The <i>Glomus sp.</i> 229456 mitochondrial genome circular-map was opened upstream of <i>rnl</i>.

<p>Genes on the outer and inner circumference are transcribed in a clockwise and counterclockwise direction, respectively. Gene and corresponding product names are <i>atp6, 8, 9,</i> ATP synthase subunit 6; <i>cob</i>, apocytochrome b; <i>cox1–3</i>, cytochrome c oxidase subunits; <i>nad1–4, 4L, 5–6</i>, NADH dehydrogenase subunits; <i>rnl, rns</i>, large and small subunit rRNAs; A–W, tRNAs, the letter corresponding to the amino acid specified by the particular tRNA followed by their anticodon. Open reading frames smaller than 100 amino acids are not shown.</p

Rapid Mitochondrial Genome Evolution through Invasion of Mobile Elements in Two Closely Related Species of Arbuscular Mycorrhizal Fungi

<div><p>Arbuscular mycorrhizal fungi (AMF) are common and important plant symbionts. They have coenocytic hyphae and form multinucleated spores. The nuclear genome of AMF is polymorphic and its organization is not well understood, which makes the development of reliable molecular markers challenging. In stark contrast, their mitochondrial genome (mtDNA) is homogeneous. To assess the intra- and inter-specific mitochondrial variability in closely related <i>Glomus species</i>, we performed 454 sequencing on total genomic DNA of <i>Glomus sp.</i> isolate DAOM-229456 and we compared its mtDNA with two <i>G. irregulare</i> isolates. We found that the mtDNA of <i>Glomus sp.</i> is homogeneous, identical in gene order and, with respect to the sequences of coding regions, almost identical t<i>o G. irregulare</i>. However, certain genomic regions vary substantially, due to insertions/deletions of elements such as introns, mitochondrial plasmid-like DNA polymerase genes and mobile open reading frames. We found no evidence of mitochondrial or cytoplasmic plasmids in <i>Glomus</i> species, and mobile ORFs in <i>Glomus</i> are responsible for the formation of four gene hybrids in <i>atp6</i>, <i>atp9</i>, <i>cox2</i>, and <i>nad</i>3, which are most probably the result of horizontal gene transfer and are expressed at the mRNA level. We found evidence for substantial sequence variation in defined regions of mtDNA, even among closely related isolates with otherwise identical coding gene sequences. This variation makes it possible to design reliable intra- and inter-specific markers.</p></div

A) Schematic alignment representation of two mitochondrial intergenic regions (<i>rnl-cox2</i> and <i>cox3-nad6</i>) showing the presence of numerous insertions and deletions (indels).

<p>The red arrows indicate the approximate position of the PCR primers that yield strain-specific markers, while the green arrows indicate the position of PCR primers that produce a size-specific marker. The yellow and orange arrows indicate potential regions to design, respectively, specific and size-specific markers in <i>G. irregulare</i> 494. <b>B</b>) Agarose gel electrophoresis figure showing the PCR results of the proposed markers on <i>Glomus sp.</i> 229456 (<i>Gs</i>) and <i>G. irregulare</i> DAOM197198 (<i>Gi</i>) respectively for each marker. Marker 1 shows the <i>Glomus sp.</i> specific amplification (156 bp), while marker 2 shows the <i>G. irregulare</i> 197198 specific marker (263 bp). The size-specific marker 3 yield a length of 160 bp for <i>Glomus sp.</i> and 226 bp for <i>G. irregulare</i> 197198. Finally, the size-specific marker 4 yield a length of 159 bp for <i>Glomus sp.</i> and 131 bp for <i>G. irregulare</i> 197198.</p

Gene and intron content in AMF and selected fungal mtDNAs.

a<p>Includes <i>nad1</i>, <i>nad2</i>, <i>nad3</i>, <i>nad4</i>, <i>nad4L</i>, <i>nad5</i> and <i>nad6</i>.</p>b<p>Only ORFs greater than 100 amino acids in length are listed, not including intronic ORFs and <i>dpo</i> and <i>rpo</i> fragments.</p>c<p>Intron I and Intron II denote introns of group I and group II, respectively.</p>d<p><i>S. cerevisiae</i> strain FY 1679 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060768#pone.0060768-Foury1" target="_blank">[57]</a>.</p

Comparative view of the three mitochondrial genomes linear map where the exons (black), introns (white), rDNA (gray), <i>dpo</i> plasmid insertions (red), ORFs (blue) and mobile endonuclease (yellow) are represented.

<p>Divergence in intron insertion pattern is indicated by projections. A hyper-variable region in the <i>cox3-rnl</i> intergene is boxed in grayscale.</p

Unrooted maximum likelihood trees obtained with the GTR+G model (5 distinct gamma categories).

<p>The first number at branches indicates ML bootstrap values with 1000 bootstrap replicates and the second number indicates posterior probability values of a MrBayes analysis with four independant chains. Bayesian inference predict similar trees (not shown). The concatenated tree of the <i>atp6</i>, <i>atp9</i>, <i>cox2</i> and <i>nad3</i> ‘core’ genes (without the duplicated C*-terminal portion) (1489 alignment positions) of selected AMF representatives (grayscale boxed) are compared with those of the <i>atp6</i> (298 alignment positions), where the red box with the asterisk point out to the reference <i>Allomyces spp.</i> HGT event (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0060768#pone-0060768-g004" target="_blank">Figure 4</a>) (A), <i>atp9</i> (51 alignment positions) (B), <i>cox2</i> (106 alignment positions) (C) and <i>nad3</i> (120 alignment positions) (D) C*-terminals. The <i>Glomus sp.</i> native C*-terminals are in blue, while the inserted C-terminals are in red.</p