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    Genebank identifiers of the nucleotide sequences of atpA, pheS and rpoA genes, used for the phylogenetic analyses. Table S2. NCBI Refseq/Genbank assembly accession numbers for the comparative genomic analysis of Leuconostoc species (29.09.2015). Table S3. L. gelidum subsp. gasicomitatum draft genomes statistics. Figure S1. Phylogenetic tree showing the relationship of L. citreum 1300_LCIT, L. gelidum subsp. gasicomitatum 1301_LGAS and L. inhae LMG 22919 genomes to other Leuconostoc species. (PDF 406 kb

    Gene map of <i>Phlebia radiata</i> mtDNA.

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    <p>Colour of the scale (kb) bar indicates orientation of transcription: clockwise (CW, white), counter-clockwise (CCW, grey). Bars mark protein-coding (blue) and RNA (red) genes, and alternative C-termini in <i>atp6</i> and <i>cox2</i> are depicted (orange). Intron type is indicated in colour: group I (light grey), group II (yellow), and uncertain (white). Within introns, the hypothetical and identified ORFs are indicated: over >200 amino-acid long ORFs (turquoise), and homing endonuclease domains GIY-YIG (black) and LAGLIDADG (dark grey). The transparent ribbon illustrates location of the 6,076 bp inversion-duplication. Asterisk indicates putative tRNA-Ile<sup>CAU</sup>. The inner circle (scale at 12 o’clock in linear units) plots nucleotide bias (G/C skew) up to hexamers along each mtDNA position; G/C (red), A/T (blue), total strand bias (black), placing <i>oriC</i> around 11∶30 o’clock as the largest bias of G over C.</p

    Schematic view of the C-termini regions of <i>P. radiata</i> mtDNA <i>atp6</i> and <i>cox2</i> genes.

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    <p>Green lines denote <i>atp6</i> coding sequence region and the last exon of <i>cox2</i>. Spheres/ovals represent LAGLIDADG 1 (green) and GIY-YIG (grey) homing endonuclease domains. <b>A)</b> Region of 201 bp (orange) with high 1 vs. 1 sequence similarity, corresponding to the 3′-end of the <i>atp6</i> gene. Codon Adaptation Index (CAI) values are shown for the <i>atp6</i> N-terminal region (blue) and for the regions of high sequence similarity. Reference codon usage is from: 1) <i>atp6</i> N-terminus, 2) <i>atp6</i> N-terminus and <i>atp8</i>-<i>9</i>, 3) <i>atp6</i> N-terminus, <i>atp8-9</i>, <i>cox1-3</i>, <i>nad1-5</i> and <i>nad4L</i>. <b>B)</b> Separated by three LAGLIDADG 1 domains and a GIY-YIG domain, two regions of high 1 vs. 1 sequence similarity (orange) exist for the last 66 bp of the <i>cox2</i> gene. Image was generated with ExPASy PROSITE MyDomains Image Creator (<a href="http://prosite.expasy.org/mydomains/" target="_blank">http://prosite.expasy.org/mydomains/</a>) and edited in Inkscape version 0.48.2 (<a href="http://inkscape.org/" target="_blank">http://inkscape.org/</a>).</p

    Introns, their lengths and types in the conserved <i>P. radiata</i> mtDNA-encoded genes.

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    <p>Homing endonuclease associations: G, GIY-YIG; L1, LAGLIDADG 1; L2, LAGLIDADG 2; R, reverse-transcriptase ORF including.</p><p>Underlined, group II intron type.</p

    Transfer RNA genes in <i>P. radiata</i> mtDNA.

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    [1]<p>tRNAscan predicts the tRNA type from the anticodon.</p>[2]<p>This tRNA was determined to be Ile through comparative means (see below).</p>[3]<p>The bit score of tRNA-Cys was below 20, which is a typical cut-off value for a pseudogene. The gene was predicted with exceptionally low score from all Basidiomycota mtDNAs.</p

    Annotated conserved protein-coding and rRNA genes, their characteristics, location and intron types in <i>P. radiata</i> mtDNA.

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    [1]<p><i>nad5</i> starts from the adjacent in frame codon to <i>nad4L</i> stop.</p>[2]<p><i>nad3</i> uses the last A of <i>nad2</i> stop codon for initiation Met’s first nt.</p>[3]<p>Based on multiple sequence alignment of <i>Basidiomycota cob</i> genes the last conserved aa of <i>P. radiata cob</i> is 43 aa before the stop codon.</p>[4]<p>Based on multiple sequence alignment of <i>Basidiomycota nad6</i> genes the last conserved aa of <i>P. radiata nad6</i> is 122 aa before the stop codon.</p>[5]<p>The codon after the putative TAG stop codon is TAA.</p><p>Empty cell, not present or observed, or unable to calculate.</p

    Contribution of the various features of <i>P. radiata</i> mtDNA to genome size.

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    <p>Conserved coding sequence refers to the conserved fungal mitochondrial proteome ORFs, rRNAs and tRNAs. Significant ORFs refer to additional identified and hypothetical protein coding sequences with E-value<0.001 obtained by BLASTp queries. Freestanding refers to intronless. Intronic significant ORFs include homing endonucleases, also exon-to-exon-fused ORFs, excluding intergenic ORF HEGs (see text).</p

    Phylogeny of fungal mitochondrial proteomes.

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    <p>The statistically most likely tree was derived by Bayesian inference from a multi-gene superalignment of mtDNA-encoded proteins (2 019 aa positions, 44 taxa). Posterior consensus support values are depicted for branching, and nodes receiving ≤0.8 support were collapsed into polytomies. The tree was rooted from mid-point. Colours refer to phyla or sub-phyla: turquoise, Chytridiomycota; yellow, Monoblepharidomycota; orange brown, Glomeromycota; dark blue, Ascomycota; pink, Ustilaginomycotina (Basidiomycota); red, Pucciniomycotina (Basidiomycota); bright green, Agaricomycotina (Basidiomycota); Blastocladiomycota node as outgroup. Scale bar indicates amino-acid substitutions per site. For species and mtDNA accession, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097141#pone-0097141-t005" target="_blank">Table 5</a>.</p

    Codon usage of the <i>P. radiata</i> mitochondrial genome protein-coding gene open reading frames in comparison to selected Basidiomycota and Ascomycota species.

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    <p>Neighbor-joining tree with topology derived from codon on codon root mean squared difference distance matrix (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097141#pone.0097141.s003" target="_blank">Table S3</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0097141#pone.0097141.s004" target="_blank">Table S4</a>). Agaricomycotina, blue; Ustilaginomycotina, red; Pucciniomycotina, black; Ascomycota species <i>Gibberella zeae = Fusarium graminearum</i>, green, as outgroup. Scale bar indicates nucleotide changes per site.</p