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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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Comparison of single gene tree topologies. The graph depicts supported relationships (>95% bootstrap support) for each pair of taxa in 790 single-copy ortholog phylogenies. Strains that clustered together as sister taxa are shown with connecting lines, where the numbers indicate the total number of trees supporting the clustering. Dotted lines represent arrangements that occurred in less than 1% of the analyzed trees (i.e., 7 or lower). Letters A–D indicate the microcluster affiliation of the strains (as in fig. 1b).
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evv079-F9: Comparison of single gene tree topologies. The graph depicts supported relationships (>95% bootstrap support) for each pair of taxa in 790 single-copy ortholog phylogenies. Strains that clustered together as sister taxa are shown with connecting lines, where the numbers indicate the total number of trees supporting the clustering. Dotted lines represent arrangements that occurred in less than 1% of the analyzed trees (i.e., 7 or lower). Letters A–D indicate the microcluster affiliation of the strains (as in fig. 1b).

Mentions: To determine whether the strains that are able to coinfect A. mellifera also recombine more frequently than other strains in their core genome, which would be indicative of long-term coexistence, we compared the topologies of all 790 single gene trees (fig. 9). None of the 790 trees supported a sister relationship for strains Fhon2 and Fhon13, nor of any of these with strain LAfl. Overall, we observed a strong coherence between the single gene and the concatenated tree topologies regarding the diversification pattern between the microclusters. For example, of the 60 trees inferred from genes longer than 2 kb, 53 supported the monophyly of the four described microclusters with high bootstrap support (>95%). Overall, only 31 of the 790 trees provided strong support (>95%) for a clustering of strains of different microcluster types. The 31 trees with a deviant topology included 9 trees in which LMbo clustered with the A-group strains (as shown for genes longer than 2 kb in supplementary fig. S12, Supplementary Material online), and 18 trees in which LAnu clustered with the B-group strains (as shown for genes longer than 2 kb in supplementary fig. S13, Supplementary Material online).Fig. 9.—


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)

Comparison of single gene tree topologies. The graph depicts supported relationships (>95% bootstrap support) for each pair of taxa in 790 single-copy ortholog phylogenies. Strains that clustered together as sister taxa are shown with connecting lines, where the numbers indicate the total number of trees supporting the clustering. Dotted lines represent arrangements that occurred in less than 1% of the analyzed trees (i.e., 7 or lower). Letters A–D indicate the microcluster affiliation of the strains (as in fig. 1b).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv079-F9: Comparison of single gene tree topologies. The graph depicts supported relationships (>95% bootstrap support) for each pair of taxa in 790 single-copy ortholog phylogenies. Strains that clustered together as sister taxa are shown with connecting lines, where the numbers indicate the total number of trees supporting the clustering. Dotted lines represent arrangements that occurred in less than 1% of the analyzed trees (i.e., 7 or lower). Letters A–D indicate the microcluster affiliation of the strains (as in fig. 1b).
Mentions: To determine whether the strains that are able to coinfect A. mellifera also recombine more frequently than other strains in their core genome, which would be indicative of long-term coexistence, we compared the topologies of all 790 single gene trees (fig. 9). None of the 790 trees supported a sister relationship for strains Fhon2 and Fhon13, nor of any of these with strain LAfl. Overall, we observed a strong coherence between the single gene and the concatenated tree topologies regarding the diversification pattern between the microclusters. For example, of the 60 trees inferred from genes longer than 2 kb, 53 supported the monophyly of the four described microclusters with high bootstrap support (>95%). Overall, only 31 of the 790 trees provided strong support (>95%) for a clustering of strains of different microcluster types. The 31 trees with a deviant topology included 9 trees in which LMbo clustered with the A-group strains (as shown for genes longer than 2 kb in supplementary fig. S12, Supplementary Material online), and 18 trees in which LAnu clustered with the B-group strains (as shown for genes longer than 2 kb in supplementary fig. S13, Supplementary Material online).Fig. 9.—

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