Separate Origins of Group I Introns in Two Mitochondrial Genes of the Katablepharid Leucocryptos marina
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{"title"=>"Separate origins of group I introns in two mitochondrial genes of the katablepharid Leucocryptos marina", "type"=>"journal", "authors"=>[{"first_name"=>"Yuki", "last_name"=>"Nishimura", "scopus_author_id"=>"55216739700"}, {"first_name"=>"Ryoma", "last_name"=>"Kamikawa", "scopus_author_id"=>"9336099100"}, {"first_name"=>"Tetsuo", "last_name"=>"Hashimoto", "scopus_author_id"=>"35205042400"}, {"first_name"=>"Yuji", "last_name"=>"Inagaki", "scopus_author_id"=>"35800053500"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0037307", "pui"=>"364803097", "sgr"=>"84860992545", "pmid"=>"22606358", "scopus"=>"2-s2.0-84860992545"}, "id"=>"aec3f553-2a3e-3fe0-8192-84ee30341cd0", "abstract"=>"Mitochondria are descendants of the endosymbiotic alpha-proteobacterium most likely engulfed by the ancestral eukaryotic cells, and the proto-mitochondrial genome should have been severely streamlined in terms of both genome size and gene repertoire. In addition, mitochondrial (mt) sequence data indicated that frequent intron gain/loss events contributed to shaping the modern mt genome organizations, resulting in the homologous introns being shared between two distantly related mt genomes. Unfortunately, the bulk of mt sequence data currently available are of phylogenetically restricted lineages, i.e., metazoans, fungi, and land plants, and are insufficient to elucidate the entire picture of intron evolution in mt genomes. In this work, we sequenced a 12 kbp-fragment of the mt genome of the katablepharid Leucocryptos marina. Among nine protein-coding genes included in the mt genome fragment, the genes encoding cytochrome b and cytochrome c oxidase subunit I (cob and cox1) were interrupted by group I introns. We further identified that the cob and cox1 introns host open reading frames for homing endonucleases (HEs) belonging to distantly related superfamilies. Phylogenetic analyses recovered an affinity between the HE in the Leucocryptos cob intron and two green algal HEs, and that between the HE in the Leucocryptos cox1 intron and a fungal HE, suggesting that the Leucocryptos cob and cox1 introns possess distinct evolutionary origins. Although the current intron (and intronic HE) data are insufficient to infer how the homologous introns were distributed to distantly related mt genomes, the results presented here successfully expanded the evolutionary dynamism of group I introns in mt genomes.", "link"=>"http://www.mendeley.com/research/separate-origins-group-i-introns-two-mitochondrial-genes-katablepharid-leucocryptos-marina", "reader_count"=>14, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>11, "Medicine and Dentistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>11}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/640106"], "description"=>"<p>Degenerate primers used for reverse-transcription PCR.</p>", "links"=>[], "tags"=>["primers", "reverse-transcription"], "article_id"=>310601, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Yuki Nishimura", "Ryoma Kamikawa", "Tetsuo Hashimoto", "Yuji Inagaki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0037307.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Degenerate_primers_used_for_reverse_transcription_PCR_/310601", "title"=>"Degenerate primers used for reverse-transcription PCR.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-11 00:10:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/640008"], "description"=>"<p><b>A.</b> Unrooted ML phylogeny inferred from the LAGLIDADG_2 alignment containing 183 amino acid positions. Thirty HEs belonging to LAGLIDADGE_2 superfamily were subjected to the ML and Bayesian methods. The HEs hosted in <i>cob</i> introns are shown in dark blue. The details of the homing positions of the HE-hosting <i>cob</i> introns (phase and codon) are given on the right side of the tree. Codon numbers are based on the <i>Saccharomyces cerevisiae cob</i> gene (GenBank accession number NC_001224). Only ML bootstrap values equal to or greater than 50% are shown. The resultant tree inferred from Bayesian analysis was essentially identical to that from the ML analysis (data not shown). The branches supported by Bayesian posterior probabilities (BPPs) equal to or greater than 0.95 were highlighted by thick lines. The GenBank accession numbers of the HE sequences used in this tree are given in brackets. <b>B.</b> Unrooted ML phylogeny inferred from the LAGLIDADG_1 alignment containing 191 amino acid positions. Twenty five HEs belonging to LAGLIDADGE_1 superfamily were subjected to the ML and Bayesian methods. The HEs hosted in <i>cox1</i> introns are shown in dark red. The details of the homing positions of the HE-hosting <i>cox1</i> introns (phase and codon) are given on the right side of the tree. Codon numbers are based on the <i>S. cerevisiae cox1</i> gene (GenBank accession number NC_001224). We are unsure the precise position of the intron identified in the <i>Flammulina velutipues cox1</i> gene, as only HE sequence has been deposited in the GenBank database (labeled with a question mark). Other details are same as described in A.