EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes
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{"title"=>"EST analysis of Ostreococcus lucimarinus, the most compact eukaryotic genome, shows an excess of introns in highly expressed genes", "type"=>"journal", "authors"=>[{"first_name"=>"William", "last_name"=>"Lanier", "scopus_author_id"=>"56212312100"}, {"first_name"=>"Ahmed", "last_name"=>"Moustafa", "scopus_author_id"=>"55251149600"}, {"first_name"=>"Debashish", "last_name"=>"Bhattacharya", "scopus_author_id"=>"7201931909"}, {"first_name"=>"Josep M.", "last_name"=>"Comeron", "scopus_author_id"=>"6701860658"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"18478122", "sgr"=>"48249153013", "scopus"=>"2-s2.0-48249153013", "isbn"=>"10.1371/journal.pone.0002171", "doi"=>"10.1371/journal.pone.0002171", "pui"=>"352068491", "issn"=>"19326203"}, "id"=>"748cf7b7-8b63-31dd-bd0c-c0e74d494641", "abstract"=>"Background: The genome of the pico-eukaryotic (bacterial-sized) prasinophyte green alga Ostreococcus lucimarinus has one of the highest gene densities known in eukaryotes, yet it contains many introns. Phylogenetic studies suggest this unusually compact genome (13.2 Mb) is an evolutionarily derived state among prasinophytes. The presence of introns in the highly reduced O. lucimarinus genome appears to be in opposition to simple explanations of genome evolution based on unidirectional tendencies, either neutral or selective. Therefore, patterns of intron retention in this species can potentially provide insights into the forces governing intron evolution. Methodology/Principal Findings: Here we studied intron features and levels of expression in O. lucimarinus using expressed sequence tags (ESTs) to annotate the current genome assembly. ESTs were assembled into unigene clusters that were mapped back to the O. lucimarinus Build 2.0 assembly using BLAST and the level of gene expression was inferred from the number of ESTs in each cluster. We find a positive correlation between expression levels and both intron number (R鈥?鈥?0.0893, p鈥?鈥?0.0005) and intron density (number of introns/kb of CDS; R鈥?鈥?0.0753, p鈥?鈥?0.005). Conclusions/Significance: In a species with a genome that has been recently subjected to a great reduction of non-coding DNA, these results imply the existence of selective/functional roles for introns that are principally detectable in highly expressed genes. In these cases, introns are likely maintained by balancing the selective forces favoring their maintenance with other mutational and/or selective forces acting on genome size.", "link"=>"http://www.mendeley.com/research/est-analysis-ostreococcus-lucimarinus-most-compact-eukaryotic-genome-shows-excess-introns-highly-exp", "reader_count"=>46, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>9, "Student > Doctoral Student"=>1, "Researcher"=>10, "Student > Ph. D. Student"=>15, "Student > Master"=>3, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>5}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>9, "Student > Doctoral Student"=>1, "Researcher"=>10, "Student > Ph. D. Student"=>15, "Student > Master"=>3, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>6, "Agricultural and Biological Sciences"=>35, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>35}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Canada"=>1, "Netherlands"=>1, "United States"=>1, "Egypt"=>1, "Brazil"=>1, "Chile"=>2, "France"=>1, "Portugal"=>1}, "group_count"=>2}

