Disparate Modes of Evolution Shaped Modern Prion (<i>PRNP</i>) and Prion-Related Doppel (<i>PRND</i>) Variation in Domestic Cattle

<div><p>Previous investigations aimed at determining whether the mammalian prion protein actually facilitates tangible molecular aspects of either a discrete or pleiotropic functional niche have been debated, especially given the apparent absence of overt behavioral or physiological phenotypes associated with several mammalian prion gene (<i>PRNP</i>) knockout experiments. Moreover, a previous evaluation of <i>PRNP</i> knockout cattle concluded that they were normal, suggesting that the bovine prion protein is physiologically dispensable. Herein, we examined the frequency and distribution of nucleotide sequence variation within the coding regions of bovine <i>PRNP</i> and the adjacent Doppel (<i>PRND</i>) gene, a proximal paralogue to <i>PRNP</i> on BTA13. Evaluation of <i>PRND</i> variation demonstrated that the gene does not depart from a strictly neutral model of molecular evolution, and would therefore not be expected to influence tests of selection within <i>PRNP</i>. Collectively, our analyses confirm that intense purifying selection is indeed occurring directly on bovine <i>PRNP</i>, which is indicative of a protein with an important role. These results suggest that the lack of observed fitness effects may not manifest in the controlled environmental conditions used to care for and raise <i>PRNP</i> knockout animals.</p></div

Tests of selection for <i>PRND</i> and <i>PRNP</i> genes.

<p>Tests of selection for <i>PRND</i> and <i>PRNP</i> genes.</p

Median joining haplotype networks for <i>PRNP</i> and <i>PRND</i>.

<p>Median joining haplotype networks were constructed for bovine <i>PRNP</i> and <i>PRND</i> using character weights of 10 for SNPs and 20 for indels. Network branch angles were adjusted to ensure clarity without modifying branch lengths.</p

<i>PRND</i> haplotype data.

<p><i>PRND</i> haplotype data.</p

Nucleotide data for <i>PRND</i> and <i>PRNP</i> genes.

<p>Nucleotide data for <i>PRND</i> and <i>PRNP</i> genes.</p

Chicken-Scarlet Macaw (<i>Ara macao</i>) Comparative Chromosome Painting (ZooFISH).

<p>Using chicken flow sorted macrochromosomes (GGA1-GGA9) as well as GGAZ and GGAW, the homologous chromosome segments of the scarlet macaw were established via fluorescent <i>in situ</i> hybridization. All flow sorted probes were validated via hybridization to chicken metaphase spreads (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062415#pone.0062415.s001" target="_blank">Figure S1</a>).</p

Whole Genome Analysis of Divergence.

<p><b>(A)</b> Genome-wide nucleotide-based divergence (CorrectedForAL) between the scarlet macaw (<i>Ara macao</i>; simple <i>de novo</i> assembly) and chicken genomes (<i>Gallus gallus</i> 2.1). <b>(B)</b> Genome-wide nucleotide-based divergence (CorrectedForAL) between the scarlet macaw (<i>Ara macao</i>; simple <i>de novo</i> assembly) and zebra finch genomes (<i>Taeniopygia guttata</i> 1.1, 3.2.4). Each histogram represents the full, ordered distribution of the composite variable defined as: . The observed ranges of the composite variable for pane <b>(A)</b> and pane <b>(B)</b> were 3.89591E-05–0.052631579, and 3.33792E-05–0.052631579, respectively. The left edges of the distributions represent extreme conservation, whereas the right edges indicate extreme putative divergence. Distributional outliers were predicted using a percentile-based approach (99.98^th and 0.02^th) to construct interval bounds capturing >99.9% of the total data points in each ordered distribution.</p

SMACv1.0 simple <i>de novo</i> outlier contigs from a genome-wide analysis of divergence with the chicken.

<p>SMACv1.0 simple <i>de novo</i> outlier contigs from a genome-wide analysis of divergence with the chicken.</p