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Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees.

Tamarit D, Ellegaard KM, Wikander J, Olofsson T, Vásquez A, Andersson SG - Genome Biol Evol (2015)

Bottom Line: A gene flux analysis, including previously sequenced Lactobacillus species as outgroups, indicated the influence of reductive evolution.We suggest that these features have resulted from a genome-wide loss of genes, with integrations of novel genes mostly occurring in regions flanking the origin of replication.The results provide an extended framework for reductive genome evolution and functional genome organization in bacteria.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden.

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Circular representation of the L. kunkeei Fhon2 genome. The color-coding from outer to inner circles represents genes in the forward and reverse strands (gray), genes present in all studied L. kunkeei but absent in all other surveyed lactobacilli (blue), genes coding for secreted proteins (green) (as found in Butler et al. [2013]), genes coding for proteins involved in amino acid metabolism (orange) and translation (red) (according to the COG database), genes found in a single copy in all surveyed lactobacilli (purple), GC content and GC skew (gray). Additional L. kunkeei genomes are shown in supplementary figure S3, Supplementary Material online.
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evv079-F3: Circular representation of the L. kunkeei Fhon2 genome. The color-coding from outer to inner circles represents genes in the forward and reverse strands (gray), genes present in all studied L. kunkeei but absent in all other surveyed lactobacilli (blue), genes coding for secreted proteins (green) (as found in Butler et al. [2013]), genes coding for proteins involved in amino acid metabolism (orange) and translation (red) (according to the COG database), genes found in a single copy in all surveyed lactobacilli (purple), GC content and GC skew (gray). Additional L. kunkeei genomes are shown in supplementary figure S3, Supplementary Material online.

Mentions: A visual inspection of the genome architecture in strain Fhon2 indicated that there was an exceptional bias in the functional organization of genes, such that conserved single-copy orthologs present in all of the currently sequenced Lactobacillus genomes were mainly situated in the chromosomal half that is flanking ter (fig. 3). In contrast, genes for metabolic processes tended to be located in the genomic half that flanks the origin of replication (fig. 3). The genes highly represented in this region code for proteins related to the metabolism of amino acids, such as ABC transporters, permeases, peptidases, and proteases.Fig. 3.—


Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees.

Tamarit D, Ellegaard KM, Wikander J, Olofsson T, Vásquez A, Andersson SG - Genome Biol Evol (2015)

Circular representation of the L. kunkeei Fhon2 genome. The color-coding from outer to inner circles represents genes in the forward and reverse strands (gray), genes present in all studied L. kunkeei but absent in all other surveyed lactobacilli (blue), genes coding for secreted proteins (green) (as found in Butler et al. [2013]), genes coding for proteins involved in amino acid metabolism (orange) and translation (red) (according to the COG database), genes found in a single copy in all surveyed lactobacilli (purple), GC content and GC skew (gray). Additional L. kunkeei genomes are shown in supplementary figure S3, Supplementary Material online.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494060&req=5

evv079-F3: Circular representation of the L. kunkeei Fhon2 genome. The color-coding from outer to inner circles represents genes in the forward and reverse strands (gray), genes present in all studied L. kunkeei but absent in all other surveyed lactobacilli (blue), genes coding for secreted proteins (green) (as found in Butler et al. [2013]), genes coding for proteins involved in amino acid metabolism (orange) and translation (red) (according to the COG database), genes found in a single copy in all surveyed lactobacilli (purple), GC content and GC skew (gray). Additional L. kunkeei genomes are shown in supplementary figure S3, Supplementary Material online.
Mentions: A visual inspection of the genome architecture in strain Fhon2 indicated that there was an exceptional bias in the functional organization of genes, such that conserved single-copy orthologs present in all of the currently sequenced Lactobacillus genomes were mainly situated in the chromosomal half that is flanking ter (fig. 3). In contrast, genes for metabolic processes tended to be located in the genomic half that flanks the origin of replication (fig. 3). The genes highly represented in this region code for proteins related to the metabolism of amino acids, such as ABC transporters, permeases, peptidases, and proteases.Fig. 3.—

Bottom Line: A gene flux analysis, including previously sequenced Lactobacillus species as outgroups, indicated the influence of reductive evolution.We suggest that these features have resulted from a genome-wide loss of genes, with integrations of novel genes mostly occurring in regions flanking the origin of replication.The results provide an extended framework for reductive genome evolution and functional genome organization in bacteria.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden.

Show MeSH