Sequence alignments of coding and non-coding regions of the MHC <i>DRB</i> gene in Alpine ibex and domestic goat.

<p>The <i>DRB</i> gene (11 kb in domestic sheep) is located on to the goat reference genome scaffold2167 at position 79'094 bp. A total of 2253 bp of the MHC <i>DRB</i> gene was sequenced including partial sequences of introns 1–4 and the complete intron 5 as well as a 3′ UTR sequence and complete sequences of exons 3, 5 and 6. Exon 6 is not shown as no polymorphism was found. Seven Alpine ibex homozygous for <i>Caib-DRB*1</i> (red), seven Alpine ibex homozygous for <i>Caib-DRB*2</i> (orange) and five domestic goat individuals selected from a screening of diverse breeds (grey) were sequenced. All seven Alpine ibex homozygous for <i>Caib-DRB*2</i> were homozygous for the same haplotype at all four loci. This haplotype was highly distinct from the haplotype carried by all seven Alpine ibex homozygous for <i>Caib-DRB*1</i>. The domestic goat VBN.4 shared a nearly identical haplotype with individuals homozygous for Caib-<i>DRB</i>*2 at all four sequenced loci (99.8% sequence identity across 2253 bp). The domestic goat VBN.4 was homozygous for the <i>DRB</i> exon 2 <i>Cahi-DRB*16</i>, which is identical to <i>Caib-DRB*2</i> (not shown). The phylogenetic trees are based on neighbor-joining. See Supporting <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004438#pgen.1004438.s015" target="_blank">Text S1</a>-<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004438#pgen.1004438.s018" target="_blank">S4</a> for full sequence alignments.