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Background  Swine brucellosis caused by  B. suis  biovar 2 is an emergent disease in domestic pigs in Europe. The emergence of this pathogen has been linked to the increase of extensive pig farms and the high density of infected wild boars ( Sus scrofa ). In Portugal and Spain, the majority of strains share specific molecular characteristics, which allowed establishing an Iberian clonal lineage. However, several strains isolated from wild boars in the North-East region of Spain are similar to strains isolated in different Central European countries.    Results  Comparative analysis of five newly fully sequenced  B. suis  biovar 2 strains belonging to the main circulating clones in Iberian Peninsula, with publicly available  Brucella  spp. genomes, revealed that strains from Iberian clonal lineage share 74% similarity with those reference genomes. Besides the 210 kb translocation event present in all biovar 2 strains, an inversion with 944 kb was presented in chromosome I of strains from the Iberian clone. At left and right crossover points, the inversion disrupted a TRAP dicarboxylate transporter, DctM subunit, and an integral membrane protein TerC. The gene  dctM  is well conserved in  Brucella  spp. except in strains from the Iberian clonal lineage. Intraspecies comparative analysis also exposed a number of biovar-, haplotype- and strain-specific insertion-deletion (INDELs) events and single nucleotide polymorphisms (SNPs) that could explain differences in virulence and host specificities. Most discriminative mutations were associated to membrane related molecules (29%) and enzymes involved in catabolism processes (20%). Molecular identification of both  B. suis  biovar 2 clonal lineages could be easily achieved using the target-PCR procedures established in this work for the evaluated INDELs.    Conclusion  Whole-genome analyses supports that the  B. suis  biovar 2 Iberian clonal lineage evolved from the Central-European lineage and suggests that the genomic specialization of this pathogen in the Iberian Peninsula is independent of a specific genomic event(s), but instead driven by allopatric speciation, resulting in the establishment of a new ecovar.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4113-8) contains supplementary material, which is available to authorized users.

Evolution and genome specialization of Brucella suis biovar 2 Iberian lineages