Data and Scripts

Raw data and scripts required to reproduce results and analyses

Supplementary tables and figures from No evidence for extrinsic post-zygotic isolation in a wild <i>Saccharomyces</i> yeast system

supplementary figures and tables supporting the result

Evidence for the Robustness of Protein Complexes to Inter-Species Hybridization

<div><p>Despite the tremendous efforts devoted to the identification of genetic incompatibilities underlying hybrid sterility and inviability, little is known about the effect of inter-species hybridization at the protein interactome level. Here, we develop a screening platform for the comparison of protein–protein interactions (PPIs) among closely related species and their hybrids. We examine <em>in vivo</em> the architecture of protein complexes in two yeast species (<em>Saccharomyces cerevisiae</em> and <em>Saccharomyces kudriavzevii</em>) that diverged 5–20 million years ago and in their F1 hybrids. We focus on 24 proteins of two large complexes: the RNA polymerase II and the nuclear pore complex (NPC), which show contrasting patterns of molecular evolution. We found that, with the exception of one PPI in the NPC sub-complex, PPIs were highly conserved between species, regardless of protein divergence. Unexpectedly, we found that the architecture of the complexes in F1 hybrids could not be distinguished from that of the parental species. Our results suggest that the conservation of PPIs in hybrids likely results from the slow evolution taking place on the very few protein residues involved in the interaction or that protein complexes are inherently robust and may accommodate protein divergence up to the level that is observed among closely related species.</p> </div

Protein divergence in the RNApII (black) and the NPC (grey) in the <i>Saccharomyces sensu stricto</i> group.

<p>Evolutionary trees were drawn for all proteins of a complex and are on the same scale (proportion of different amino acids). Distribution of protein divergence between <i>Scer</i> and <i>Skud</i> was calculated from multiple-sequence alignments available for 5261 orthologous proteins <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003161#pgen.1003161-Scannell1" target="_blank">[23]</a>. Arrows indicate protein divergence covered by the two complexes.</p

The NPC and RNApII networks are largely conserved between <i>Scer</i> and <i>Skud</i>.

<p>(<i>A</i>) Comparison of SI values (strains growth signal index; log₁₀) between species. Grey dotted lines indicate SI threshold values (<i>t</i>). SI values were considered to correspond to interactions when greater than <i>t</i> in both species (purple) or specific to one species when greater than <i>t</i> only in <i>Scer</i> (red), or only in <i>Skud</i> (blue). Black dotted lines indicate 5%, 1% and 0.1% threshold above which SI residuals significantly deviate from the <i>Scer-Skud</i> regression (black line). (<i>B</i>) Overlapped networks of <i>Scer</i> and <i>Skud</i>. Only SI above <i>t</i> and comparable interactions are represented. Line width is proportional to SI values measured between proteins in <i>Scer</i> (red) and <i>Skud</i> (blue) in the NPC (left) and the RNApII (right). Interactions appear in purple when <i>Scer</i> and <i>Skud</i> SI values overlap. Different degrees of purple depend on whether the interaction could be tested in reciprocal ways or not. (<i>C</i>) Venn diagram indicating the overlap of PPIs detected by PCA of other methods (BioGRID) in <i>Scer</i>, and by PCA in <i>Skud</i>. Reciprocal combinations of PPIs were collapsed. (<i>D</i>) Representation of PPIs shared (purple lines) or unique to <i>Scer</i> (red lines) or <i>Skud</i> (blue lines) in the NPC. Only proteins involving divergences in PPIs are showed. Only the difference in the Nup120-Nup145 PPI was significant (**: <i>p</i><0.01).</p

The absence of Nup120-Nup145C interaction in <i>Skud</i> is likely a PPI loss.

