Mitochondrial genome rearrangements observed among <i>Helotiales</i> and <i>Peltigerales</i>.

<p>The second truncated copy of <i>atp9</i> in <i>S. borealis</i> mtDNA is marked by an asterisk.</p

Genome organisation of the region around <i>atp9</i> genes for the helotialean species.

<p>Boxes represent ORFs and tRNA genes (blue, tRNA genes; yellow, <i>atp</i> ORFs and gene fragments; green, <i>cob</i> ORFs and gene fragments; black, inserts in truncated copies of genes; red, intronic HEG-like ORFs; grey, other ORFs). The second truncated copies of <i>atp6</i> and <i>atp9</i> are shown as atp6_tr and atp9_tr, respectively.</p

The phylogenetic tree was calculated from the multiple sequence alignment of concatenated mtDNA-encoded proteins of 51 fungal species.

<p>A dataset of 14 proteins was used, and topology was inferred using Bayesian method. Numbers above the nodes indicate bootstrap support values. The tree is drawn to scale, with branch lengths measured by the number of substitutions per site. Species analysed are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107536#pone.0107536.s005" target="_blank">Table S3</a>; only the <i>Ascomycota</i> branch of the whole tree is shown.</p

Map of the mitochondrial genome of <i>S. borealis</i>.

<p>The first ring from the outside represents the <i>S. borealis</i> core mitochondrial protein-coding genes and <i>rps3</i> (blue boxes). The second ring from the outside represents the hypothetical ORFs in red, ORFs for proteins containing GIY-YIG domains in orange, ORFs for proteins containing LAGLIDADG domains in purple, and fragments of DNA polymerase B and RNA polymerase genes in black. Full-size boxes indicate proteins containing complete GIY-YIG or LAGLIDADG domains, and half-size boxes indicate incomplete domains. The third ring represents the <i>rns</i> and <i>rnl</i> genes in yellow, <i>rnpB</i> in black and tRNA genes in green. Exons are indicated by dark colours, and introns are in light colours. All genes are oriented clockwise except for one fragment of DNA polymerase B (22818–21772 nt).</p

Genes encoding 14 typical mitochondrial proteins and the ribosomal RNA subunits in <i>S. borealis</i> mitochondrial genome.

<p>Genes encoding 14 typical mitochondrial proteins and the ribosomal RNA subunits in <i>S. borealis</i> mitochondrial genome.</p

Structure of the <i>S. borealis cox1</i> gene introns 1 (A) and 8 (B).

<p>Introns are represented by black horizontal bars; the sizes are drawn to scale. Red arrows show HEG-like ORFs. Green and blue rectangles show, respectively, catalytic GIY-YIG_bI1_like (cd10445) and LAGLIDADG_1 (pfam00961) domains. Nucleotide sequence similarity is indicated by grey areas between introns. Sbor – <i>S. borealis</i>, Bfuc – <i>B. fuckeliana</i>, Pmal – <i>P. malacea</i>, Pans – <i>P. anserina</i>.</p

Location of introns in the mtDNAs of Helotiales and Peltigerales species.

<p>Plus (+) and minus (−) symbols indicate, respectively, presence or absence of orthologues intron in particular position. H and eH in parentheses represents the presence of the putative functional and eroded HEG-like ORFs, respectively.</p><p>Sbor – <i>S. borealis</i> F-4128, Bfuc - <i>B. fuckeliana</i> B05.10, Pmal – <i>P. malacea</i> DB3992, Pmem – <i>P. membranacea</i> LA-31632, Rcom – <i>R. commune</i> UK7, Rorth - <i>R. orthosporum</i> 04CH-BAR-A.1.1.3.</p><p>*The intron positions are indicated relative to the amino acid sequences of reference intronless genes of <i>P. subalpina</i> UAMH 11012. For <i>cox1</i> introns the nomenclature of insertion sites suggested by Ferandon et al (2010) is shown in parentheses.</p><p>**Total number of introns in analysed genes. Note the absences of introns in the <i>atp8</i> and <i>atp9</i> genes in all analysed species.</p><p>Location of introns in the mtDNAs of Helotiales and Peltigerales species.</p

The 203 kbp Mitochondrial Genome of the Phytopathogenic Fungus <i>Sclerotinia borealis</i> Reveals Multiple Invasions of Introns and Genomic Duplications

