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{"title"=>"Evidence for a fourteenth mtDNA-encoded protein in the female-transmitted mtDNA of marine mussels (Bivalvia: Mytilidae)", "type"=>"journal", "authors"=>[{"first_name"=>"Sophie", "last_name"=>"Breton", "scopus_author_id"=>"7006942775"}, {"first_name"=>"Fabrizio", "last_name"=>"Ghiselli", "scopus_author_id"=>"22134229700"}, {"first_name"=>"Marco", "last_name"=>"Passamonti", "scopus_author_id"=>"7004682936"}, {"first_name"=>"Liliana", "last_name"=>"Milani", "scopus_author_id"=>"22135824200"}, {"first_name"=>"Donald T.", "last_name"=>"Stewart", "scopus_author_id"=>"55817300500"}, {"first_name"=>"Walter R.", "last_name"=>"Hoeh", "scopus_author_id"=>"6603677407"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-79955682606", "doi"=>"10.1371/journal.pone.0019365", "pui"=>"361717700", "issn"=>"19326203", "pmid"=>"21556327", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"79955682606"}, "id"=>"beb81e79-0427-3a86-a3c5-aa26bcc828aa", "abstract"=>"BACKGROUND: A novel feature for animal mitochondrial genomes has been recently established: i.e., the presence of additional, lineage-specific, mtDNA-encoded proteins with functional significance. This feature has been observed in freshwater mussels with doubly uniparental inheritance of mtDNA (DUI). The latter unique system of mtDNA transmission, which also exists in some marine mussels and marine clams, is characterized by one mt genome inherited from the female parent (F mtDNA) and one mt genome inherited from the male parent (M mtDNA). In freshwater mussels, the novel mtDNA-encoded proteins have been shown to be mt genome-specific (i.e., one novel protein for F genomes and one novel protein for M genomes). It has been hypothesized that these novel, F- and M-specific, mtDNA-encoded proteins (and/or other F- and/or M-specific mtDNA sequences) could be responsible for the different modes of mtDNA transmission in bivalves but this remains to be demonstrated.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: We investigated all complete (or nearly complete) female- and male-transmitted marine mussel mtDNAs previously sequenced for the presence of ORFs that could have functional importance in these bivalves. Our results confirm the presence of a novel F genome-specific mt ORF, of significant length (>100aa) and located in the control region, that most likely has functional significance in marine mussels. The identification of this ORF in five Mytilus species suggests that it has been maintained in the mytilid lineage (subfamily Mytilinae) for ∼13 million years. Furthermore, this ORF likely has a homologue in the F mt genome of Musculista senhousia, a DUI-containing mytilid species in the subfamily Crenellinae. We present evidence supporting the functionality of this F-specific ORF at the transcriptional, amino acid and nucleotide levels.\\n\\nCONCLUSIONS/SIGNIFICANCE: Our results offer support for the hypothesis that \"novel F genome-specific mitochondrial genes\" are involved in key biological functions in bivalve species with DUI.", "link"=>"http://www.mendeley.com/research/evidence-fourteenth-mtdnaencoded-protein-femaletransmitted-mtdna-marine-mussels-bivalvia-mytilidae", "reader_count"=>36, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>4, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>4, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>29, "Immunology and Microbiology"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>29}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Czech Republic"=>1, "Brazil"=>1, "Spain"=>1}, "group_count"=>1}

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• http://doi.org/10.1111/jzs.12354
• http://doi.org/10.1007/s10750-020-04196-z
• http://doi.org/10.1186/s12864-016-2986-6
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• {"month"=>"9", "year"=>"2020", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"3"}
• {"month"=>"10", "year"=>"2020", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"7"}
• {"month"=>"11", "year"=>"2020", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"0"}
• {"month"=>"12", "year"=>"2020", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"3"}
• {"month"=>"1", "year"=>"2021", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"1"}
• {"month"=>"2", "year"=>"2021", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"3"}

Figshare

