Expected (<i>H_e</i>) and observed (<i>H_o</i>) heterozygosity for <i>TLR9</i> gene, in relation to seropositivity for <i>Small Ruminant Lentivirus</i> (<i>SRLV</i>), <i>C. abortus</i> (<i>CA</i>) or <i>M. avium</i> subsp. <i>paratuberculosis</i> (<i>MAP</i>) in three sheep flocks from different breeds.

<p>Expected (<i>H_e</i>) and observed (<i>H_o</i>) heterozygosity for <i>TLR9</i> gene, in relation to seropositivity for <i>Small Ruminant Lentivirus</i> (<i>SRLV</i>), <i>C. abortus</i> (<i>CA</i>) or <i>M. avium</i> subsp. <i>paratuberculosis</i> (<i>MAP</i>) in three sheep flocks from different breeds.</p

Association of <i>ΤLR9</i> genotypes with seroprevalence for <i>Small Ruminant Lentivirus</i> (<i>SRLV</i>), <i>C. abortus</i> (<i>CA</i>) or <i>M. avium</i> subsp. <i>paratuberculosis</i> (<i>MAP</i>) in three sheep flocks from different breeds.

<p>+: seropositive animals,</p><p>−: seronegative animals.</p

SNPs and alleles identified in ovine <i>TLR9</i> and <i>MyD88</i> genes.

a<p>Numbering corresponds to NM_001011555.1 <i>TLR9</i> and to NM_001166183.1 <i>MyD88</i> sequences, counting as position 1 the nucleotide A of the ATG codon.</p>b<p>Alleles 05–11 correspond to <i>TLR9</i> and alleles 01–02 to <i>MyD88</i>.</p

RNA-Seq identified SNPs that were further validated by Sanger sequencing in other individuals of the two lineages.

<p>Shaded boxes correspond to SNPs that Sanger sequencing failed to validate.</p

The rate of total and non-synonymous differentiating mutations, respectively, for the three energy producing procedures.

<p>In the OXPHOS, rates are also presented for each of the five complexes separately, distinguishing between nuclear and mtDNA-encoded genes.</p

The list of genes involved in cellular energetics that were targeted in the current analysis.

<p>Genes involved in Oxidative Phosphorylation are also separated by Complex (Complexes I-V). Genes encoded by the mtDNA are presented as underlined.</p

RNA-seq analysis pipeline.

<p>Schematic representation of the bioinformatics pipeline used in RNA-Seq analysis and SNP detection in nuclear-encoded genes.</p

Pair-wise analysis of the MHC class II frequencies in controls, total patients and WNND/WNF* subpopulations.

<p>P values in bold indicate significance.</p

Pair-wise analysis of homozygous/heterozygous state in controls, total WNV cases and WNND/WNF^* subpopulations.

<p><i>P</i> values in bold indicate significance^.</p

The official nomenclature of the identified alleles and their frequency in European populations together with the respective allelic frequencies found in this study (column Greece) [24].

<p>The official nomenclature of the identified alleles and their frequency in European populations together with the respective allelic frequencies found in this study (column Greece) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0165952#pone.0165952.ref024" target="_blank">24</a>].</p