Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.
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 o...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2017-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5268413?pdf=render |
| _version_ | 1818840516938170368 |
|---|---|
| author | Rafael A Baraúna Rommel T J Ramos Adonney A O Veras Kenny C Pinheiro Leandro J Benevides Marcus V C Viana Luís C Guimarães Judy M Edman Sharon J Spier Vasco Azevedo Artur Silva |
| author_facet | Rafael A Baraúna Rommel T J Ramos Adonney A O Veras Kenny C Pinheiro Leandro J Benevides Marcus V C Viana Luís C Guimarães Judy M Edman Sharon J Spier Vasco Azevedo Artur Silva |
| author_sort | Rafael A Baraúna |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-19T04:11:26Z |
| format | Article |
| id | doaj.art-fa1847e41221417e87ca4573138d8409 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-19T04:11:26Z |
| publishDate | 2017-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-fa1847e41221417e87ca4573138d84092022-12-21T20:36:24ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01121e017067610.1371/journal.pone.0170676Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.Rafael A BaraúnaRommel T J RamosAdonney A O VerasKenny C PinheiroLeandro J BenevidesMarcus V C VianaLuís C GuimarãesJudy M EdmanSharon J SpierVasco AzevedoArtur SilvaSeven 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.http://europepmc.org/articles/PMC5268413?pdf=render |
| spellingShingle | Rafael A Baraúna Rommel T J Ramos Adonney A O Veras Kenny C Pinheiro Leandro J Benevides Marcus V C Viana Luís C Guimarães Judy M Edman Sharon J Spier Vasco Azevedo Artur Silva Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics. PLoS ONE |
| title | Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics. |
| title_full | Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics. |
| title_fullStr | Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics. |
| title_full_unstemmed | Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics. |
| title_short | Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics. |
| title_sort | assessing the genotypic differences between strains of corynebacterium pseudotuberculosis biovar equi through comparative genomics |
| url | http://europepmc.org/articles/PMC5268413?pdf=render |
| work_keys_str_mv | AT rafaelabarauna assessingthegenotypicdifferencesbetweenstrainsofcorynebacteriumpseudotuberculosisbiovarequithroughcomparativegenomics AT rommeltjramos assessingthegenotypicdifferencesbetweenstrainsofcorynebacteriumpseudotuberculosisbiovarequithroughcomparativegenomics AT adonneyaoveras assessingthegenotypicdifferencesbetweenstrainsofcorynebacteriumpseudotuberculosisbiovarequithroughcomparativegenomics AT kennycpinheiro assessingthegenotypicdifferencesbetweenstrainsofcorynebacteriumpseudotuberculosisbiovarequithroughcomparativegenomics AT leandrojbenevides assessingthegenotypicdifferencesbetweenstrainsofcorynebacteriumpseudotuberculosisbiovarequithroughcomparativegenomics AT marcusvcviana assessingthegenotypicdifferencesbetweenstrainsofcorynebacteriumpseudotuberculosisbiovarequithroughcomparativegenomics AT luiscguimaraes assessingthegenotypicdifferencesbetweenstrainsofcorynebacteriumpseudotuberculosisbiovarequithroughcomparativegenomics AT judymedman assessingthegenotypicdifferencesbetweenstrainsofcorynebacteriumpseudotuberculosisbiovarequithroughcomparativegenomics AT sharonjspier assessingthegenotypicdifferencesbetweenstrainsofcorynebacteriumpseudotuberculosisbiovarequithroughcomparativegenomics AT vascoazevedo assessingthegenotypicdifferencesbetweenstrainsofcorynebacteriumpseudotuberculosisbiovarequithroughcomparativegenomics AT artursilva assessingthegenotypicdifferencesbetweenstrainsofcorynebacteriumpseudotuberculosisbiovarequithroughcomparativegenomics |