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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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Comparative alignments of the L. kunkeei genomes. The color bars and boxes represent phages (pink); plasmids (green); genes identified to be present in all L. kunkeei genomes, but no other lactobacilli for which complete genome data are present (blue); and the contiguous giant genes (yellow), which are also unique for these genomes. Asterisks represent CRISPR-cas loci, with colors representing different CRISPR types. The alternating horizontal grayscale boxes represent putatively adjacent contigs. Gray links between genomes represent BLASTn nucleotide similarity of at least 80% identity for alignments longer than 300 bases. The tree topology and the microclusters (letters A–D) are as in figure 1b.
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evv079-F4: Comparative alignments of the L. kunkeei genomes. The color bars and boxes represent phages (pink); plasmids (green); genes identified to be present in all L. kunkeei genomes, but no other lactobacilli for which complete genome data are present (blue); and the contiguous giant genes (yellow), which are also unique for these genomes. Asterisks represent CRISPR-cas loci, with colors representing different CRISPR types. The alternating horizontal grayscale boxes represent putatively adjacent contigs. Gray links between genomes represent BLASTn nucleotide similarity of at least 80% identity for alignments longer than 300 bases. The tree topology and the microclusters (letters A–D) are as in figure 1b.

Mentions: A similar bias was also observed for the recently acquired and variably present genes located near ori versus the conserved ancestral genes located near ter. Thus, 40 of the 50 genes present in all strains of L. kunkeei but in no other Lactobacillus genomes were flanking ori, of which 20 were clustered in a 100-kb segment (fig. 4). These genes were often of short, but similar sizes and showed atypically high sequence divergence levels between L. apinorum Fhon13 and the L. kunkeei strains.Fig. 4.—


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)

Comparative alignments of the L. kunkeei genomes. The color bars and boxes represent phages (pink); plasmids (green); genes identified to be present in all L. kunkeei genomes, but no other lactobacilli for which complete genome data are present (blue); and the contiguous giant genes (yellow), which are also unique for these genomes. Asterisks represent CRISPR-cas loci, with colors representing different CRISPR types. The alternating horizontal grayscale boxes represent putatively adjacent contigs. Gray links between genomes represent BLASTn nucleotide similarity of at least 80% identity for alignments longer than 300 bases. The tree topology and the microclusters (letters A–D) are as in figure 1b.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv079-F4: Comparative alignments of the L. kunkeei genomes. The color bars and boxes represent phages (pink); plasmids (green); genes identified to be present in all L. kunkeei genomes, but no other lactobacilli for which complete genome data are present (blue); and the contiguous giant genes (yellow), which are also unique for these genomes. Asterisks represent CRISPR-cas loci, with colors representing different CRISPR types. The alternating horizontal grayscale boxes represent putatively adjacent contigs. Gray links between genomes represent BLASTn nucleotide similarity of at least 80% identity for alignments longer than 300 bases. The tree topology and the microclusters (letters A–D) are as in figure 1b.
Mentions: A similar bias was also observed for the recently acquired and variably present genes located near ori versus the conserved ancestral genes located near ter. Thus, 40 of the 50 genes present in all strains of L. kunkeei but in no other Lactobacillus genomes were flanking ori, of which 20 were clustered in a 100-kb segment (fig. 4). These genes were often of short, but similar sizes and showed atypically high sequence divergence levels between L. apinorum Fhon13 and the L. kunkeei strains.Fig. 4.—

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