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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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Coinfections inferred from PCR screening of multiple isolates. The phylogeny was inferred from a fragment of the recG gene for multiple L. kunkeei strains. The colors in the external nodes represent sequences obtained from hosts that belong to the described microclusters: A (blue), B (green), C (orange), D (red), and LAdo (purple). The same colors in the branches represent the microcluster to which the last well-supported ancestor of each of the sequences coming from the genomic data belongs, and all its descendants. The phylogeny was inferred with the maximum-likelihood method.
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evv079-F8: Coinfections inferred from PCR screening of multiple isolates. The phylogeny was inferred from a fragment of the recG gene for multiple L. kunkeei strains. The colors in the external nodes represent sequences obtained from hosts that belong to the described microclusters: A (blue), B (green), C (orange), D (red), and LAdo (purple). The same colors in the branches represent the microcluster to which the last well-supported ancestor of each of the sequences coming from the genomic data belongs, and all its descendants. The phylogeny was inferred with the maximum-likelihood method.

Mentions: Given the lack of codiversification between bacterial strains and hosts, we speculated that strains of different genotypes might be present in each host species. If so, there was a risk that we had sampled only a subset of the available strains as genome sequence data were obtained from only one isolate per host. To test for such potentially missed diversity, we amplified with PCR variable segments of the lepA and recG genes from 27 additional isolates from managed and wild subspecies of A. mellifera in Sweden, Kenya and United States, and from 60 isolates from the other 9 host species (supplementary table S8, Supplementary Material online). Overall, we found that most sequences from each host were of the same genotype as those of the sequenced genomes (fig. 8 and supplementary fig. S9, Supplementary Material online), suggesting that the strains selected for sequencing represent the most abundant strains in each host species sample. In cases where the sampling had been done from multiple sites for a given host species (honey, beebread, and/or the honey crop), the same genotype was normally recovered.Fig. 8.—


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)

Coinfections inferred from PCR screening of multiple isolates. The phylogeny was inferred from a fragment of the recG gene for multiple L. kunkeei strains. The colors in the external nodes represent sequences obtained from hosts that belong to the described microclusters: A (blue), B (green), C (orange), D (red), and LAdo (purple). The same colors in the branches represent the microcluster to which the last well-supported ancestor of each of the sequences coming from the genomic data belongs, and all its descendants. The phylogeny was inferred with the maximum-likelihood method.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv079-F8: Coinfections inferred from PCR screening of multiple isolates. The phylogeny was inferred from a fragment of the recG gene for multiple L. kunkeei strains. The colors in the external nodes represent sequences obtained from hosts that belong to the described microclusters: A (blue), B (green), C (orange), D (red), and LAdo (purple). The same colors in the branches represent the microcluster to which the last well-supported ancestor of each of the sequences coming from the genomic data belongs, and all its descendants. The phylogeny was inferred with the maximum-likelihood method.
Mentions: Given the lack of codiversification between bacterial strains and hosts, we speculated that strains of different genotypes might be present in each host species. If so, there was a risk that we had sampled only a subset of the available strains as genome sequence data were obtained from only one isolate per host. To test for such potentially missed diversity, we amplified with PCR variable segments of the lepA and recG genes from 27 additional isolates from managed and wild subspecies of A. mellifera in Sweden, Kenya and United States, and from 60 isolates from the other 9 host species (supplementary table S8, Supplementary Material online). Overall, we found that most sequences from each host were of the same genotype as those of the sequenced genomes (fig. 8 and supplementary fig. S9, Supplementary Material online), suggesting that the strains selected for sequencing represent the most abundant strains in each host species sample. In cases where the sampling had been done from multiple sites for a given host species (honey, beebread, and/or the honey crop), the same genotype was normally recovered.Fig. 8.—

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