• {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/391095/Figure_S1.doc", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/391157/Figure_S2.doc", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/391228/Figure_S3.doc", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/391368/Figure_S4.tif"], "description"=>"<div><h3>Background</h3><p>A novel feature for animal mitochondrial genomes has been recently established: i.e., the presence of additional, lineage-specific, mtDNA-encoded proteins with functional significance. This feature has been observed in freshwater mussels with doubly uniparental inheritance of mtDNA (DUI). The latter unique system of mtDNA transmission, which also exists in some marine mussels and marine clams, is characterized by one mt genome inherited from the female parent (F mtDNA) and one mt genome inherited from the male parent (M mtDNA). In freshwater mussels, the novel mtDNA-encoded proteins have been shown to be mt genome-specific (i.e., one novel protein for F genomes and one novel protein for M genomes). It has been hypothesized that these novel, F- and M-specific, mtDNA-encoded proteins (and/or other F- and/or M-specific mtDNA sequences) could be responsible for the different modes of mtDNA transmission in bivalves but this remains to be demonstrated.</p> <h3>Methodology/Principal Findings</h3><p>We investigated all complete (or nearly complete) female- and male-transmitted marine mussel mtDNAs previously sequenced for the presence of ORFs that could have functional importance in these bivalves. Our results confirm the presence of a novel F genome-specific mt ORF, of significant length (>100aa) and located in the control region, that most likely has functional significance in marine mussels. The identification of this ORF in five <em>Mytilus</em> species suggests that it has been maintained in the mytilid lineage (subfamily Mytilinae) for ∼13 million years. Furthermore, this ORF likely has a homologue in the F mt genome of <em>Musculista senhousia</em>, a DUI-containing mytilid species in the subfamily Crenellinae. We present evidence supporting the functionality of this F-specific ORF at the transcriptional, amino acid and nucleotide levels.</p> <h3>Conclusions/Significance</h3><p>Our results offer support for the hypothesis that “novel F genome-specific mitochondrial genes” are involved in key biological functions in bivalve species with DUI.</p> </div>", "links"=>[], "tags"=>["fourteenth", "mtdna-encoded", "female-transmitted", "mtdna", "mussels"], "article_id"=>137244, "categories"=>["Biological Sciences", "Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Sophie Breton", "Fabrizio Ghiselli", "Marco Passamonti", "Liliana Milani", "Donald T. Stewart", "Walter R. Hoeh"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0019365"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/Evidence_for_a_Fourteenth_mtDNA_Encoded_Protein_in_the_Female_Transmitted_mtDNA_of_Marine_Mussels_Bivalvia_Mytilidae_/137244", "title"=>"Evidence for a Fourteenth mtDNA-Encoded Protein in the Female-Transmitted mtDNA of Marine Mussels (Bivalvia: Mytilidae)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-04-27 02:00:44"}
• {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/780387/Figure_1.tif"], "description"=>"<p>All genes are encoded on the same strand. Gene identities: <i>nd1-6</i> and <i>nd4l</i>, NADH dehydrogenase subunits 1–6 and 4L; <i>cytb</i>, cytochrome b; <i>cox1-3</i>, cytochrome c oxidase subunits I–III; <i>atp6-8</i>, ATP synthase subunit 6 and 8 (protein-coding genes in white); 12SrRNA and 16SrRNA, small and large subunits of ribosomal RNA (in light gray). Transfer RNA genes are depicted by one-letter amino acid codes (in gray). The red and blue lines at the inner periphery of the ring represent EST sequences for the F and M mt genomes of <i>M. edulis/M. galloprovincialis</i>, respectively. Schematics of the structure of a typical F-type (left) and M-type (right) control regions, which are located between the 16SrRNA and trnY genes, are shown. The F-<i>ORF-VD1</i> is identified in the F-type control region. CR, control region; CD, conserved domain; VD1, variable domain 1; VD2, variable domain 2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Cao2\" target=\"_blank\">[39]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Cao3\" target=\"_blank\">[40]</a>. The mean size of each domain of the CR is shown. *The “standard” F-type CR of <i>M. trossulus</i>, which is a F/M recombinant CR, is not presented.</p>", "links"=>[], "tags"=>["mitochondrial"], "article_id"=>450761, "categories"=>["Biological Sciences", "Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Sophie Breton", "Fabrizio Ghiselli", "Marco Passamonti", "Liliana Milani", "Donald T. Stewart", "Walter R. Hoeh"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0019365.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_A_typical_Mytilus_mitochondrial_genome_/450761", "title"=>"A typical <i>Mytilus</i> mitochondrial genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-27 00:12:41"}
