Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice
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{"title"=>"Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice", "type"=>"journal", "authors"=>[{"first_name"=>"Carene", "last_name"=>"Rizzon", "scopus_author_id"=>"6602532790"}, {"first_name"=>"Loic", "last_name"=>"Ponger", "scopus_author_id"=>"6506794383"}, {"first_name"=>"Brandon S.", "last_name"=>"Gaut", "scopus_author_id"=>"7005950294"}], "year"=>2006, "source"=>"PLoS Computational Biology", "identifiers"=>{"scopus"=>"2-s2.0-33749357831", "pui"=>"44495715", "doi"=>"10.1371/journal.pcbi.0020115", "issn"=>"1553734X", "isbn"=>"1553-7358 (Electronic)", "pmid"=>"16948529", "sgr"=>"33749357831"}, "id"=>"539b0e48-e79f-37bf-a8da-99baa5173815", "abstract"=>"In Arabidopsis, tandemly arrayed genes (TAGs) comprise >10% of the genes in the genome. These duplicated genes represent a rich template for genetic innovation, but little is known of the evolutionary forces governing their generation and maintenance. Here we compare the organization and evolution of TAGs between Arabidopsis and rice, two plant genomes that diverged ~150 million years ago. TAGs from the two genomes are similar in a number of respects, including the proportion of genes that are tandemly arrayed, the number of genes within an array, the number of tandem arrays, and the dearth of TAGs relative to single copy genes in centromeric regions. Analysis of recombination rates along rice chromosomes confirms a positive correlation between the occurrence of TAGs and recombination rate, as found in Arabidopsis. TAGs are also biased functionally relative to duplicated, nontandemly arrayed genes. In both genomes, TAGs are enriched for genes that encode membrane proteins and function in \"abiotic and biotic stress\" but underrepresented for genes involved in transcription and DNA or RNA binding functions. We speculate that these observations reflect an evolutionary trend in which successful tandem duplication involves genes either at the end of biochemical pathways or in flexible steps in a pathway, for which fluctuation in copy number is unlikely to affect downstream genes. Despite differences in the age distribution of tandem arrays, the striking similarities between rice and Arabidopsis indicate similar mechanisms of TAG generation and maintenance.", "link"=>"http://www.mendeley.com/research/striking-similarities-genomic-distribution-tandemly-arrayed-genes-arabidopsis-rice", "reader_count"=>99, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>12, "Researcher"=>27, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>3, "Student > Master"=>5, "Other"=>4, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>12, "Researcher"=>27, "Student > Doctoral Student"=>6, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>3, "Student > Master"=>5, "Other"=>4, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>9, "Mathematics"=>1, "Agricultural and Biological Sciences"=>85, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>85}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Austria"=>1, "Belgium"=>1, "United States"=>4, "Italy"=>1, "France"=>3, "Bulgaria"=>1, "Germany"=>2, "Spain"=>1, "India"=>1}, "group_count"=>4}

