List of complete mtDNA sequences included in Figure 1.

a<p>Family ID numbers correspond to the numbers in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042242#pone-0042242-g001" target="_blank">Figure 1</a>.</p>b<p>This family is originally from Lebanon.</p>c<p>This family is originally from Turkey.</p>d<p>This family is originally from Benin.</p>e<p>Haplogroup classification based on the most updated human mitochondrial phylogeny <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042242#pone.0042242-vanOven1" target="_blank">[35]</a>.</p>f<p>Nucleotide positions and changes refer to rCRS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042242#pone.0042242-Andrews1" target="_blank">[57]</a>. The non-synonymous nucleotide changes at nps 8860 (8860G) and 15326 (15326G), present in all LHON samples, are not included because they are private mutations of the reference sequence. LHON mutations are in bold, while those with a possible synergistic effect are underlined.</p>g<p>Only the entire mitochondrial sequence #6 was already published (Olivieri et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042242#pone.0042242-Olivieri1" target="_blank">[44]</a>).</p

Phylogenetic tree of 16 complete mtDNA sequences from LHON patients.

<p>Rare LHON mutations are shown in bold. The position of rCRS <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042242#pone.0042242-Andrews1" target="_blank">[57]</a> is indicated for reading off sequence motifs. Mutations are shown on the branches; they are transitions unless a base is explicitly indicated. The prefix @ designates reversions, while suffixes indicate: transversions (to A, G, C, or T), indels (+, d), gene locus (∼t, tRNA; ∼r, rRNA), synonymous or non-synonymous changes (s or ns) and heteroplasmies (h). Recurrent mutations are underlined. One mtDNA sequence (I; black circle) from a control subject (GenBank accession number FJ190383) was also included to illustrate that sequences 11 and 12 acquired independently the LHON mutation m.14568C>T. The haplogroup affiliation of each haplotype is based on mutational motifs and follows the most updated human phylogeny <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042242#pone.0042242-vanOven1" target="_blank">[35]</a>.</p

RFLP evaluation of heteroplasmy.

<p>Electrophoresis on Metaphor gel of the restriction fragments is shown. Wild type and mutant fragments are indicated with the corresponding size, expressed as base pairs (bps). Non affected negative control individual is indicated as C. DNA samples were extracted from whole blood, except when indicated: whole blood is indicated as B, urinary epithelium is indicated as U, platelet fraction is indicated as P, hairs are indicated as H and skeletal muscle is indicated as M. Molecular weight marker is indicated as MWM.</p

Sequence alignment and conservation analysis of ND1, ND4L and ND6 protein sequences.

<p>Alignments of protein sequences from eukaryotes and mammals, including <i>Homo sapiens,</i> are reported. The upper lines represent the human sequence with the amino acid changes induced by the corresponding LHON mutation. Mutated positions are in bold and indicated by an asterisk. Different shading corresponds to increasing conservation levels: amino acid conservation between 70% and 90% are highlighted in light grey, amino acid conservation between 90% and 99% are highlighted in dark grey, and invariant positions (100% conservation) are highlighted in black. Alignment gaps are indicated by a hyphen (-).</p

Conservation analysis of rare primary LHON mutations.

a<p>The GenBank database was searched on March 2^nd 2012 when a total of 10,304 mtDNA coding regions were deposited.</p