednoël", "Tifenn Donnart", "Caroline Esnault", "Paula Graça", "Dominique Higuet", "Eric Bonnivard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057675.g001", "stats"=>{"downloads"=>1, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CoRex_A_and_GyRex_B_retrotransposons_annotation_/644398", "title"=>"CoRex (A) and GyRex (B) retrotransposons annotation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-05 10:54:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/977073"], "description"=>"<p>The crustacean elements are indicated in bold and the four <i>R. exoculata</i> elements (GyRex) are highlighted in grey. Statistical support (>50%) comes from non parametric bootstrapping using 100 replicates. DIRS1-like sequences were used as outgroup.</p>", "links"=>[], "tags"=>["relationships", "gypsy", "retrotransposons", "inferred", "neighbor-joining", "amino"], "article_id"=>644401, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Mathieu Piednoël", "Tifenn Donnart", "Caroline Esnault", "Paula Graça", "Dominique Higuet", "Eric Bonnivard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057675.g003", "stats"=>{"downloads"=>1, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_among_Gypsy_retrotransposons_inferred_from_Neighbor_Joining_analysis_of_RT_RH_amino_acid_sequences_/644401", "title"=>"Phylogenetic relationships among Gypsy retrotransposons inferred from Neighbor-Joining analysis of RT/RH amino acid sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-05 10:54:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/977075"], "description"=>"<p>The crustacean elements are indicated in bold and the three <i>R. exoculata</i> elements (CoRex) are highlighted in grey. Statistical support (>50%) comes from non parametric bootstrapping using 100 replicates. Gypsy sequences were used as outgroup.</p>", "links"=>[], "tags"=>["relationships", "copia", "retrotransposons", "inferred", "neighbor-joining", "amino"], "article_id"=>644402, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Mathieu Piednoël", "Tifenn Donnart", "Caroline Esnault", "Paula Graça", "Dominique Higuet", "Eric Bonnivard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057675.g004", "stats"=>{"downloads"=>1, "page_views"=>45, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_among_Copia_retrotransposons_inferred_from_Neighbor_Joining_analysis_of_RT_RH_amino_acid_sequences_/644402", "title"=>"Phylogenetic relationships among Copia retrotransposons inferred from Neighbor-Joining analysis of RT/RH amino acid sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-05 10:55:11"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[302, 488, 607, 717, 832, 931, 1024, 1117, 1212, 1302, 1389, 1469, 1535]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[281, 484, 611, 728, 835, 934, 1030, 1123, 1214, 1299, 1383, 1464]}]}
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