Sequence types (STs) identified at both side of the Pacific Ocean and route for the movement of waters associated with El Niño event (red arrow).

<p>STs in red indicate those genetic variants detected both in Asia and Peru (ST189a), including the ST189 for the strain 090–96 with the <i>recA</i> insertion.</p

Schematic representation of the <i>recA</i> gene region between four <i>V</i>. <i>parahaemolyticus</i> genomes.

<p>Comparison includes RIMD2210633 (prototypic “pandemic” strain O3:K6), BB22OP (closest relative ST88), strains 090–96 (Peruvian, fragmented <i>recA</i> gene), and S134 (Chinese strain containing a similar insert at <i>recA</i> gene). Predicted genes are depicted by horizontal arrows and named according the legend. Red bars represent inverted regions flanking the insertion. The percentage DNA sequence identity is indicated in grey bars and represents the BLASTn matches between sequences.</p

<i>V</i>. <i>parahaemolyticus</i> “snapshot” of CC345 obtained using eBURST v3.

<p>Other CCs were defined using stringent criteria (6/7 shared alleles) (Figure B in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117485#pone.0117485.s001" target="_blank">S1 File</a>). Among those groups or CCs, ST345 was identified as the predicted clonal ancestor of CC345. STs that are SLV of each other are shown connected by lines (black). DLV STs are shown as connected light gray lines. CC—Clonal Complex. R- Recombination event and the number of SNPs between ST345 (founder) and the other STs are between brackets. All the differences were located at the <i>recA</i> allele, except for ST812 that were located at the <i>gyrB</i> allele.</p

NeighborNet graph generated using the BIGSdb Genome Comparator tool implemented within the PubMLST website [34,35] with 2005 variable loci identified after using as a reference (ref) RIMD2210633 chromosome I (3079 genes) of available <i>V</i>. <i>parahaemolyticus</i> genomes at Genbank (Table A in S1 File for the list of the strains) and strain 090–96 (Peru 1996), showing that this strain is closed related to BB22OP (ST88) and the two other ST189 strains and far related to other strains containing fragmented <i>recA</i> genes with similar insertion (S130 and S134, both ST527).

<p>This clearly suggests acquisition of this region by HGT. A similar graph was obtained with chromosome II of the same strain as reference (data not shown). Distances between taxa are calculated as the number of loci with different allele sequences.</p

<i>V</i>. <i>parahaemolyticus</i> strains with <i>recA</i> allele 107 available at the MLST <i>V</i>. <i>parahaemolyticus</i> database.

<p>C- Clinical. E- Environmental.</p><p><i>V</i>. <i>parahaemolyticus</i> strains with <i>recA</i> allele 107 available at the MLST <i>V</i>. <i>parahaemolyticus</i> database.</p

Summary report of the <i>de novo</i> assembly of 090–96.

<p>* The N50 statistic is calculated by summing the lengths of the biggest contigs until 50% of the total genome length has been reached. The smallest contig within this set is reported the N50 value of a <i>de novo</i> assembly.</p><p>Summary report of the <i>de novo</i> assembly of 090–96.</p

Annotation of the <i>recA</i> region from the genome of strain 090–96 by RAST server [22].

<p>This region was identified in contig0035 (JFFP01000036) of the assembled shotgun genome. In bold fonts are the inserted genes probably by HGT. In green fonts are the two <i>recA</i> fragments resultants from the split of the original <i>recA</i>3.</p><p>^aOrder of the genes shown on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117485#pone.0117485.g002" target="_blank">Fig. 2</a>.</p><p>Annotation of the <i>recA</i> region from the genome of strain 090–96 by RAST server [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0117485#pone.0117485.ref022" target="_blank">22</a>].</p

MLST majority consensus phylogeny.

<p>A majority consensus phylogeny of 77 <i>V. parahaemolyticus</i> isolates based on 7 concatenated housekeeping loci (<i>dna</i>E, <i>gyr</i>B, <i>rec</i>A, <i>dtd</i>S, <i>pnt</i>A, <i>pry</i>C and <i>tna</i>A) and representing 3,682 total nucleotides was constructed using the Bayesian Markov chain Monte Carlo (MCMC) method as implemented in MrBayes v3.2. The 77 isolates included in this phylogeny were separated into three major clusters (I, II, III) and 12 distinct clades (1–12). Sequence typing (ST) designations for MLST analysis describe the 24 MLST sequence types comprising each of the 12 clades. Distinct clades clearly highlighted by alternating blue and gray shading. Nodes are labeled with posterior probabilities (0–1) while cladogram shading is indicative of branches with weak support (red) and strong support (black).</p

Results of the Pairwise Homoplasy Index (φ_w)^a and Sawyer’s Run Test^b for homologous recombination performed on individual loci included in the MLST scheme (<i>dna</i>E, <i>gyr</i>B, <i>rec</i>A, <i>dtd</i>S, <i>pnt</i>A, <i>pry</i>C and <i>tna</i>A).

a<p>mean Pairwise Homoplasy Index, see reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055726#pone.0055726-Bruen1" target="_blank">[48]</a>.</p>b<p>sum of squared lengths of condensed fragments (SSCF) and sum of squared lengths of uncondensed fragments (SSUF), see reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055726#pone.0055726-Sawyer1" target="_blank">[49]</a>.</p>*<p>significance declared at P<0.05.</p

Summary of loci statistics included in the MLST scheme (<i>dna</i>E, <i>gyr</i>B, <i>rec</i>A, <i>dtd</i>S, <i>pnt</i>A, <i>pry</i>C and <i>tna</i>A) such as fragment length, number of alleles and polymorphic sites, nucleotide diversity (π), rates of nonsynonymous (<i>d</i>_N) and synonymous (<i>d</i>_S) mutations, and tests of selection (<i>d</i>_N/<i>d</i>_S).

a<p>Rate of nonsynonymous (<i>d</i>_N) and synonymous (<i>d</i>_S) substitutions where <i>d</i>_N/<i>d</i>_S<1 indicates that the loci is subject to purifying selection.</p