• {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/780529/Figure_2.tif"], "description"=>"<p>Three of more identical amino acids within a column are highlighted in blue. Conservation (Cons.) score values and quality (Qual.) of the alignment are indicated. Dashes (–) denote a missing residue at this position in comparison with other sequence(s). Mca, <i>M. californianus</i>; Mco, <i>M. coruscus</i>; Med, <i>M. edulis</i>; Mga, <i>M. galloprovincialis</i>; Mse, <i>M. senhousia</i>; Mtr, <i>M. trossulus</i>.</p>", "links"=>[], "tags"=>["alignment", "translated", "f-specific", "orf", "sequences", "mytilid"], "article_id"=>450889, "categories"=>["Biological Sciences", "Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Sophie Breton", "Fabrizio Ghiselli", "Marco Passamonti", "Liliana Milani", "Donald T. Stewart", "Walter R. Hoeh"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0019365.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_T_COFFEE_alignment_of_the_translated_F_specific_ORF_sequences_of_mytilid_mussels_/450889", "title"=>"T-COFFEE alignment of the translated F-specific ORF sequences of mytilid mussels.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-27 00:14:49"}
• {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/780636/Figure_3.tif"], "description"=>"<p>(A) Overall amino acid composition of <i>Mytilus</i> spp. F-<i>ORF-VD1</i> and <i>M. senhousia</i> F-<i>ORF</i> protein sequences. (B) Composition of chemically equivalent amino acids of <i>Mytilus</i> spp. F-<i>ORF-VD1</i> and <i>M. senhousia</i> F-<i>ORF</i> protein sequences. (C) Overall amino acid composition of <i>Mytilus</i> spp. F-<i>ATP8</i> and <i>M. senhousia</i> F-<i>ATP8</i> protein sequences. (D) Composition of chemically equivalent amino acids of <i>Mytilus</i> spp. F-<i>ATP8</i> and <i>M. senhousia</i> F-<i>ATP8</i> protein sequences (<i>M. coruscus atp8</i> sequence is not available in GenBank). (E) Overall amino acid composition of the putative <i>Mytilus</i> spp. M-<i>ORF-VD1</i> (*mean values for several M-<i>ORF-VD1</i> GenBank sequences for each species). (F) Composition of chemically equivalent amino acids of the putative <i>Mytilus</i> spp. M-<i>ORF-VD1</i> (such ORF has not been found in <i>M. senhousia</i>). Amino acid composition is reported as percentage. Mca, <i>M. californianus</i>; Mco, <i>M. coruscus</i>; Med, <i>M. edulis</i>; Mga, <i>M. galloprovincialis</i>; Mse, <i>M. senhousia</i>; Mtr, <i>M. trossulus</i>.</p>", "links"=>[], "tags"=>["mytilid", "f-specific", "protein-coding", "putative"], "article_id"=>451003, "categories"=>["Biological Sciences", "Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Sophie Breton", "Fabrizio Ghiselli", "Marco Passamonti", "Liliana Milani", "Donald T. Stewart", "Walter R. Hoeh"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0019365.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Amino_acid_composition_of_mytilid_F_specific_ORFs_protein_coding_gene_ATP8_and_putative_M_ORF_VD1_/451003", "title"=>"Amino acid composition of mytilid F-specific ORFs, protein-coding gene <i>ATP8</i> and putative M-<i>ORF-VD1</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-27 00:16:43"}
• {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/780724/Figure_4.tif"], "description"=>"<p>(A) Profiles for each species were calculated by the method of Kyte and Doolittle <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Kyte1\" target=\"_blank\">[104]</a>. Numbers below profiles designate amino acid positions in each protein. Predicted transmembrane domains according to TMpred <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Hoffmann2\" target=\"_blank\">[102]</a> (all with significant scores >500) are shown in light gray (It has to be noted that a single TMH in the N terminal portion of each F-<i>ORF</i> proteins has also been identified using HMMTOP <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Tusndy1\" target=\"_blank\">[101]</a>). (B) T-COFFEE alignment of the translated N terminal portions of mytilid F-specific ORF sequences. Predicted transmembrane domains according to TMpred <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Hoffmann2\" target=\"_blank\">[102]</a> are shown in light gray. (C) Kyte and Doolittle profiles for the F-<i>ORF</i> protein alignment with the homologous amino acid sites in the same position on the x axis. The predicted transmembrane domain according to TMpred <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Hoffmann2\" target=\"_blank\">[102]</a> is shown in light gray. Mca, <i>M. californianus</i>; Mco, <i>M. coruscus</i>; Med, <i>M. edulis</i>; Mga, <i>M. galloprovincialis</i>; Mse, <i>M. senhousia</i>; Mtr, <i>M. trossulus</i>.</p>", "links"=>[], "tags"=>["hydropathy"], "article_id"=>451095, "categories"=>["Biological Sciences", "Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Sophie Breton", "Fabrizio Ghiselli", "Marco Passamonti", "Liliana Milani", "Donald T. Stewart", "Walter R. Hoeh"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0019365.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Comparisons_of_Mytilus_spp_F_ORF_VD1_and_M_senhousia_F_ORF_hydropathy_profiles_/451095", "title"=>"Comparisons of <i>Mytilus</i> spp. F-<i>ORF-VD1</i> and <i>M. senhousia</i> F-<i>ORF</i> hydropathy profiles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-27 00:18:15"}