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  • {"files"=>["https://ndownloader.figshare.com/files/931280"], "description"=>"<p>Summary statistics of predicted introns in O. lucimarinus.</p>", "links"=>[], "tags"=>["introns"], "article_id"=>601728, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["William Lanier", "Ahmed Moustafa", "Debashish Bhattacharya", "Josep M. Comeron"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002171.t002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_statistics_of_predicted_introns_in_O_lucimarinus_/601728", "title"=>"Summary statistics of predicted introns in O. lucimarinus.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-14 00:28:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/931169"], "description"=>"<p>Putative exon-junction associated proteins in <i>Arabidopsis</i>, their corresponding locus, best hit to protein model in the <i>Ostreococcus lucimarinus</i> Build 2.0, and respective e-value. The proposed <i>Arabidopsis</i> EJC protein families have been grouped together.</p>", "links"=>[], "tags"=>["exon-junction"], "article_id"=>601613, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["William Lanier", "Ahmed Moustafa", "Debashish Bhattacharya", "Josep M. Comeron"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002171.t005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Putative_exon_junction_associated_proteins_/601613", "title"=>"Putative exon-junction associated proteins.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-14 00:26:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/931256"], "description"=>"1<p>Number of sequenced clones within assembled unigene clusters used as a measure of gene expression.</p>2<p>Length of the open reading frame.</p>*<p>, <i>p</i><0.05;</p>**<p>, <i>p</i><0.005;</p>***<p>, <i>p</i><0.0005;</p><p>n.s., <i>p</i>>0.05</p>", "links"=>[], "tags"=>["coefficient", "est-annotated", "introns"], "article_id"=>601706, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["William Lanier", "Ahmed Moustafa", "Debashish Bhattacharya", "Josep M. Comeron"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002171.t003", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Spearman_s_rank_correlation_coefficient_analysis_of_EST_annotated_introns_in_O_lucimarinus_/601706", "title"=>"Spearman's rank correlation coefficient analysis of EST-annotated introns in O. lucimarinus.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-14 00:28:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/460009", "https://ndownloader.figshare.com/files/460033"], "description"=>"<div><h3>Background</h3><p>The genome of the pico-eukaryotic (bacterial-sized) prasinophyte green alga <em>Ostreococcus lucimarinus</em> has one of the highest gene densities known in eukaryotes, yet it contains many introns. Phylogenetic studies suggest this unusually compact genome (13.2 Mb) is an evolutionarily derived state among prasinophytes. The presence of introns in the highly reduced <em>O. lucimarinus</em> genome appears to be in opposition to simple explanations of genome evolution based on unidirectional tendencies, either neutral or selective. Therefore, patterns of intron retention in this species can potentially provide insights into the forces governing intron evolution.</p><h3>Methodology/Principal Findings</h3><p>Here we studied intron features and levels of expression in <em>O. lucimarinus</em> using expressed sequence tags (ESTs) to annotate the current genome assembly. ESTs were assembled into unigene clusters that were mapped back to the <em>O. lucimarinus</em> Build 2.0 assembly using BLAST and the level of gene expression was inferred from the number of ESTs in each cluster. We find a positive correlation between expression levels and both intron number (R = +0.0893, <em>p</em> = <0.0005) and intron density (number of introns/kb of CDS; R = +0.0753, <em>p</em> = <0.005).</p><h3>Conclusions/Significance</h3><p>In a species with a genome that has been recently subjected to a great reduction of non-coding DNA, these results imply the existence of selective/functional roles for introns that are principally detectable in highly expressed genes. In these cases, introns are likely maintained by balancing the selective forces favoring their maintenance with other mutational and/or selective forces acting on genome size.</p></div>", "links"=>[], "tags"=>["est", "compact", "eukaryotic", "shows", "excess", "introns", "expressed", "genes"], "article_id"=>150632, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["William Lanier", "Ahmed Moustafa", "Debashish Bhattacharya", "Josep M. Comeron"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0002171.s001", "https://dx.doi.org/10.1371/journal.pone.0002171.s002"], "stats"=>{"downloads"=>7, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/EST_Analysis_of_Ostreococcus_lucimarinus_the_Most_Compact_Eukaryotic_Genome_Shows_an_Excess_of_Introns_in_Highly_Expressed_Genes/150632", "title"=>"EST Analysis of <em>Ostreococcus lucimarinus,</em> the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-05-14 00:10:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/931009"], "description"=>"<p>The prasinophyte green algal genus <i>Ostreococcus</i> is the smallest-known free-living eukaryotes, with an average size of 0.8 μm. (a) Image of <i>Ostreococcus</i> strain RCC 143 kindly provided by W. Eikrem and J. Throndsen (University of Oslo) (image also available in Wiki Commons). (b) and (c) Histograms showing the frequency and length distribution for clustered contigs (b) and longest open reading frames (c) for the <i>Ostreococcus lucimarinus</i> EST library.</p>", "links"=>[], "tags"=>["ostreococcus", "clustered", "contigs"], "article_id"=>601457, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["William Lanier", "Ahmed Moustafa", "Debashish Bhattacharya", "Josep M. Comeron"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002171.g001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ostreococcus_lucimarinus_and_length_distribution_of_clustered_contigs_and_open_reading_frames_/601457", "title"=>"<i> Ostreococcus lucimarinus</i> and length distribution of clustered contigs and open reading frames.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-14 00:24:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/931227"], "description"=>"<p>Genes predicted for O. lucimarinus Build 2.0 in relation to the unigene clusters mapped, mapped clusters with introns, and the ratio of unigene clusters mapped per genes predicted in the currently genome assembly.</p>", "links"=>[], "tags"=>["genes", "est-annotated"], "article_id"=>601675, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["William Lanier", "Ahmed Moustafa", "Debashish Bhattacharya", "Josep M. Comeron"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002171.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_genes_predicted_and_EST_annotated_mapped_for_O_lucimarinus_/601675", "title"=>"Summary of genes predicted and EST-annotated (mapped) for O. lucimarinus.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-14 00:27:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/931195"], "description"=>"<p>Summary statistics for cluster lengths and longest open reading frames (LORFs) for all unigene clusters.</p>", "links"=>[], "tags"=>["lengths", "longest", "frames", "unigene"], "article_id"=>601642, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["William Lanier", "Ahmed Moustafa", "Debashish Bhattacharya", "Josep M. Comeron"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002171.t004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_statistics_for_cluster_lengths_and_longest_open_reading_frames_LORFs_for_all_unigene_clusters_/601642", "title"=>"Summary statistics for cluster lengths and longest open reading frames (LORFs) for all unigene clusters.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-14 00:27:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/931097"], "description"=>"<p>(a) Mean expression values and +/− standard errors for clusters lacking introns and all clusters containing introns. Expression values are in terms of the number of sequenced clones represented within a single unigene cluster. Boxplots showing the clustered contig lengths (b) and longest open reading frames (c) for contigs without introns (red, n = 265), contigs with introns (green, n = 1405), the combined data set of intron containing and intronless contigs (blue n = 1670), and for the complete EST library (yellow, n = 2050).</p>", "links"=>[], "tags"=>["intron", "containing", "intronless", "genes"], "article_id"=>601541, "categories"=>["Evolutionary Biology", "Genetics"], "users"=>["William Lanier", "Ahmed Moustafa", "Debashish Bhattacharya", "Josep M. Comeron"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0002171.g002", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Levels_of_gene_expression_for_intron_containing_and_intronless_genes_in_Ostreococcus_lucimarinus_/601541", "title"=>"Levels of gene expression for intron containing and intronless genes in <i>Ostreococcus lucimarinus.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-14 00:25:41"}

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

Relative Metric

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