Horizontal gene transfer of selenoprotein genes reflects adaptation to stress conditions.

<p><b>(a)</b> Phylogeny of formate dehydrogenase α subunit (<i>fdhA</i>). Closest non-redundant hits (BLASTp against NCBI nr) to the P1 selenoprotein sequence are shown. <b>(b)</b> Phylogeny of formylmethanofuran dehydrogenase β subunit (<i>fmdB</i>). Closest non-redundant hits to the P2 selenoprotein sequence are shown. Asterisk indicates a similar formylmethanofuran dehydrogenase operon structure as in P2 (<i>fmdD</i>-<i>fmdB</i>-<i>fmdA</i>-<i>fmdC</i>). In both <b>(a)</b> and <b>(b)</b>, genes are color-coded by organism as follows: Planctomycetes [blue], Proteobacteria [purple], Acidobacteria [orange], Thermotogae [light blue], Firmicutes [black], and Archaea [red], Synergistetes [cyan], unclassified [gray]. Sequences containing selenocysteine are marked with [U] and cysteine-containing sequences are marked with [C]. Node support is from 1000 bootstrap iterations.</p

Phylogenies of polysaccharide-degrading enzymes indicate host adaptation.

<p><b>(a)</b> Phylogeny of P3 α-L fucosidases (GH29). The genes included in the phylogeny are top hits having >50% sequence identity at 80% query coverage that were determined by BLASTp of each of the eight P3 fucosidases to the NCBI nr database and to the genomes included in this study. <b>(b)</b> Phylogeny of PL6 and PL14 alginate lyases. The genes included in the phylogeny are top hits having >50% sequence identity at 80% query coverage that was determined by the BLASTp of each of the P1, P2 and P3 alginate lyases to the NCBI nr database and to the genomes included in this study. In both <b>(a)</b> and <b>(b)</b>, genes are color-coded by organism as follows: Planctomycetes [blue], Bacteroidetes [green], Proteobacteria [purple], Verrucomicrobia [red-orange], Armatimonadetes [magenta], Gemmatimonadetes [brown], unclassified [gray]. Node support is from 1000 bootstrap iterations.</p

Changing context of sulfatase genes in operons.

<p><b>(a)</b> Changing genetic context of individual sulfatase genes of a co-oriented P2 sulfatase gene cluster, resembling an operon. Adjacent genes are joined by a black line, and all genes are color-coded by predicted function as given on the right-hand side of the figure. P1 and <i>R</i>. <i>rubra</i> homologs for individual sulfatase genes in the P2 operon are shown. For each homolog, the immediate context of adjacent, co-oriented genes within their respective genomes is also shown. Reciprocal best-hit genes across organisms are connected by thick colored lines (gray, green, cyan). ORF lengths and intergenic distances are not drawn to scale. <b>(b)</b> A heterophyletic gene cluster resembling an operon in P3. Seven consecutive genes are color-coded by predicted function as given on the right-hand side of the figure. The distribution of top 10 BLASTp hits across various bacterial phyla is provided for each gene.</p

Distribution of COG functional categories in paralogous gene families.

<p><b>(a)</b> Distribution across families containing only singletons, or with 2–5 members or 6+ members. Paralogous gene families were identified using a network-based approach (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151883#pone.0151883.s021" target="_blank">S1 Text</a>). <b>(b)</b> Definition of COG categories on the x-axis of <b>(a)</b> (and also in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151883#pone.0151883.s007" target="_blank">S4 Fig</a>).</p

Phylogeny of three novel planctomycetes and related species.

<p>The phylogeny shown is based on concatenated protein-coding sequences of 39 highly conserved, single-copy genes (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151883#pone.0151883.s012" target="_blank">S1 Table</a>). Consensus maximum likelihood trees from 1000 bootstrap iterations are shown. Internal nodes are color-coded (indicated to the left of each tree) based on bootstrap support values. Taxa are color-coded by the type of habitat from which they were isolated: marine [blue], freshwater [orange], marine/brackish [purple], soil [green].</p

Cell wall degradation enzymes in planctomycetes and related species.

<p>The number of BLASTp hits (e-value < 1e-10) is shown for selected GH and PL domains, which are involved in the degradation of algal, fungal, and vascular plant cell walls. The rows are ordered according to the phylogeny in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0151883#pone.0151883.g001" target="_blank">Fig 1</a>. Entries for P1, P2 and P3 are bolded in cases where the number of members within a CAZY category has a percent rank among all shown species that is greater than 75%.</p

Sulfatase gene distribution and sub-classification in Planctomycetes and related strains.

<p><b>(a)</b> Number of sulfatase genes in various Planctomycetes and related strains. Only sulfatase genes encoding the active site and ≥350 amino acid residues were included. <b>(b)</b> Functional subclasses of sulfatases present in P1, P2, P3, <i>R</i>. <i>baltica</i> and <i>R</i>. <i>maiorica</i>. For each organism, the total number of sulfatases (≥350 residues) is divided into the following subclasses: choline/iduronate-2-sulfatases, mucin-desulfating sulfatases, heparan-N-sulfatases, and unclassified sulfatases including general arylsulfatases and galactosamine N-acetyl-6-sulfate sulfatases.</p

Properties of 9 bacterial genome assemblies including 8 Planctomycetes and 1 marine Bacteroidetes.

<p>P1, P2 and P3 were sequenced from a blade of <i>Porphyra umbilicalis</i>. Strains of <i>R</i>. <i>baltica</i>, <i>P</i>. <i>mikurensis</i> and <i>Z</i>. <i>galactanivorans</i> (Bacteroidetes) were also present on the blade (based on 16S rDNA analysis). <i>P</i>. <i>staleyi</i>, <i>R</i>. <i>maiorica</i> and <i>B</i>. <i>marina</i> are the closest known relatives of P1, P2 and P3, respectively.</p