IADR Abstract Archives
The Core and Pan Genomes of Porphyromonas gingivalis
Objectives: The goals of this study were to determine the core and pan genomes of P. gingivalis, to determine the relatedness of the 26 strains included and to identify unique genes present in different strains of this species.
Methods: : Draft genomes of nine[RC1] novel clinical isolates were produced via PacBio SMRT technology. Publicly available genomes of 17 P. gingivalis strains were obtained from NCBI. For uniform comparison, all new and existing genomes were annotated by Prokka software (v. 1.11). Genomes were compared using Roary software (v. 3.3.4) to determine the core (genes conserved across ≥ 99% of strains) and pan (all genes –core, accessory or unique– present within any included strains) genomes. Harvest software (v 1.1.2) was used to generate cladograms to illustrate the relatedness of the strains.
Results: Bioinformatics analysis revealed that the pan genome of this collection of strains consists of 1339 core genes (conserved in ≥99% of strains), 39 soft core genes (95-99%), 1210 shell genes (15-95%) and 2941 cloud genes (0-15%), for a total of 5529 genes present in these 26 isolates of P. gingivalis. The data are consistent with an “open” pan genome, where inclusion of additional strain genomes increases the pan genome with no apparent limit. The cladograms depicted the presence of multiple clades, with strains W12, A7436, AJW4, W83 and W50 in one clade; strains 33277, 381, HG66 and A7A1-28 in a second clade; and multiple “fresh” isolates, including TDC60, in a third clade.
Conclusions: These data demonstrate the diversity among the genomes of P. gingivalis, as well as the relative relatedness of one strain to another. These data should be considered by all who study this species, with regards to both common and unique phenotypes present among strains/isolates of P. gingivalis.
Methods: : Draft genomes of nine[RC1] novel clinical isolates were produced via PacBio SMRT technology. Publicly available genomes of 17 P. gingivalis strains were obtained from NCBI. For uniform comparison, all new and existing genomes were annotated by Prokka software (v. 1.11). Genomes were compared using Roary software (v. 3.3.4) to determine the core (genes conserved across ≥ 99% of strains) and pan (all genes –core, accessory or unique– present within any included strains) genomes. Harvest software (v 1.1.2) was used to generate cladograms to illustrate the relatedness of the strains.
Results: Bioinformatics analysis revealed that the pan genome of this collection of strains consists of 1339 core genes (conserved in ≥99% of strains), 39 soft core genes (95-99%), 1210 shell genes (15-95%) and 2941 cloud genes (0-15%), for a total of 5529 genes present in these 26 isolates of P. gingivalis. The data are consistent with an “open” pan genome, where inclusion of additional strain genomes increases the pan genome with no apparent limit. The cladograms depicted the presence of multiple clades, with strains W12, A7436, AJW4, W83 and W50 in one clade; strains 33277, 381, HG66 and A7A1-28 in a second clade; and multiple “fresh” isolates, including TDC60, in a third clade.
Conclusions: These data demonstrate the diversity among the genomes of P. gingivalis, as well as the relative relatedness of one strain to another. These data should be considered by all who study this species, with regards to both common and unique phenotypes present among strains/isolates of P. gingivalis.