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Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis.

Kittichotirat W, Bumgarner RE, Asikainen S, Chen C - PLoS ONE (2011)

Bottom Line: The genomic differences were occasionally greater for strains of the same serotypes than strains of different serotypes.Cumulatively, 777 strain-specific genes were found on these islands and represented 61% of the flexible gene pool.Moreover, the genomic variation within each clonal lineage of A. actinomycetemcomitans (as defined by serotype grouping) may be greater than between clonal lineages.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, Washington, United States of America.

ABSTRACT

Background: Aggregatibacter actinomycetemcomitans is genetically heterogeneous and comprises distinct clonal lineages that may have different virulence potentials. However, limited information of the strain-to-strain genomic variations is available.

Methodology/principal findings: The genome sequences of 11 A. actinomycetemcomitans strains (serotypes a-f) were generated de novo, annotated and combined with three previously sequenced genomes (serotypes a-c) for comparative genomic analysis. Two major groups were identified; serotypes a, d, e, and f, and serotypes b and c. A serotype e strain was found to be distinct from both groups. The size of the pangenome was 3,301 genes, which included 2,034 core genes and 1,267 flexible genes. The number of core genes is estimated to stabilize at 2,060, while the size of the pangenome is estimated to increase by 16 genes with every additional strain sequenced in the future. Within each strain 16.7-29.4% of the genome belonged to the flexible gene pool. Between any two strains 0.4-19.5% of the genomes were different. The genomic differences were occasionally greater for strains of the same serotypes than strains of different serotypes. Furthermore, 171 genomic islands were identified. Cumulatively, 777 strain-specific genes were found on these islands and represented 61% of the flexible gene pool.

Conclusions/significance: Substantial genomic differences were detected among A. actinomycetemcomitans strains. Genomic islands account for more than half of the flexible genes. The phenotype and virulence of A. actinomycetemcomitans may not be defined by any single strain. Moreover, the genomic variation within each clonal lineage of A. actinomycetemcomitans (as defined by serotype grouping) may be greater than between clonal lineages. The large genomic data set in this study will be useful to further examine the molecular basis of variable virulence among A. actinomycetemcomitans strains.

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Related in: MedlinePlus

Classification of core and flexible genes in A. actinomycetemcomitans.Genes were classified by the COG super-functional category (A) and the COG functional category (B). As expected, the core genome is better represented by genes that provide the essential cell function for the bacterium whereas the vast majority of the variable genome is made up of poorly characterized genes. Poorly characterized genes also represented about one third of the core genome. This suggests that more studies are still needed to understand the basic biology of this bacterial species.
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pone-0022420-g003: Classification of core and flexible genes in A. actinomycetemcomitans.Genes were classified by the COG super-functional category (A) and the COG functional category (B). As expected, the core genome is better represented by genes that provide the essential cell function for the bacterium whereas the vast majority of the variable genome is made up of poorly characterized genes. Poorly characterized genes also represented about one third of the core genome. This suggests that more studies are still needed to understand the basic biology of this bacterial species.

Mentions: The distribution patterns of the flexible genes (subgrouped based on the numbers of strains sharing the genes) in individual strains are illustrated in Figure S2. Within each strain 16.7–29.4% of the genome belonged to the flexible gene pool. Figure 3 shows the functional classification of core and flexible genes by COG super-functional (Figure 3A) or functional category (Figure 3B). As expected, the vast majority of genes making up the core genome belonged to the groups of housekeeping functions. As is common in most bacteria, about one-fourth of the shared genes were assigned to the category of poorly characterized proteins, suggesting that many aspects of basic A. actinomycetemcomitans biology still need to be explored. Genes associated with housekeeping functions were also found within the flexible gene pool but less well-represented there, whereas poorly characterized genes comprised the majority of the flexible pool; 951 out of 1,267 (75%) flexible genes were classified as poorly characterized (Figure 3A). One hundred and sixty-seven of the remaining 316 flexible genes (53%) are associated with mobile and extrachromosomal elements.


Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis.

