Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution
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{"title"=>"Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution", "type"=>"journal", "authors"=>[{"first_name"=>"Pierre Marc", "last_name"=>"Delaux", "scopus_author_id"=>"37099528100"}, {"first_name"=>"Kranthi", "last_name"=>"Varala", "scopus_author_id"=>"16644102200"}, {"first_name"=>"Patrick P.", "last_name"=>"Edger", "scopus_author_id"=>"35078331000"}, {"first_name"=>"Gloria M.", "last_name"=>"Coruzzi", "scopus_author_id"=>"7102139927"}, {"first_name"=>"J. Chris", "last_name"=>"Pires", "scopus_author_id"=>"7102586164"}, {"first_name"=>"Jean Michel", "last_name"=>"Ané", "scopus_author_id"=>"6603641183"}], "year"=>2014, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537404", "scopus"=>"2-s2.0-84905454834", "sgr"=>"84905454834", "pui"=>"373701243", "isbn"=>"1553-7390", "pmid"=>"25032823", "doi"=>"10.1371/journal.pgen.1004487"}, "id"=>"1dd3815b-6816-32cf-8b39-a6e4a4c6bc59", "abstract"=>"Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant-microbe symbiosis, arbuscular mycorrhization (AM), as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales). Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.", "link"=>"http://www.mendeley.com/research/comparative-phylogenomics-uncovers-impact-symbiotic-associations-host-genome-evolution", "reader_count"=>196, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>14, "Student > Doctoral Student"=>17, "Researcher"=>41, "Student > Ph. D. Student"=>73, "Student > Postgraduate"=>4, "Student > Master"=>15, "Other"=>2, "Student > Bachelor"=>20, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>14, "Student > Doctoral Student"=>17, "Researcher"=>41, "Student > Ph. D. Student"=>73, "Student > Postgraduate"=>4, "Student > Master"=>15, "Other"=>2, "Student > Bachelor"=>20, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Engineering"=>1, "Environmental Science"=>5, "Biochemistry, Genetics and Molecular Biology"=>25, "Agricultural and Biological Sciences"=>155, "Medicine and Dentistry"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>155}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>25}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>5}}, "reader_count_by_country"=>{"Netherlands"=>5, "Czech Republic"=>1, "United States"=>12, "Ireland"=>1, "Taiwan"=>1, "Mexico"=>1, "United Kingdom"=>1, "France"=>1, "Germany"=>2}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1598451"], "description"=>"<p>A) Genes requires for both root nodule and AM symbioses are present in the <i>Lupinus albus</i> transcriptome and the <i>Lupinus angustifolius</i> genome whereas genes only required for AM symbiosis (indicated in red) are not detected. Both classes of genes are present in genomes and transcriptomes of host legumes. B) <i>RAM2</i> and <i>DMI1</i> can be amplified by PCR from genomic DNA of host legume species whereas only <i>DMI1</i> can be amplified from <i>Lupinus sericeus</i>, <i>Lupinus luteus</i>, or <i>Lupinus albus</i>.</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "Comparative genomics", "Genome evolution", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "microbiology", "Plant microbiology", "organisms", "plants", "Flowering plants", "Plant science", "genes", "arbuscular", "mycorrhizal", "symbiosis", "genus"], "article_id"=>1108699, "categories"=>["Biological Sciences"], "users"=>["Pierre-Marc Delaux", "Kranthi Varala", "Patrick P. Edger", "Gloria M. Coruzzi", "J. Chris Pires", "Jean-Michel Ané"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004487.g004", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Loss_of_genes_specifically_required_for_arbuscular_mycorrhizal_AM_symbiosis_in_the_genus_Lupinus_/1108699", "title"=>"Loss of genes specifically required for arbuscular mycorrhizal (AM) symbiosis in the genus <i>Lupinus</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-17 03:18:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1598444"], "description"=>"<p>Conserved genes are present in both host and non-host Brassicales species. In contrast, ‘symbiosis-specific’ ones are not detected in the genomes and transcriptomes of species having diverged after the loss of the AM symbiosis (red star).</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "Comparative genomics", "Genome evolution", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "microbiology", "Plant microbiology", "organisms", "plants", "Flowering plants", "Plant science", "genes"], "article_id"=>1108692, "categories"=>["Biological Sciences"], "users"=>["Pierre-Marc Delaux", "Kranthi Varala", "Patrick P. Edger", "Gloria M. Coruzzi", "J. Chris Pires", "Jean-Michel Ané"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004487.g002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Loss_of_the_8216_symbiosis_specific_8217_genes_in_the_order_Brassicales_/1108692", "title"=>"Loss of the ‘symbiosis-specific’ genes in the order Brassicales.