Features of the DS durum wheat genetic map.

<p>Features of the DS durum wheat genetic map.</p

Efficiency of the genotyping by capture protocol.

<p>Efficiency of the genotyping by capture protocol.</p

Description of the bait design.

<p>Orange lines represent the durum wheat genome, with the targeted SNP in brackets. Bait sequences are represented in grey. The number of SNPs targeted by each type of bait is specified.</p

Polymorphisms available for bait design.

<p>Polymorphisms available for bait design.</p

Correlations between putative physical and genetic positions.

<p>The 14 durum wheat chromosomes are shown separately, with the putative physical position on the X-axis (bp) and the genetic position on the Y-axis (cM). The chromosome name is given at the top left of each plot. The number of markers is given in brackets. A red line represents the fitted polynomial model and a grey area represents the 95% confidence interval. The two vertical grey lines are maximum and minimum values of the physical positions.</p

Detection of a bonus SNP on the homeolog of a targeted contig.

<p>A portion of A and B genomes were represented, with an SNP on the A genome (in red) and an SNP on the B genome (in blue). Divergences between both genomes are represented in green. The bait shown in grey was designed initially to capture a portion of the A genome, but captured also the homeologous portion of the B genome, with the related bonus SNP.</p

Patterns of codon preference among the 11 studied species.

<p>The colour scale indicates the magnitude of Δ RSCU, the difference in the Relative Synonymous Codon Usage between highly and lowly expressed genes. The greenest codons are the most preferred and the reddest the least preferred. Codons ending in G or C are in red and those ending in A or T in blue.</p

Combined effect of GC3 and expression level on DoS statistics.

<p>The DoS statistics was computed on W/S (gBGC) or U/P (SCU) changes for four gene categories: GC-rich and highly expressed, GC-rich and lowly expressed, GC-poor and highly expressed, GC-poor and lowly expressed.</p

Schematic presentation of the method to estimate recent and ancestral gBGC or SCU.

<p>In addition to polymorphic derived mutations used to infer recent gBGC or selection (<i>B</i>₁/<i>S</i>₁) as in [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006799#pgen.1006799.ref038" target="_blank">38</a>] we also consider substitutions (<i>i</i>.<i>e</i>. fixed derived mutations) on the branch leading to the focal species. Each box corresponds to a site position in a sequence alignment. Both kinds of mutations are polarized with the two same outgroups and are thus sensitive to the same probability of polarization error. We assume that gBGC and selection may have change so that fixed mutations may have undergo a different intensity. Note that these two <i>B</i> or <i>S</i> values correspond to average of potentially more complex variations over the two periods.</p

GC3 and gBGC gradients along genes.

<p>A: gBGC strength estimations (4<i>N</i>_<i>e</i><i>b</i>) for first exons (252 first bp of contigs) and rest of gene. Error bars indicate the 95% confidence intervals. With the exception of <i>D</i>. <i>abyssinica</i> and <i>S</i>. <i>pimpinellifolium</i>, all species exhibit stronger gBGC in the first exons compared to the rest of genes. B. Correlations between GC3 and gBGC strength in first exons (red) and rest of genes (blue). Each dot corresponds to one species. GC3 and 4<i>N</i>_<i>e</i><i>b</i> tend to be positively correlated in both regions: ρ_Spearman = 0.591, p-value = 0.061 for first exons and ρ_Spearman = 0.382, p-value = 0.248 for the rest of genes. C. Comparison of 4Neb estimates between first exons and rest of genes for Commelinids (all Monocots with the exception of <i>D</i>. <i>abyssinica</i>, left panel) and other species (right panel). 4<i>N</i>_<i>e</i><i>b</i> values are higher in first exons compared to rest of genes in Commelinids species, while other species exhibit no differences between first exons and rest of genes.</p