Kittichotirat W, Bumgarner RE, Asikainen S, Chen C - PLoS ONE (2011)

Classification of core and flexible genes in A. actinomycetemcomitans.Genes were classified by the COG super-functional category (A) and the COG functional category (B). As expected, the core genome is better represented by genes that provide the essential cell function for the bacterium whereas the vast majority of the variable genome is made up of poorly characterized genes. Poorly characterized genes also represented about one third of the core genome. This suggests that more studies are still needed to understand the basic biology of this bacterial species.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3139650&req=5

pone-0022420-g003: Classification of core and flexible genes in A. actinomycetemcomitans.Genes were classified by the COG super-functional category (A) and the COG functional category (B). As expected, the core genome is better represented by genes that provide the essential cell function for the bacterium whereas the vast majority of the variable genome is made up of poorly characterized genes. Poorly characterized genes also represented about one third of the core genome. This suggests that more studies are still needed to understand the basic biology of this bacterial species.
Mentions: The distribution patterns of the flexible genes (subgrouped based on the numbers of strains sharing the genes) in individual strains are illustrated in Figure S2. Within each strain 16.7–29.4% of the genome belonged to the flexible gene pool. Figure 3 shows the functional classification of core and flexible genes by COG super-functional (Figure 3A) or functional category (Figure 3B). As expected, the vast majority of genes making up the core genome belonged to the groups of housekeeping functions. As is common in most bacteria, about one-fourth of the shared genes were assigned to the category of poorly characterized proteins, suggesting that many aspects of basic A. actinomycetemcomitans biology still need to be explored. Genes associated with housekeeping functions were also found within the flexible gene pool but less well-represented there, whereas poorly characterized genes comprised the majority of the flexible pool; 951 out of 1,267 (75%) flexible genes were classified as poorly characterized (Figure 3A). One hundred and sixty-seven of the remaining 316 flexible genes (53%) are associated with mobile and extrachromosomal elements.

Bottom Line: The genomic differences were occasionally greater for strains of the same serotypes than strains of different serotypes.Cumulatively, 777 strain-specific genes were found on these islands and represented 61% of the flexible gene pool.Moreover, the genomic variation within each clonal lineage of A. actinomycetemcomitans (as defined by serotype grouping) may be greater than between clonal lineages.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, University of Washington, Seattle, Washington, United States of America.

ABSTRACT

Background: Aggregatibacter actinomycetemcomitans is genetically heterogeneous and comprises distinct clonal lineages that may have different virulence potentials. However, limited information of the strain-to-strain genomic variations is available.

Methodology/principal findings: The genome sequences of 11 A. actinomycetemcomitans strains (serotypes a-f) were generated de novo, annotated and combined with three previously sequenced genomes (serotypes a-c) for comparative genomic analysis. Two major groups were identified; serotypes a, d, e, and f, and serotypes b and c. A serotype e strain was found to be distinct from both groups. The size of the pangenome was 3,301 genes, which included 2,034 core genes and 1,267 flexible genes. The number of core genes is estimated to stabilize at 2,060, while the size of the pangenome is estimated to increase by 16 genes with every additional strain sequenced in the future. Within each strain 16.7-29.4% of the genome belonged to the flexible gene pool. Between any two strains 0.4-19.5% of the genomes were different. The genomic differences were occasionally greater for strains of the same serotypes than strains of different serotypes. Furthermore, 171 genomic islands were identified. Cumulatively, 777 strain-specific genes were found on these islands and represented 61% of the flexible gene pool.

Conclusions/significance: Substantial genomic differences were detected among A. actinomycetemcomitans strains. Genomic islands account for more than half of the flexible genes. The phenotype and virulence of A. actinomycetemcomitans may not be defined by any single strain. Moreover, the genomic variation within each clonal lineage of A. actinomycetemcomitans (as defined by serotype grouping) may be greater than between clonal lineages. The large genomic data set in this study will be useful to further examine the molecular basis of variable virulence among A. actinomycetemcomitans strains.

Show MeSH
Related in: MedlinePlus