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  • {"files"=>["https://ndownloader.figshare.com/files/956635"], "description"=>"<div><p>Only the H/0 datasets are shown.</p><p>The asterisks above the bars indicate significance of the χ<sup>2</sup> tests, under the null hypothesis that TAGs and duplicated non-TAG genes have the same proportion.</p><p>*, <i>p</i> < 0.05; **, <i>p</i> > 0.01; ***, <i>p</i> < 0.001. Bonferonni-corrected for 92 tests.</p></div>", "links"=>[], "tags"=>["genes", "mf", "categories"], "article_id"=>626912, "categories"=>["Biological Sciences", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Carene Rizzon", "Loic Ponger", "Brandon S Gaut"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0020115.g005", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_of_Genes_in_the_GO_MF_categories_in_Arabidopsis_and_Rice_Based_on_the_H_0_Dataset_/626912", "title"=>"Frequency of Genes in the GO MF categories in <i>Arabidopsis</i> and Rice, Based on the H/0 Dataset", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 13:15:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/956444"], "description"=>"<p>(A) A. thaliana. (B) O. sativa.</p>", "links"=>[], "tags"=>["tags"], "article_id"=>626722, "categories"=>["Biological Sciences", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Carene Rizzon", "Loic Ponger", "Brandon S Gaut"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0020115.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_Size_of_TAGs_for_the_H_0_Dataset_/626722", "title"=>"Distribution of the Size of TAGs for the H/0 Dataset", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 13:13:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/956596"], "description"=>"<p>Histogram of the distribution of Ks values for TAG pairs (dots) and duplicated non-TAG gene pairs (bars) in <i>Arabidopsis</i> and in rice for the H/0 dataset are in panels (A) and (B), respectively. Results for the L/0 dataset are provided in panels (C) and (D).</p>", "links"=>[], "tags"=>["ks", "pairs", "duplicated", "non-tag"], "article_id"=>626871, "categories"=>["Biological Sciences", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Carene Rizzon", "Loic Ponger", "Brandon S Gaut"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0020115.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_Ks_Values_between_TAG_Pairs_and_between_Duplicated_Non_TAG_Gene_Pairs_/626871", "title"=>"Distribution of Ks Values between TAG Pairs and between Duplicated Non-TAG Gene Pairs", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 13:14:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/956485"], "description"=>"<div><p>Recombination estimates are represented by the black lines. Density estimates are based on the H/0 dataset (blue lines) and H/10 dataset (pink lines).</p><p>Centromere positions are marked in orange.</p></div>", "links"=>[], "tags"=>["estimates", "tags"], "article_id"=>626760, "categories"=>["Biological Sciences", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Carene Rizzon", "Loic Ponger", "Brandon S Gaut"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0020115.g002", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Recombination_Rate_Estimates_and_Density_of_TAGs_Number_of_TAGs_Total_Number_of_Genes_along_O_sativa_Chromosome_/626760", "title"=>"Recombination Rate Estimates and Density of TAGs (Number of TAGs/Total Number of Genes) along O. sativa Chromosome", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 13:13:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/470669", "https://ndownloader.figshare.com/files/470728", "https://ndownloader.figshare.com/files/470791"], "description"=>"<div><p>In <em>Arabidopsis,</em> tandemly arrayed genes (TAGs) comprise >10% of the genes in the genome. These duplicated genes represent a rich template for genetic innovation, but little is known of the evolutionary forces governing their generation and maintenance. Here we compare the organization and evolution of TAGs between <em>Arabidopsis</em> and rice, two plant genomes that diverged ~150 million years ago. TAGs from the two genomes are similar in a number of respects, including the proportion of genes that are tandemly arrayed, the number of genes within an array, the number of tandem arrays, and the dearth of TAGs relative to single copy genes in centromeric regions. Analysis of recombination rates along rice chromosomes confirms a positive correlation between the occurrence of TAGs and recombination rate, as found in <em>Arabidopsis.</em> TAGs are also biased functionally relative to duplicated, nontandemly arrayed genes. In both genomes, TAGs are enriched for genes that encode membrane proteins and function in “abiotic and biotic stress” but underrepresented for genes involved in transcription and DNA or RNA binding functions. We speculate that these observations reflect an evolutionary trend in which successful tandem duplication involves genes either at the end of biochemical pathways or in flexible steps in a pathway, for which fluctuation in copy number is unlikely to affect downstream genes. Despite differences in the age distribution of tandem arrays, the striking similarities between rice and <em>Arabidopsis</em> indicate similar mechanisms of TAG generation and maintenance.</p></div>", "links"=>[], "tags"=>["similarities", "genomic", "tandemly", "arrayed", "genes"], "article_id"=>152818, "categories"=>["Biological Sciences", "Genetics", "Cell Biology", "Evolutionary Biology"], "users"=>["Carene Rizzon", "Loic Ponger", "Brandon S Gaut"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.0020115.st001", "https://dx.doi.org/10.1371/journal.pcbi.0020115.st002", "https://dx.doi.org/10.1371/journal.pcbi.0020115.st003"], "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Striking_Similarities_in_the_Genomic_Distribution_of_Tandemly_Arrayed_Genes_in_Arabidopsis_and_Rice/152818", "title"=>"Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in <em>Arabidopsis</em> and Rice", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2006-09-01 00:46:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/956564"], "description"=>"<p>TAG Gene Density Plotted against Recombination Rate in O. sativa for the L/0 Dataset and the H/0 Dataset</p>", "links"=>[], "tags"=>["plotted", "recombination", "dataset"], "article_id"=>626845, "categories"=>["Biological Sciences", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Carene Rizzon", "Loic Ponger", "Brandon S Gaut"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0020115.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TAG_Gene_Density_Plotted_against_Recombination_Rate_in_O_sativa_for_the_L_0_Dataset_and_the_H_0_Dataset_/626845", "title"=>"TAG Gene Density Plotted against Recombination Rate in O. sativa for the L/0 Dataset and the H/0 Dataset", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 13:14:34"}

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  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"5"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"6"}
  • {"unique-ip"=>"12", "full-text"=>"13", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"7"}
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  • {"unique-ip"=>"12", "full-text"=>"11", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"10"}
  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"4", "year"=>"2015", "month"=>"11"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"12"}
  • {"unique-ip"=>"11", "full-text"=>"10", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2016", "month"=>"1"}
  • {"unique-ip"=>"11", "full-text"=>"12", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
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  • {"unique-ip"=>"11", "full-text"=>"16", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"5"}
  • {"unique-ip"=>"16", "full-text"=>"18", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
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  • {"unique-ip"=>"9", "full-text"=>"7", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
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  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"4", "full-text"=>"6", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
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  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"11", "full-text"=>"16", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
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Relative Metric

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