</p>", "links"=>[], "tags"=>["phylogenetic", "analyses", "homing", "endonuclease"], "article_id"=>310498, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Yuki Nishimura", "Ryoma Kamikawa", "Tetsuo Hashimoto", "Yuji Inagaki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0037307.g003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_ML_phylogenetic_analyses_of_homing_endonuclease_HE_sequences_/310498", "title"=>"Maximum-likelihood (ML) phylogenetic analyses of homing endonuclease (HE) sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-11 00:08:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/639809"], "description"=>"<p>Protein-coding genes (and their directions) are shown by arrows. Abbreviations; <i>nad11</i>, NADH dehydrogenase subunit 11; <i>nad1</i>, NADH dehydrogenase subunit 1; <i>nad6</i>, NADH dehydrogenase subunit 6; <i>atp6</i>, ATP synthase F0 subunit 6; <i>nad7</i>, NADH dehydrogenase subunit 7; <i>cox2</i>, cytochrome <i>c</i> oxidase subunit 2; <i>cox3</i>, cytochrome <i>c</i> oxidase subunit 3; <i>cob</i>, cytochrome <i>b</i>; <i>cox1</i>, cytochrome <i>c</i> oxidase subunit 1. Introns inserted in the <i>cob</i> and <i>cox1</i> genes are shown as triangles. The genes initially amplified by reverse transcriptase PCR are shown in orange, while those amplified from genomic DNA were in green. The 5′ terminus of the <i>nad11</i> gene and the 3′ terminus of the <i>cox1</i> gene were not determined in the current study (highlighted by dotted lines).</p>", "links"=>[], "tags"=>["mitochondrial", "genome", "katablepharid"], "article_id"=>310300, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Yuki Nishimura", "Ryoma Kamikawa", "Tetsuo Hashimoto", "Yuji Inagaki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0037307.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primary_structure_of_the_partial_mitochondrial_genome_of_the_katablepharid_Leucocryptos_marina_/310300", "title"=>"Primary structure of the partial mitochondrial genome of the katablepharid <i>Leucocryptos marina</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-11 00:05:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/330091", "https://ndownloader.figshare.com/files/330133", "https://ndownloader.figshare.com/files/330175"], "description"=>"<div><p>Mitochondria are descendants of the endosymbiotic α-proteobacterium most likely engulfed by the ancestral eukaryotic cells, and the proto-mitochondrial genome should have been severely streamlined in terms of both genome size and gene repertoire. In addition, mitochondrial (mt) sequence data indicated that frequent intron gain/loss events contributed to shaping the modern mt genome organizations, resulting in the homologous introns being shared between two distantly related mt genomes. Unfortunately, the bulk of mt sequence data currently available are of phylogenetically restricted lineages, <em>i.e.</em>, metazoans, fungi, and land plants, and are insufficient to elucidate the entire picture of intron evolution in mt genomes. In this work, we sequenced a 12 kbp-fragment of the mt genome of the katablepharid <em>Leucocryptos marina</em>. Among nine protein-coding genes included in the mt genome fragment, the genes encoding cytochrome <em>b</em> and cytochrome <em>c</em> oxidase subunit I (<em>cob</em> and <em>cox1</em>) were interrupted by group I introns. We further identified that the <em>cob</em> and <em>cox1</em> introns host open reading frames for homing endonucleases (HEs) belonging to distantly related superfamilies. Phylogenetic analyses recovered an affinity between the HE in the <em>Leucocryptos cob</em> intron and two green algal HEs, and that between the HE in the <em>Leucocryptos cox1</em> intron and a fungal HE, suggesting that the <em>Leucocryptos cob</em> and <em>cox1</em> introns possess distinct evolutionary origins. Although the current intron (and intronic HE) data are insufficient to infer how the homologous introns were distributed to distantly related mt genomes, the results presented here successfully expanded the evolutionary dynamism of group I introns in mt genomes.</p> </div>", "links"=>[], "tags"=>["origins", "introns", "mitochondrial", "genes", "katablepharid"], "article_id"=>125186, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Yuki Nishimura", "Ryoma Kamikawa", "Tetsuo Hashimoto", "Yuji Inagaki"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0037307.s001", "https://dx.doi.org/10.1371/journal.pone.0037307.s002", "https://dx.doi.org/10.1371/journal.pone.0037307.s003"], "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Separate_Origins_of_Group_I_Introns_in_Two_Mitochondrial_Genes_of_the_Katablepharid_Leucocryptos_marina_/125186", "title"=>"Separate Origins of Group I Introns in Two Mitochondrial Genes of the Katablepharid <em>Leucocryptos marina</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-05-11 01:26:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/639861"], "description"=>"<p><b>A.</b> Secondary structure of the <i>Leucocryptos cob</i> intron. Putative Watson–Crick and wobble base pairs are shown by lines and open circles, respectively. Capital and small letters represent intron and exon nucleotides, respectively. Double helical structures, which are characteristic to group I introns, are labeled as P1–P10. The open reading frame (ORF) for a LAGLIDADG-type homing endonuclease (closed box; 217 amino acid residues) was found in the 718 nucleotide-long loop region between P1 and P2. <b>B.</b> Secondary structure of the <i>Leucocryptos cox1</i> intron. The details of this figure are same as described in A, except the ORF for a LAGLIDADG-type homing endonuclease (closed box; 267 amino acid residues) was found in the 827 nucleotide-long loop region between P1 and P10. P9.1 and P7.1, which are absent in the <i>Leucocryptos cob</i> intron, are shaded.</p>", "links"=>[], "tags"=>["structures", "intron"], "article_id"=>310357, "categories"=>["Biological Sciences", "Genetics", "Microbiology", "Evolutionary Biology"], "users"=>["Yuki Nishimura", "Ryoma Kamikawa", "Tetsuo Hashimoto", "Yuji Inagaki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0037307.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Putative_secondary_structures_of_the_group_I_intron_RNAs_/310357", "title"=>"Putative secondary structures of the group I intron RNAs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-11 00:05:57"}

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Relative Metric

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