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-17 03:18:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1598453", "https://ndownloader.figshare.com/files/1598454", "https://ndownloader.figshare.com/files/1598455", "https://ndownloader.figshare.com/files/1598456", "https://ndownloader.figshare.com/files/1598457", "https://ndownloader.figshare.com/files/1598458", "https://ndownloader.figshare.com/files/1598459", "https://ndownloader.figshare.com/files/1598460", "https://ndownloader.figshare.com/files/1598461", "https://ndownloader.figshare.com/files/1598462", "https://ndownloader.figshare.com/files/1598463", "https://ndownloader.figshare.com/files/1598464", "https://ndownloader.figshare.com/files/1598465", "https://ndownloader.figshare.com/files/1598466", "https://ndownloader.figshare.com/files/1598467", "https://ndownloader.figshare.com/files/1598468", "https://ndownloader.figshare.com/files/1598469", "https://ndownloader.figshare.com/files/1598470", "https://ndownloader.figshare.com/files/1598471", "https://ndownloader.figshare.com/files/1598472", "https://ndownloader.figshare.com/files/1598473", "https://ndownloader.figshare.com/files/1598474", "https://ndownloader.figshare.com/files/1598475", "https://ndownloader.figshare.com/files/1598476", "https://ndownloader.figshare.com/files/1598477", "https://ndownloader.figshare.com/files/1598478", "https://ndownloader.figshare.com/files/1598479", "https://ndownloader.figshare.com/files/1598480"], "description"=>"<div><p>Mutualistic symbioses between eukaryotes and beneficial microorganisms of their microbiome play an essential role in nutrition, protection against disease, and development of the host. However, the impact of beneficial symbionts on the evolution of host genomes remains poorly characterized. Here we used the independent loss of the most widespread plant–microbe symbiosis, arbuscular mycorrhization (AM), as a model to address this question. Using a large phenotypic approach and phylogenetic analyses, we present evidence that loss of AM symbiosis correlates with the loss of many symbiotic genes in the Arabidopsis lineage (Brassicales). Then, by analyzing the genome and/or transcriptomes of nine other phylogenetically divergent non-host plants, we show that this correlation occurred in a convergent manner in four additional plant lineages, demonstrating the existence of an evolutionary pattern specific to symbiotic genes. Finally, we use a global comparative phylogenomic approach to track this evolutionary pattern among land plants. Based on this approach, we identify a set of 174 highly conserved genes and demonstrate enrichment in symbiosis-related genes. Our findings are consistent with the hypothesis that beneficial symbionts maintain purifying selection on host gene networks during the evolution of entire lineages.</p></div>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "Comparative genomics", "Genome evolution", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "microbiology", "Plant microbiology", "organisms", "plants", "Flowering plants", "Plant science", "phylogenomics", "uncovers", "symbiotic", "associations", "genome"], "article_id"=>1108701, "categories"=>["Biological Sciences"], "users"=>["Pierre-Marc Delaux", "Kranthi Varala", "Patrick P. Edger", "Gloria M. Coruzzi", "J. Chris Pires", "Jean-Michel Ané"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004487.s001", "https://dx.doi.org/10.1371/journal.pgen.1004487.s002", "https://dx.doi.org/10.1371/journal.pgen.1004487.s003", "https://dx.doi.org/10.1371/journal.pgen.1004487.s004", "https://dx.doi.org/10.1371/journal.pgen.1004487.s005", "https://dx.doi.org/10.1371/journal.pgen.1004487.s006", "https://dx.doi.org/10.1371/journal.pgen.1004487.s007", "https://dx.doi.org/10.1371/journal.pgen.1004487.s008", "https://dx.doi.org/10.1371/journal.pgen.1004487.s009", "https://dx.doi.org/10.1371/journal.pgen.1004487.s010", "https://dx.doi.org/10.1371/journal.pgen.1004487.s011", "https://dx.doi.org/10.1371/journal.pgen.1004487.s012", "https://dx.doi.org/10.1371/journal.pgen.1004487.s013", "https://dx.doi.org/10.1371/journal.pgen.1004487.s014", "https://dx.doi.org/10.1371/journal.pgen.1004487.s015", "https://dx.doi.org/10.1371/journal.pgen.1004487.s016", "https://dx.doi.org/10.1371/journal.pgen.1004487.s017", "https://dx.doi.org/10.1371/journal.pgen.1004487.s018", "https://dx.doi.org/10.1371/journal.pgen.1004487.s019", "https://dx.doi.org/10.1371/journal.pgen.1004487.s020", "https://dx.doi.org/10.1371/journal.pgen.1004487.s021", "https://dx.doi.org/10.1371/journal.pgen.1004487.s022", "https://dx.doi.org/10.1371/journal.pgen.1004487.s023", "https://dx.doi.org/10.1371/journal.pgen.1004487.s024", "https://dx.doi.org/10.1371/journal.pgen.1004487.s025", "https://dx.doi.org/10.1371/journal.pgen.1004487.s026", "https://dx.doi.org/10.1371/journal.pgen.1004487.s027", "https://dx.doi.org/10.1371/journal.pgen.1004487.s028"], "stats"=>{"downloads"=>167, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_Phylogenomics_Uncovers_the_Impact_of_Symbiotic_Associations_on_Host_Genome_Evolution_/1108701", "title"=>"Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-07-17 