• {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/780814/Figure_5.tif"], "description"=>"<p>The F-<i>ORF-VD1</i> is identified in the F-type control region. The amino acids that constitute the putative transmembrane helix are indicated in boldface type and bigger characters. The stretch of ∼60 residues showing the greatest similarity among the species is underlined. Dashes (–) denote the missing amino acid residues in the truncated F-<i>ORF-VD1</i>. CD, conserved domain; VD1, variable domain 1; VD2, variable domain 2 <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Cao2\" target=\"_blank\">[39]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Cao3\" target=\"_blank\">[40]</a>. *The “standard” F-type CR of <i>M. trossulus</i>, which is a F/M recombinant CR, is not presented.</p>", "links"=>[], "tags"=>["f-type", "recently-masculinized", "venetis", "et", "m-type"], "article_id"=>451178, "categories"=>["Biological Sciences", "Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Sophie Breton", "Fabrizio Ghiselli", "Marco Passamonti", "Liliana Milani", "Donald T. Stewart", "Walter R. Hoeh"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0019365.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Schematics_of_the_structure_of_a_typical_F_type_above_recently_masculinized_center_according_to_Venetis_et_al_47_and_typical_M_type_below_control_regions_/451178", "title"=>"Schematics of the structure of a typical F-type (above), recently-masculinized (center, according to Venetis et al. [<b>47</b>]) and typical M-type (below) control regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-27 00:19:38"}
• {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/780867/Table_4.xls"], "description"=>"<p>Note.—No <i>ATP8</i> sequence is available for <i>M. coruscus</i>. Amino acid identities % are given for the total number of aligned amino acids.</p>", "links"=>[], "tags"=>["comparisons", "mytilid", "lineage", "evolving", "amino"], "article_id"=>451237, "categories"=>["Biological Sciences", "Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Sophie Breton", "Fabrizio Ghiselli", "Marco Passamonti", "Liliana Milani", "Donald T. Stewart", "Walter R. Hoeh"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0019365.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Interspecies_comparisons_in_the_mytilid_F_lineage_Mytilus_spp_and_Musculista_senhousia_for_the_fast_evolving_F_ORF_VD1_F_ORF_and_ATP8_genes_amino_acid_identities_/451237", "title"=>"Interspecies comparisons in the mytilid F lineage (<i>Mytilus</i> spp. and <i>Musculista senhousia</i>) for the fast evolving F-<i>ORF-VD1</i> & F-<i>ORF</i> and <i>ATP8</i> genes: % amino acid identities.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-04-27 00:20:37"}
• {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/780911/Table_5.xls"], "description"=>"<p>Note.— The divergence in synonymous sites (K_S) and the divergence in nonsynonymous sites (K_A) have been calculated by the modified Nei-Gojobori method with Jukes-Cantor correction. Within species comparisons have been calculated using D-loop sequences from the following studies: <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Cao2\" target=\"_blank\">[39]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Cao3\" target=\"_blank\">[40]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Burzyski2\" target=\"_blank\">[45]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Burzyski3\" target=\"_blank\">[46]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Beagley1\" target=\"_blank\">[55]</a>–<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Filipowicz1\" target=\"_blank\">[57]</a>; Barna and Showman unpublished.</p>", "links"=>[], "tags"=>["comparisons", "lineage", "evolving", "selective", "pressures", "synonymous", "nonsynonymous"], "article_id"=>451271, "categories"=>["Biological Sciences", "Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Sophie Breton", "Fabrizio Ghiselli", "Marco Passamonti", "Liliana Milani", "Donald T. Stewart", "Walter R. Hoeh"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0019365.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_DNA_comparisons_in_the_Mytilus_F_lineage_for_the_fast_evolving_F_orf_vd1_gene_selective_pressures_at_synonymous_and_nonsynonymous_sites_/451271", "title"=>"DNA comparisons in the <i>Mytilus</i> F lineage for the fast evolving F-<i>orf-vd1</i> gene: selective pressures at synonymous and nonsynonymous sites.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-04-27 00:21:11"}
