<i>In planta</i> performances of multiplex HRM analysis for discrimination of <i>P. savastanoi</i> pathovars.

<p>Normalized and difference plots obtained in multiplex HRM assay, performed using the couple of primer pairs for SNP markers C2/L1 on Oleander plants inoculated with <i>Psn23</i>. Pure genomic DNAs from <i>Psv5</i>, <i>Psn23</i>, and <i>Psf134</i> were also tested as controls. On each plot different colors indicate distinct profiles, generated by <i>Psv5</i>, <i>Psn23</i> and <i>Psf134</i> (red, blue and green trace, respectively). Three <i>Psn23</i> artificially infected plants were tested for each of the three independent Real-Time PCR runs performed. RFU: Relative fluorescence units. Green and red columns represent pre- and post-melting normalization regions.</p

Normalized HRM plots related to the ten SNPs analyzed in this study.

<p>Normalized HRM plots of the amplicons obtained from the 56 <i>P. savastanoi</i> strains using the nine primer pairs. For each amplicon, the corresponding SNP marker is reported on the upper-right corner of the plot. Different colors are used to indicate distinct profiles, corresponding to the HRMA-based clustering of the 56 <i>P. savastanoi</i> strains into pathovars or SGs. RFU: Relative fluorescence units. Green and red columns represent pre- and post-melting normalization regions.</p

Details and performances of the nine primer pairs used in this study for the identification and genotyping of <i>P. savastanoi</i> by HRMA.

a<p>In bold the two variants for each SNP marker are shown.</p>b<p>Pre- and post-melt temperatures used to normalize HRM data.</p>c<p>LLOD = Lower Limit Of Detection.</p

<i>P. savastanoi</i> strains used in this study with the designation of their geographical origin, the variants for each SNP marker examined and their SNP-group.

a<p>CFBP, Collection Française de Bactéries Phytopathogènes, INRA, Angers, France; ITM, Culture collection of Istituto Tossine e Micotossine da Parassiti vegetali, C.N.R., Bari, Italy (from A. Sisto); LPVM, Culture Collection of Laboratorio di Patologia Vegetale Molecolare, Dipartimento di Biotecnologie Agrarie, Università degli Studi di Firenze; NCPPB, National Collection of Plant Pathogenic Bacteria, York, UK (<a href="http://www.nctc.org.uk" target="_blank">http://www.nctc.org.uk</a>); PD, Culture collection of Plant Protection Service, Wageningen, The Netherlands; PVBa, Culture Collection of Dipartimento di Patologia Vegetale, Università degli Studi di Bari, Italy (from A. Sisto); ES, MC and AG, from E. Santilli, M. Cerboneschi and A. Gori, respectively.</p>b<p>Code used at LPVM for strains ITM317, NCPPB1006 and ES23 are <i>Psv5</i>, <i>Psf134</i> and <i>Psn23</i>, respectively.</p>c<p>SG = SNP-group.</p

Bayesian inference tree.

<p>ITS1 Bayesian inference tree illustrating the phylogenetic relationships among <i>Eunicella</i> species. Numbers near nodes are posterior probability (PP) values. ST mean ‘sequence type’ to refer to every distinct type of ITS-1 sequence detected, as proposed by [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160678#pone.0160678.ref052" target="_blank">52</a>].</p

Genetic diversity of <i>Eunicella singularis</i> at six microsatellite loci; H_O: observed heterozygosity, H_E: unbiased expected heterozygosity, Ar: allelic richness, Ap: private allelic richness, F_IS: Weir and Cockerham’s [35] estimate fixation index with significant values in bold (0.05 threshold after FDR correction).

<p>Genetic diversity of <i>Eunicella singularis</i> at six microsatellite loci; H_O: observed heterozygosity, H_E: unbiased expected heterozygosity, Ar: allelic richness, Ap: private allelic richness, F_IS: Weir and Cockerham’s [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160678#pone.0160678.ref035" target="_blank">35</a>] estimate fixation index with significant values in bold (0.05 threshold after FDR correction).</p

Colonies of <i>Eunicella singularis</i> from 10 to 60 meter depth sampled in Cap de Creus; <i>Eunicella cavolinii</i> from Elba Island at 18–20 m depth, <i>E</i>. <i>verrucosa</i> from Tarragona at 13–17 m depth, and <i>E</i>. <i>racemosa</i> along the Morocco coast.

<p>Reprinted from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160678#pone.0160678.ref016" target="_blank">16</a>], under a CC BY license, with permission from SPRINGER, original copyright 2012</p

Geographical coordinates of the sampling locations and depth range at which <i>E</i>. <i>singularis</i> colonies were collected.

<p>N: numbers of analysed colonies.</p

Population structure as inferred by the STRUCTURE analysis for K = 2 (A) and K = 4 (B) clusters in <i>E</i>. <i>singularis</i>.

<p>Individuals are represented by vertical bars; the colours correspond to different genetic clusters, and the colours proportions of the individuals indicate their membership (from 0 to 1) in the corresponding cluster. Each graph corresponds to the combination of ten different runs obtained for each K value. Population codes are indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0160678#pone.0160678.t001" target="_blank">Table 1</a>.</p

Subdivision of the <i>Eunicella singularis</i> colonies according to the DAPC method.

<p>Colonies from different sites are indicated with different colours, dots represent individual colonies. A barplot of eigenvalues for the discriminant analysis is displayed in inset. Eigenvalues show the amount of genetic information contained in each successive principal component with x and y-axes constituting the first two principal components, respectively.</p