03:18:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1598452"], "description"=>"<p>The number of genes present in the list after removing those present in non-host species (Excluded species). Symbiosis-related genes are genes required for AM symbiosis (Symbiotic genes) and genes up-regulated in arbuscules according to <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004487#pgen.1004487-Gomez1\" target=\"_blank\">[41]</a>.</p>°<p>Determined by χ<sup>2</sup> test as described in the <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004487#s4\" target=\"_blank\">Materials and Methods</a> section.</p><p>*Species with only transcriptomes available.</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "Comparative genomics", "Genome evolution", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "microbiology", "Plant microbiology", "organisms", "plants", "Flowering plants", "Plant science", "phylogenomic", "symbiotic", "pathways"], "article_id"=>1108700, "categories"=>["Biological Sciences"], "users"=>["Pierre-Marc Delaux", "Kranthi Varala", "Patrick P. Edger", "Gloria M. Coruzzi", "J. Chris Pires", "Jean-Michel Ané"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004487.t001", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_phylogenomic_identification_of_new_symbiotic_pathways_in_Medicago_/1108700", "title"=>"Comparative phylogenomic identification of new symbiotic pathways in Medicago.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-17 03:18:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1598447"], "description"=>"<p>A) Conserved genes are present in both host and non-host species. In contrast, ‘symbiosis-specific’ ones are not detected in the genomes and transcriptomes of non-host ones. B) The basal Orobanchaceae <i>Lindenbergia philippensis</i> associates with the AM fungus <i>Glomus intraradices</i> leading to the development of vesicles, arbuscules, and intra-radical hyphae.</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "Comparative genomics", "Genome evolution", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "microbiology", "Plant microbiology", "organisms", "plants", "Flowering plants", "Plant science", "genes", "non-host", "flowering"], "article_id"=>1108695, "categories"=>["Biological Sciences"], "users"=>["Pierre-Marc Delaux", "Kranthi Varala", "Patrick P. Edger", "Gloria M. Coruzzi", "J. Chris Pires", "Jean-Michel Ané"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004487.g003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Convergent_loss_of_8216_symbiosis_specific_8217_genes_in_non_host_flowering_plant_species_/1108695", "title"=>"Convergent loss of ‘symbiosis-specific’ genes in non-host flowering plant species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-17 03:18:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1598442"], "description"=>"<p>A) For each tested species the symbiotic behavior, host (H) or non-host (NH) is indicated. The probability of having AM symbiosis in ancestral taxa, which were inferred using the maximum likelihood method in Mesquite version 2.75, is indicated for each interior node. Red star indicates the loss of AM symbiosis before the divergence of the Limnanthaceae. B) <i>Moringa oleifera</i> (left) develops a <i>bona fide</i> association with the AM fungus <i>Glomus intraradices</i> whereas <i>Limnanthes douglasii</i> (right) does not.</p>", "links"=>[], "tags"=>["biotechnology", "Plant biotechnology", "Plant genomics", "Computational biology", "Comparative genomics", "Genome evolution", "Evolutionary biology", "Organismal evolution", "Plant evolution", "genetics", "Plant genetics", "microbiology", "Plant microbiology", "organisms", "plants", "Flowering plants", "Plant science", "arbuscular", "mycorrhizal", "symbiosis"], "article_id"=>1108690, "categories"=>["Biological Sciences"], "users"=>["Pierre-Marc Delaux", "Kranthi Varala", "Patrick P. Edger", "Gloria M. Coruzzi", "J. Chris Pires", "Jean-Michel Ané"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004487.g001", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Loss_of_the_arbuscular_mycorrhizal_AM_symbiosis_in_the_order_Brassicales_/1108690", "title"=>"Loss of the arbuscular mycorrhizal (AM) symbiosis in the order Brassicales.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-17 03:18:13"}

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[291]}, {"subject_area"=>"/Biology and life sciences/Mycology", "average_usage"=>[348, 543]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[310]}]}

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