• {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/780942/Table_2.xls"], "description"=>"<p>Note.— F = Female genomes; M = Male genomes; RM* = These genomes are recently-masculinized genomes (see text for details).</p>a<p>These complete <i>M. trossulus</i> mtDNAs correspond to or have high affinity with the corresponding ancestral <i>M. trossulus</i> genomes from North America <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Breton4\" target=\"_blank\">[30]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Zbawicka2\" target=\"_blank\">[97]</a>.</p>b<p>DNA divergences based on partial <i>cox1</i> sequences <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Hoeh1\" target=\"_blank\">[42]</a>. Sequence divergences are given in percentages nucleotide difference for the total number of aligned nucleotides.</p><p>CR and of the F-specific ORF in the unassigned region UR2 of <i>Musculista senhousia</i>.</p>", "links"=>[], "tags"=>["characteristics", "orfs", "vd1"], "article_id"=>451310, "categories"=>["Biological Sciences", "Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Sophie Breton", "Fabrizio Ghiselli", "Marco Passamonti", "Liliana Milani", "Donald T. Stewart", "Walter R. Hoeh"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0019365.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_General_Characteristics_of_F_and_M_ORFs_in_the_VD1_domain_of_the_Mytilus_spp_/451310", "title"=>"General Characteristics of F and M ORFs in the VD1 domain of the <i>Mytilus</i> spp.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-04-27 00:21:50"}
• {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/780977/Table_3.xls"], "description"=>"<p>F-<i>orf-vd1</i> and “M-<i>orf-vd1</i>” and for <i>Musculista senhousia</i> F-<i>orf</i>.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "cell biology", "Evolutionary biology", "Biochemistry"], "article_id"=>451345, "categories"=>["Biological Sciences", "Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Sophie Breton", "Fabrizio Ghiselli", "Marco Passamonti", "Liliana Milani", "Donald T. Stewart", "Walter R. Hoeh"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0019365.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Testcode_results_for_Mytilus_spp_/451345", "title"=>"Testcode results for <i>Mytilus</i> spp.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-04-27 00:22:25"}
• {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/781008/Table_1.xls"], "description"=>"<p>Note.—F = Female genomes; M = Male genomes; RM* = These genomes are recently-masculinized genomes (see text for details).</p>a<p>These complete mtDNAs from Baltic <i>M. trossulus</i> derive throught recent introgression from <i>M. edulis</i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Zbawicka1\" target=\"_blank\">[96]</a>.</p>b<p>These complete <i>M. trossulus</i> mtDNAs correspond to or have high affinity with the corresponding ancestral <i>M. trossulus</i> genomes from North America <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Breton4\" target=\"_blank\">[30]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019365#pone.0019365-Zbawicka2\" target=\"_blank\">[97]</a>.</p>", "links"=>[], "tags"=>["mitochondrial", "genome", "sequences", "mytilid", "dui"], "article_id"=>451375, "categories"=>["Biological Sciences", "Biochemistry", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Sophie Breton", "Fabrizio Ghiselli", "Marco Passamonti", "Liliana Milani", "Donald T. Stewart", "Walter R. Hoeh"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0019365.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Complete_mitochondrial_genome_sequences_of_mytilid_species_with_DUI_used_in_this_study_/451375", "title"=>"Complete mitochondrial genome sequences of mytilid species with DUI used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-04-27 00:22:55"}

PMC Usage Stats | Further Information

• {"scanned-page-browse"=>"0", "month"=>"5", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"12", "unique-ip"=>"14", "pdf"=>"4", "year"=>"2011", "figure"=>"1", "scanned-summary"=>"0", "supp-data"=>"2"}
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Relative Metric

{"start_date"=>"2011-01-01T00:00:00Z", "end_date"=>"2011-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[290, 559, 698, 813, 927, 1028, 1121, 1206, 1289, 1360, 1433, 1501, 1569, 1637, 1707, 1774, 1841, 1911, 1974, 2038, 2103, 2161, 2219, 2280, 2345, 2406, 2466, 2529, 2592, 2654, 2713, 2772, 2835, 2893, 2954, 3020, 3071]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[330, 550, 674, 772, 863, 958, 1034, 1108, 1180, 1252, 1324, 1393, 1460, 1526, 1597, 1664, 1725, 1783, 1848, 1901, 1974, 2049, 2125, 2185, 2260, 2326, 2383, 2440, 2511, 2581, 2647, 2711, 2760, 2815, 2874, 2928, 3008]}]}

F1000Prime