<div><p>Here we report the complete sequence of the mitochondrial (mt) genome of the necrotrophic phytopathogenic fungus <i>Sclerotinia borealis</i>, a member of the order <i>Helotiales</i> of Ascomycetes. The 203,051 bp long mtDNA of <i>S. borealis</i> represents one of the largest sequenced fungal mt genomes. The large size is mostly determined by the presence of mobile genetic elements, which include 61 introns. Introns contain a total of 125,394 bp, are scattered throughout the genome, and are found in 12 protein-coding genes and in the ribosomal RNA genes. Most introns contain complete or truncated ORFs that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Integrations of mobile elements are also evidenced by the presence of two regions similar to fragments of inverton-like plasmids. Although duplications of some short genome regions, resulting in the appearance of truncated extra copies of genes, did occur, we found no evidences of extensive accumulation of repeat sequences accounting for mitochondrial genome size expansion in some other fungi. Comparisons of mtDNA of <i>S. borealis</i> with other members of the order <i>Helotiales</i> reveal considerable gene order conservation and a dynamic pattern of intron acquisition and loss during evolution. Our data are consistent with the hypothesis that horizontal DNA transfer has played a significant role in the evolution and size expansion of the <i>S. borealis</i> mt genome.</p></div

Image_3_Whole-Genome Analysis of Three Yeast Strains Used for Production of Sherry-Like Wines Revealed Genetic Traits Specific to Flor Yeasts.PDF

<p>Flor yeast strains represent a specialized group of Saccharomyces cerevisiae yeasts used for biological wine aging. We have sequenced the genomes of three flor strains originated from different geographic regions and used for production of sherry-like wines in Russia. According to the obtained phylogeny of 118 yeast strains, flor strains form very tight cluster adjacent to the main wine clade. SNP analysis versus available genomes of wine and flor strains revealed 2,270 genetic variants in 1,337 loci specific to flor strains. Gene ontology analysis in combination with gene content evaluation revealed a complex landscape of possibly adaptive genetic changes in flor yeast, related to genes associated with cell morphology, mitotic cell cycle, ion homeostasis, DNA repair, carbohydrate metabolism, lipid metabolism, and cell wall biogenesis. Pangenomic analysis discovered the presence of several well-known “non-reference” loci of potential industrial importance. Events of gene loss included deletions of asparaginase genes, maltose utilization locus, and FRE-FIT locus involved in iron transport. The latter in combination with a flor-yeast-specific mutation in the Aft1 transcription factor gene is likely to be responsible for the discovered phenotype of increased iron sensitivity and improved iron uptake of analyzed strains. Expansion of the coding region of the FLO11 flocullin gene and alteration of the balance between members of the FLO gene family are likely to positively affect the well-known propensity of flor strains for velum formation. Our study provides new insights in the nature of genetic variation in flor yeast strains and demonstrates that different adaptive properties of flor yeast strains could have evolved through different mechanisms of genetic variation.</p

Image_4_Whole-Genome Analysis of Three Yeast Strains Used for Production of Sherry-Like Wines Revealed Genetic Traits Specific to Flor Yeasts.PDF

<p>Flor yeast strains represent a specialized group of Saccharomyces cerevisiae yeasts used for biological wine aging. We have sequenced the genomes of three flor strains originated from different geographic regions and used for production of sherry-like wines in Russia. According to the obtained phylogeny of 118 yeast strains, flor strains form very tight cluster adjacent to the main wine clade. SNP analysis versus available genomes of wine and flor strains revealed 2,270 genetic variants in 1,337 loci specific to flor strains. Gene ontology analysis in combination with gene content evaluation revealed a complex landscape of possibly adaptive genetic changes in flor yeast, related to genes associated with cell morphology, mitotic cell cycle, ion homeostasis, DNA repair, carbohydrate metabolism, lipid metabolism, and cell wall biogenesis. Pangenomic analysis discovered the presence of several well-known “non-reference” loci of potential industrial importance. Events of gene loss included deletions of asparaginase genes, maltose utilization locus, and FRE-FIT locus involved in iron transport. The latter in combination with a flor-yeast-specific mutation in the Aft1 transcription factor gene is likely to be responsible for the discovered phenotype of increased iron sensitivity and improved iron uptake of analyzed strains. Expansion of the coding region of the FLO11 flocullin gene and alteration of the balance between members of the FLO gene family are likely to positively affect the well-known propensity of flor strains for velum formation. Our study provides new insights in the nature of genetic variation in flor yeast strains and demonstrates that different adaptive properties of flor yeast strains could have evolved through different mechanisms of genetic variation.</p