78 research outputs found

    Sequences alignment of cyanobacterial 16S rRNA genes from relevant strains

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    Alignment (Fasta file) of 16S rRNA gene sequences from cyanobacterial strains included in the online database CyanoType

    16S rRNA gene sequences alignment of a subset of relevant cyanobacterial strains

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    Alignment (Fasta file) of a subset of 16S rRNA gene sequences from cyanobacterial strains included in the online database CyanoTyp

    Phylogenetic tree of cyanobacterial 16S rRNA gene sequences from relevant strains

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    Maximum-Likelihood phylogenetic tree (Newick format) with relevant cyanobacterial strains included in the online database CyanoTyp

    Bacterial community assemblage retrieved from seawater and sponges, shown as percentage.

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    <p>Total number of clones from each source is represented in parenthesis. Values in bold represent the most dominant bacterial group found in association with source. Values with asterisk show the unique bacterial lineage from sponges.</p

    Principal Coordinate Analysis (PCoA) plot based on weighted unifrac distances.

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    <p>16s rRNA sequences are binned according to sample source using a category mapping file. The percentage variation explained with first two principal components (P1 and P2).</p

    Sponge-associated bacteria among the host sponges <i>H. perlevis</i>, <i>P. penicillus</i> and <i>O</i>. <i>papilla</i> and its similarity with globally distributed related and unrelated host sponges.

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    <p>(A) Global map depicting the location of host sponges harboring bacterial assemblage similar to the retrieved microbes from the present study. Colored triangle on the map shows the sponge species from other studies. (B–C) Sponge associated bacteria from different hosts determined by isolation and uncultured techniques, represented as a pie chart <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080653#pone.0080653-Ondov1" target="_blank">[73]</a> showing its abundance and affiliation with microbes found in association with globally distributed host sponges.</p

    Phylogeny and diversity of bacterial isolates from marine sponges <i>H. perlevis</i> (HM), <i>P. penicillus</i> (PL) and <i>O. papilla</i> (OP).

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    <p>(<b>A</b>) Maximum-likelihood phylogenetic tree of nearly full length 16S rRNA gene sequences (ca. 1400 bp) using <i>Prochlorococcus marinus</i> as an outgroup. Sponge-derived bacterial isolates obtained from this study are highlighted in bold. The closest relatives retrieved through the BLAST search (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080653#pone.0080653.s004" target="_blank">Table S1</a>) with their GenBank accession numbers are represented. Dashed box delimit the sponge-associated bacterial groups (i.e. the grouping of bacteria retrieved from this study with the previously reported microbes from other sponges). Bootstrap node support values >50% are represented. (<b>B</b>) Stacked histogram showing the relative abundance of 16S rRNA diversity recovered from the sponge sources.</p

    Adaptation of the Mitochondrial Genome in Cephalopods: Enhancing Proton Translocation Channels and the Subunit Interactions

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    <div><p>Mitochondrial protein-coding genes (mt genes) encode subunits forming complexes of crucial cellular pathways, including those involved in the vital process of oxidative phosphorylation (OXPHOS). Despite the vital role of the mitochondrial genome (mt genome) in the survival of organisms, little is known with respect to its adaptive implications within marine invertebrates. The molluscan Class Cephalopoda is represented by a marine group of species known to occupy contrasting environments ranging from the intertidal to the deep sea, having distinct metabolic requirements, varied body shapes and highly advanced visual and nervous systems that make them highly competitive and successful worldwide predators. Thus, cephalopods are valuable models for testing natural selection acting on their mitochondrial subunits (mt subunits). Here, we used concatenated mt genes from 17 fully sequenced mt genomes of diverse cephalopod species to generate a robust mitochondrial phylogeny for the Class Cephalopoda. We followed an integrative approach considering several branches of interest–covering cephalopods with distinct morphologies, metabolic rates and habitats–to identify sites under positive selection and localize them in the respective protein alignment and/or tridimensional structure of the mt subunits. Our results revealed significant adaptive variation in several mt subunits involved in the energy production pathway of cephalopods: ND5 and ND6 from Complex I, CYTB from Complex III, COX2 and COX3 from Complex IV, and in ATP8 from Complex V. Furthermore, we identified relevant sites involved in protein-interactions, lining proton translocation channels, as well as disease/deficiencies related sites in the aforementioned complexes. A particular case, revealed by this study, is the involvement of some positively selected sites, found in Octopoda lineage in lining proton translocation channels (site 74 from ND5) and in interactions between subunits (site 507 from ND5) of Complex I.</p></div
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