title: Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.
abstract: Seven genomes of Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp. This bacterium is the causative agent of disease known as "pigeon fever" which commonly affects horses worldwide. The pangenome of biovar equi was calculated and two phylogenomic approaches were used to identify clustering patterns within Corynebacterium genus. Furthermore, other comparative analyses were performed including the prediction of genomic islands and prophages, and SNP-based phylogeny. In the phylogenomic tree, C. pseudotuberculosis was divided into two distinct clades, one formed by nitrate non-reducing species (biovar ovis) and another formed by nitrate-reducing species (biovar equi). In the latter group, the strains isolated from California were more related to each other, while the strains CIP 52.97 and 1/06-A formed the outermost clade of the biovar equi. A total of 1,355 core genes were identified, corresponding to 42.5% of the pangenome. This pangenome has one of the smallest core genomes described in the literature, suggesting a high genetic variability of biovar equi of C. pseudotuberculosis. The analysis of the similarity between the resistance islands identified a higher proximity between the strains that caused more severe infectious conditions (infection in the internal organs). Pathogenicity islands were largely conserved between strains. Several genes that modulate the pathogenicity of C. pseudotuberculosis were described including peptidases, recombination enzymes, micoside synthesis enzymes, bacteriocins with antimicrobial activity and several others. Finally, no genotypic differences were observed between the strains that caused the three different types of infection (external abscess formation, infection with abscess formation in the internal organs, and ulcerative lymphangitis). Instead, it was noted that there is a higher phenetic correlation between strains isolated at California compared to the other strains. Additionally, high variability of resistance islands suggests gene acquisition through several events of horizontal gene transfer.
authors.affiliation: Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Rafael A
authors.identifier: http://orcid.org/0000-0002-7837-7380
authors.initials: RA
authors.lastname: Baraúna
authors.affiliation: Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Rommel T J
authors.initials: RT
authors.lastname: Ramos
authors.affiliation: Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Adonney A O
authors.initials: AA
authors.lastname: Veras
authors.affiliation: Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Kenny C
authors.initials: KC
authors.lastname: Pinheiro
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Leandro J
authors.initials: LJ
authors.lastname: Benevides
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Marcus V C
authors.identifier: http://orcid.org/0000-0002-7017-6437
authors.initials: MV
authors.lastname: Viana
authors.affiliation: Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Luís C
authors.identifier: http://orcid.org/0000-0002-7147-9448
authors.initials: LC
authors.lastname: Guimarães
authors.affiliation: School of Veterinary Medicine, Department of Medicine and Epidemiology, University of California Davis, Davis, California, United States of America.
authors.forename: Judy M
authors.initials: JM
authors.lastname: Edman
authors.affiliation: School of Veterinary Medicine, Department of Medicine and Epidemiology, University of California Davis, Davis, California, United States of America.
authors.forename: Sharon J
authors.initials: SJ
authors.lastname: Spier
authors.affiliation: Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
authors.affiliation: Laboratory of Genomics and Bioinformatics, Center of Genomics and Systems Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
mesh_terms: D000818:Animals; D003354:Corynebacterium Infections / Q000235:genetics* / Q000382:microbiology; D016925:Corynebacterium pseudotuberculosis / Q000235:genetics* / Q000472:pathogenicity; D016680:Genome, Bacterial / Q000235:genetics*; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006734:Horse Diseases / Q000235:genetics* / Q000382:microbiology; D006736:Horses / Q000382:microbiology; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D016929:Rhodococcus equi / Q000235:genetics* / Q000472:pathogenicity