title: In silicoComparison of 19Porphyromonas gingivalisStrains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics.
abstract: Currently, genome sequences of a total of 19Porphyromonas gingivalisstrains are available, including eight completed genomes (strains W83, ATCC 33277, TDC60, HG66, A7436, AJW4, 381, and A7A1-28) and 11 high-coverage draft sequences (JCVI SC001, F0185, F0566, F0568, F0569, F0570, SJD2, W4087, W50, Ando, and MP4-504) that are assembled into fewer than 300 contigs. The objective was to compare these genomes at both nucleotide and protein sequence levels in order to understand their phylogenetic and functional relatedness. Four copies of16S rRNAgene sequences were identified in each of the eight complete genomes and one in the other 11 unfinished genomes. These 4316S rRNAsequences represent only 24 unique sequences and the derived phylogenetic tree suggests a possible evolutionary history for these strains. Phylogenomic comparison based on shared proteins and whole genome nucleotide sequences consistently showed two groups with closely related members: one consisted of ATCC 33277, 381, and HG66, another of W83, W50, and A7436. At least 1,037 core/shared proteins were identified in the 19P. gingivalisgenomes based on the most stringent detecting parameters. Comparative functional genomics based on genome-wide comparisons between NCBI and RAST annotations, as well as additional approaches, revealed functions that are unique or missing in individualP. gingivalisstrains, or species-specific in allP. gingivalisstrains, when compared to a neighboring speciesP. asaccharolytica. All the comparative results of this study are available online for download at ftp://www.homd.org/publication_data/20160425/.
authors.affiliation: Department of Microbiology, The Forsyth Institute Cambridge, MA, USA.
authors.forename: Tsute
authors.initials: T
authors.lastname: Chen
authors.affiliation: Department of Oral Biology, University of Oslo Oslo, Norway.
authors.forename: Huma
authors.initials: H
authors.lastname: Siddiqui
authors.affiliation: Department of Oral Biology, University of Oslo Oslo, Norway.
authors.forename: Ingar
authors.initials: I
authors.lastname: Olsen
mesh_terms: D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D016966:Porphyromonas gingivalis / Q000145:classification* / Q000235:genetics*; D012336:RNA, Ribosomal, 16S; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: Porphyromonas gingivalis; comparative genomics; phylogenetics; phylogenomics