Features of the DS durum wheat genetic map.

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

Efficiency of the genotyping by capture protocol.

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

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

Polymorphisms available for bait design.

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

Prevalence of virulence factor genes in major African and French Clonal Complexes causing meningitis.

<p><u>Legend:</u></p><p>^a Genotypic analysis performed using the following parameters: clonal complexes (CC) defined as MLVA types having a maximum distance of changes at 2 loci and a minimum cluster size of 2 types</p><p>^b PMEN clones listed in <a href="http://www.sph.emory.edu/PMEN/" target="_blank">www.sph.emory.edu/PMEN/</a>.</p><p>^c<i>pspA</i> not typable in 3 African and 3 French isolates, both families present in 1 French isolate, no family 3 identified</p><p>^d<i>nanA</i> and <i>nanB</i> not reported because present in 100% of the strain collection</p><p>^e Presence of a truncated gene with lower PM amplified product in 6 French isolates</p><p>Abbreviations: MLVA = Multi Locus Variable number tandem repeats Analysis, Sp = serotype, CC = Clonal Complex, CSF = cerebrospinal fluid, N = number, PMEN = pneumococcal molecular epidemiological network; <i>ply</i> coding for Pneumolysin, <i>pspA</i> for Pneumococcal surface protein A (all types+ family 1/2), <i>pspC</i> for Pneumococcal surface protein C (all types and group 4), <i>pavA</i> for Pneumococcal adhesion and virulence A, <i>lytA</i> for Autolysin A, <i>phtA</i>, <i>B</i>, <i>D</i>, <i>E</i> for Polyhistidine triad complex A, B, D, E, <i>nanA</i>, <i>B</i>, <i>C</i> for Neuraminidase A, B, C, <i>rrgA</i> for detection of Pilus-1 islet, <i>sipA</i> for detection of Pilus2 islet, <i>pcpA</i> for Pneumococcal choline binding protein A, <i>psrp</i> for Pneumococcal serine-rich protein.</p><p>Prevalence of virulence factor genes in major African and French Clonal Complexes causing meningitis.</p

Prevalence of vaccine candidate antigens among invasive isolates according to PCV13 (VTs) or non-PCV13 (NVTs) serotypes inside the French (3.a) and African (3.b) collections.

<p>It illustrates the theoretical coverage achievable by each antigen in a monovalent or combined (PhtD+PcpA) hypothetical vaccination in terms of percentage of IPD strains circulating at the time of the study likely to express the vaccine-included protein. The <i>ply</i> gene is not represented since present by definition in 100% of our collection. The prevalence of the combination <i>phtD</i> + <i>pcpA</i> genes was arbitrarily calculated taking into account the presence of at least one of the two genes. Abbreviations: Sp = serotype, IPD = invasive pneumococcal disease, N = number, PCV13 = 13 valent pneumococcal conjugate vaccine, VT = PCV13 included serotype, NVT = non-PCV13 included serotype.</p

Distribution of Sp1 isolates (N = 136) according to virulence genes profile by (A)) unweighted pair group method with arithmetic mean (UPGMA) dendrogram based on similarity matrix (B) Multi-Dimensional Scaling (MDS) based on similarity matrix.

<p>2.A: Every row represents one strain, the dark plot means the presence of the gene, colour represents the country of isolation (blue = France, red = Africa).2.B: MDS is a visualization method displaying in <i>3</i>-dimensional space the information contained in the similarity matrix. Every dot represents a group of strains sharing an identical combination of virulence genes. The more different the gene combinations are, the more distant the dots are. Colours represent the region of isolation (blue = France, red = Africa).</p

Minimum spanning tree of Sp1 invasive isolates according to MLVA genotypes and either continent of origin (1a, N = 136) or <i>ply</i> allele (1b, N = 62).

<p>The size of the circle reflects the number of isolates identified, the distance between circles reflects the degree of genetic divergence, the circle colors represent either the continent (1.a) or the <i>ply</i> allele type (1.b), the colours outside of circles indicate major clonal groupings (MLVA CCs). MLVA = Multi locus variable number tandem repeats analysis, CC = Clonal Complex, N = number.</p