Bayesian tree constructed on the concatenated sequences of <i>cts</i>, <i>gyrB</i>, <i>rpoD</i> and <i>gapA</i> (1465bp).

<p>Bootstrap values are indicated at each node, while names at the branches indicate the name of the strains. Pathovar affiliations are reported for some of the <i>Pseudomonas syringae</i> strains belonging to different phylogenetic groups. Sequences for the different <i>P</i>. <i>syringae</i> strains and their phylogroup affiliation were described previously by Berge et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147584#pone.0147584.ref046" target="_blank">46</a>]. MLST sequences of the Pav strains isolated previously from Greece and Italy were reported by Wang et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147584#pone.0147584.ref018" target="_blank">18</a>]. Sequences for PavCRAFRUec1, PavCRAFRUec2 and PavCRAFRUec3 are published by Marcelletti and Scortichini [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0147584#pone.0147584.ref041" target="_blank">41</a>]. <i>Pseudomonas aeruginona</i> (PAO1) was used as an outgroup. Triangles with different colours are used to label strains in the following way. Blue triangles: strains isolated in this study, red triangles: strains isolated in central Italy during the first epidemic, and green triangles: strains isolated in Greece.</p

Length of external and internal necroses developed on hazelnut plants (cv. Tonda Gentile Romana) inoculated through leaf scar.

<p>The length was measured after 4 weeks post infection. The reference strains of <i>Pseudomonas avellanae</i> (NCPPB 3487 (= BPIC631) and NCPPB 3489) previously isolated in Greece from bacterial canker symptoms produced mild external and internal necroses, together with the strain PaVT10 isolated in this study. The rest of the strains tested in this study caused only weak necrosis on the inoculated plants. The error bars represent the standard error of the measurements.</p

Isolation of <i>Pseudomonas avellanae</i> (Pav) from hazelnut twigs collected from 2010 to 2012.

<p>Samples were collected from March to August, each year. The average percentage of Pav isolation for the three years is calculated by the ratio between the number of Pav-positive samples and the total number of samples used for isolation.</p

Characteristic hazelnut decline symptoms observed on hazelnut plants (cv. Tonda Gentile Romana).

<p>Decline began with sudden wilting of a stem (A) while the rest was still intact. Successively, decline affected the whole branch which manifested the dieback while the remaining branch manifested suffering state with pale green foliage (B). When the bark of branch bearing pale green foliage was excised, discoloration of cambium could be observed (C). During the end of vegetative phase complete plant death occurred although leaves were still attached (D). The following year, also the plants present in the proximity of the plant that showed initial decline symptoms appeared completely affected (E).</p

An example of BOX PCR fingerprint patterns obtained for genomic DNAs of <i>Pseudomonas avellanae</i> strains isolated from <i>Corylus avellana</i> by using the BOX primer set.

<p>Lanes from left to right—M: molecular size marker (1-kb ladder), 1: strain PaVT1, 2: strain PaVT2, 3: strain PaVT5, 4: strain PaVT6, 5: strain PaVT8, 6: strain PaVT10, 7: strain PaVT17, 8: strain PaVT24, 9: strain PaVT25, 10: strain PaVT28, 11: strain PaVT29, 12: strain NCPPB 3489, 13: strain NCPPB 3487 and m: molecular size marker (100bp ladder). All strains isolated in this study were clonal and no diversity was observed among them.</p

A very young hazelnut plantation (4 year old plants, cv. Tonda gentile Romana) completely decimated by hazelnut decline phenomenon.

<p>The young plants were planted in the same plot where severely affected old plants (15-year-old) were removed.</p

Incidence of hazelnut decline (%) across the study sites in the province of Viterbo.

<p>The circle size inside the map indicates the different hazelnut decline incidence.</p

A User's Guide to a Data Base of the Diversity of <i>Pseudomonas syringae</i> and Its Application to Classifying Strains in This Phylogenetic Complex

<div><p>The <i>Pseudomonas syringae</i> complex is composed of numerous genetic lineages of strains from both agricultural and environmental habitats including habitats closely linked to the water cycle. The new insights from the discovery of this bacterial species in habitats outside of agricultural contexts <i>per se</i> have led to the revelation of a wide diversity of strains in this complex beyond what was known from agricultural contexts. Here, through Multi Locus Sequence Typing (MLST) of 216 strains, we identified 23 clades within 13 phylogroups among which the seven previously described <i>P. syringae</i> phylogroups were included. The phylogeny of the core genome of 29 strains representing nine phylogroups was similar to the phylogeny obtained with MLST thereby confirming the robustness of MLST-phylogroups. We show that phenotypic traits rarely provide a satisfactory means for classification of strains even if some combinations are highly probable in some phylogroups. We demonstrate that the citrate synthase (<i>ct</i>s) housekeeping gene can accurately predict the phylogenetic affiliation for more than 97% of strains tested. We propose a list of <i>cts</i> sequences to be used as a simple tool for quickly and precisely classifying new strains. Finally, our analysis leads to predictions about the diversity of <i>P. syringae</i> that is yet to be discovered. We present here an expandable framework mainly based on <i>cts</i> genetic analysis into which more diversity can be integrated.</p></div

Data_Sheet_1_A Genomic Map of Climate Adaptation in Arabidopsis thaliana at a Micro-Geographic Scale.DOCX

<p>Understanding the genetic bases underlying climate adaptation is a key element to predict the potential of species to face climate warming. Although substantial climate variation is observed at a micro-geographic scale, most genomic maps of climate adaptation have been established at broader geographical scales. Here, by using a Pool-Seq approach combined with a Bayesian hierarchical model that control for confounding by population structure, we performed a genome–environment association (GEA) analysis to investigate the genetic basis of adaptation to six climate variables in 168 natural populations of Arabidopsis thaliana distributed in south-west of France. Climate variation among the 168 populations represented up to 24% of climate variation among 521 European locations where A. thaliana inhabits. We identified neat and strong peaks of association, with most of the associated SNPs being significantly enriched in likely functional variants and/or in the extreme tail of genetic differentiation among populations. Furthermore, genes involved in transcriptional mechanisms appear predominant in plant functions associated with local climate adaptation. Globally, our results suggest that climate adaptation is an important driver of genomic variation in A. thaliana at a small spatial scale and mainly involves genome-wide changes in fundamental mechanisms of gene regulation. The identification of climate-adaptive genetic loci at a micro-geographic scale also highlights the importance to include within-species genetic diversity in ecological niche models for projecting potential species distributional shifts over short geographic distances.</p

Bayesian phylogeny of the core genome of 29 <i>P. syringae</i> strains.

<p>An un-rooted tree was constructed on 107 open reading frames (64,000 bp) common to 29 <i>P. syringae</i> strains. Bootstrap values are indicated at each node and strain names are indicated at tree branches. Phylogroup and clade names are also indicated in the tree.</p