<p>(<i>A</i>) Spot assays on Methotrexate medium (six days of growth at 30°C) to dissect the interaction in <i>Scer</i> (red), <i>Skud</i> (blue), <i>Suva</i> (yellow) and their hybrids. The interaction between Nup145C from <i>Scer</i> and Nup120 from <i>Scer</i>, <i>Skud</i> or <i>Suva</i> is detected, whereas it is lost when Nup145C comes from <i>Skud</i>. The interaction was also absent when it involved Nup120 from <i>Skud</i> and Nup145 from <i>Suva</i>. (<i>B</i>) Schematic structure of the <i>Scer</i> Nup120-Nup85-Nup145 sub-complex adapted from Fernandez-Martinez <i>et al. </i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003161#pgen.1003161-FernandezMartinez1" target="_blank">[43]</a>. The three interacting domains are indicated in black. (<i>C</i>) Interactions between Nup85 and Nup145C or Nup120 in three species and their hybrids confirm that not all Nup145C interactions are lost. (<i>D</i>) Evolutionary tree of <i>Scer</i>, <i>Skud</i> and <i>Suva</i> and schematic representation of Nup145-Nup120-Nup85 interactions in species and hybrids according to spot assays (<i>A–C</i>), revealing several other loss of interaction in hybrids with <i>Suva</i>. Line width is proportional to the number of spot growth observed for each interaction. (<i>E</i>) Similar growth for BY4741 <i>Scer</i> wild type (WT) and modified strains (Δ<i>Skud-NUP145</i>) suggest that <i>Skud-Nup145</i> complements the absence of <i>Scer-Nup145</i> (YPD medium, two days of growth at 30°C), as <i>Nup145</i> is essential for growth in <i>Scer</i>.</p

The NPC and RNApII are robust to hybridization.

<p>SI values compared between <i>Scer</i> (red) or <i>Skud</i> (blue) and <i>Scer-Skud</i> hybrids (green). Examples of proteins Nup82 (<i>A–B</i>) and Nup145 (<i>E–F</i>) in the NPC and Rpb3 (<i>C–D</i>) in the RNApII. Segment width is proportional to SI (dotted line if SI<<i>t</i>). For each comparison, networks on left show interactions measured between the protein of interest tagged in <i>MATa</i> (center) and other proteins of the same complex tagged in <i>MATα</i>. Networks on right show the reciprocal interactions. The protein of interest comes from <i>Scer</i> (red ring) or <i>Skud</i> (blue ring) and is in the species background (outer ring) or in the hybrid background (inner ring). Asterisks indicate whether the SI value measured in hybrid is significantly different from that measured in species (*: <i>p</i><0.05; **: <i>p</i><0.01; ***: <i>p</i><0.001). Only the absence of <i>Scer</i>Nup120-<i>Skud</i>Nup145 is significant in reciprocal comparisons (<i>E</i>). Protein names were blurred when strains were unavailable.</p

Supplemental Material for Wolters et al., 2018

Figure S1: Mitochondrial Recombinants<br>Tables S1-11. All growth measures used for analyses are provided in Tables S6, S7 and S8.<br><br><br

cohort SNP file

variant file of all strains, contains all single nucleotide polymorphic sites that are bi-allelic only

<i>S</i>. <i>eubayanus</i> distribution and phylogeography.

<p>A) Geographic distribution of <i>S</i>. <i>eubayanus</i> isolates. B) Maximum-Likelihood (ML) phylogenetic tree reconstructed using the concatenated multi-locus Dataset A (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006155#pgen.1006155.s001" target="_blank">S1 Text</a>). Bar colors are defined in the legend in panel A. Asterisks highlight new isolates or strains not previously studied together [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006155#pgen.1006155.ref020" target="_blank">20</a>]. EU: Europe; QI: Qinghai (China); LA: Lanin (Argentina); NC: North Carolina (USA); NH: Nahuel Huapi (Argentina); NZ: New Zealand; SH: Shaanxi (China); SI: Sichuan (China); T: Tibet (China); VP: Villa Pehuenia (Argentina); WA: Washington (USA). C) ML phylogenetic tree reconstructed using the complete genome sequence data. Phylogenetic trees were rooted using <i>S</i>. <i>uvarum</i> (CBS7001) as the outgroup. The scale bars show the number of substitutions per site. The strain FM1318 is a monosporic derivative of CRUB1568^T (= CBS12357^T = PYCC6148^T). Bootstrap values above 50 are reported at their corresponding nodes. D) Neighbor-Net phylogenetic network reconstructed with the SNP dataset. In phylogenetic networks, incongruent data are represented by nodes subtended by multiple edges. Blue and red arrows indicate the fractional genomic contributions from PB-1 and PA-2, respectively. The scale bar represents the number of substitutions. Note that the admixed strains from Wisconsin [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006155#pgen.1006155.ref020" target="_blank">20</a>] and New Brunswick (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006155#pgen.1006155.g002" target="_blank">Fig 2</a>) are only shown in panel D to avoid implying a linear bifurcating ancestry.</p