Positive Selection of the Chromo and Chromo Shadow Domains of <i>rhino</i>

<div><p>(A) An amino acid alignment of the chromo domain of different <i>Drosophila</i> species is shown with the distantly related <i>HP1A</i> and human <i>HP1α</i> chromo domains for comparison. The neighbor-joining tree based on this alignment (shown on the left) recapitulates known <i>Drosophila</i> phylogeny. Amino acids of the <i>HP1A</i> chromo domain that are involved in binding to H3K9me are color coded: Blue amino acids form an aromatic cage that recognize K9me, and pink amino acids form a complementary surface for recognition of the H3 peptide [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010009#pgen-0010009-b45" target="_blank">45</a>]. The corresponding DNA sequence alignment was used in a PAML analysis. Three codons that have been under repeated and strong positive selection are indicated by arrows. The corresponding positions (red) are indicated on the known structure of the <i>Drosophila </i><i>HP1A</i> chromo domain (light blue) bound to H3K9me (purple) [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010009#pgen-0010009-b45" target="_blank">45</a>].</p> <p>(B) Amino acid alignment of representative chromo shadow domains of <i>rhino</i> orthologs from <i>Drosophila</i>. The neighbor-joining tree based on this alignment also recapitulates <i>Drosophila</i> phylogeny. Amino acids of mouse <i>HP1β</i> known to be involved in dimerization are shown in pink and those required for the shadow fold in blue [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010009#pgen-0010009-b46" target="_blank">46</a>]. We use arrows to indicate codons identified as being under positive selection by our PAML analysis. Corresponding positions of the mouse <i>HP1β</i> chromo shadow domain are indicated (red) on one of the shadow domains (light blue) of the dimer [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0010009#pgen-0010009-b46" target="_blank">46</a>]. These positions are shown in yellow on the other shadow domain (green).</p>