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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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Phylogenetic relationships of the L. kunkeei species complex. The phylogenetic trees were inferred from (a) 16 S rRNA sequences and (b) a concatenated nucleotide alignment of 790 genes single-copy orthologs in the L. kunkeei species complex and L. sanfranciscensis. For ease of visualization, only the subtrees including the L. kunkeei clade are shown. Nodes with bootstrap support values of 100% are indicated with asterisks. The ancestral node in (a) was supported by 92% bootstrap support. The trees were inferred with the maximum-likelihood method. The same topology of the tree presented in (b) and similar branch lengths were obtained by Bayesian analysis, in which all nodes had a posterior probability of 1. Abbreviations of strain names are defined in table 1.
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evv079-F1: Phylogenetic relationships of the L. kunkeei species complex. The phylogenetic trees were inferred from (a) 16 S rRNA sequences and (b) a concatenated nucleotide alignment of 790 genes single-copy orthologs in the L. kunkeei species complex and L. sanfranciscensis. For ease of visualization, only the subtrees including the L. kunkeei clade are shown. Nodes with bootstrap support values of 100% are indicated with asterisks. The ancestral node in (a) was supported by 92% bootstrap support. The trees were inferred with the maximum-likelihood method. The same topology of the tree presented in (b) and similar branch lengths were obtained by Bayesian analysis, in which all nodes had a posterior probability of 1. Abbreviations of strain names are defined in table 1.

Mentions: A comparison of a 1,408-bp-long alignment of the 16 S rRNA gene showed that eight of the isolated strains were identical to the type strain, L. kunkeei YH15, whereas strain LAdo contained a single polymorphism, and strains LAko and LAnu shared another polymorphism. Strain Fhon13 showed 98.8% sequence identity (17 polymorphisms) in the 16 S rRNA gene to L. kunkeei YH-15. An rRNA-based maximum-likelihood phylogeny showed that L. kunkeei and L. apinorum Fhon13 were related to Lactobacillus ozensis, Lactobacillus lindneri, Lactobacillus sanfranciscensis, and Lactobacillus fructivorans (fig. 1a). For the purpose of this discussion, we have considered L. apinorum Fhon13 to be a member of the L. kunkeei species complex.Fig. 1.—


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)

Phylogenetic relationships of the L. kunkeei species complex. The phylogenetic trees were inferred from (a) 16 S rRNA sequences and (b) a concatenated nucleotide alignment of 790 genes single-copy orthologs in the L. kunkeei species complex and L. sanfranciscensis. For ease of visualization, only the subtrees including the L. kunkeei clade are shown. Nodes with bootstrap support values of 100% are indicated with asterisks. The ancestral node in (a) was supported by 92% bootstrap support. The trees were inferred with the maximum-likelihood method. The same topology of the tree presented in (b) and similar branch lengths were obtained by Bayesian analysis, in which all nodes had a posterior probability of 1. Abbreviations of strain names are defined in table 1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv079-F1: Phylogenetic relationships of the L. kunkeei species complex. The phylogenetic trees were inferred from (a) 16 S rRNA sequences and (b) a concatenated nucleotide alignment of 790 genes single-copy orthologs in the L. kunkeei species complex and L. sanfranciscensis. For ease of visualization, only the subtrees including the L. kunkeei clade are shown. Nodes with bootstrap support values of 100% are indicated with asterisks. The ancestral node in (a) was supported by 92% bootstrap support. The trees were inferred with the maximum-likelihood method. The same topology of the tree presented in (b) and similar branch lengths were obtained by Bayesian analysis, in which all nodes had a posterior probability of 1. Abbreviations of strain names are defined in table 1.
Mentions: A comparison of a 1,408-bp-long alignment of the 16 S rRNA gene showed that eight of the isolated strains were identical to the type strain, L. kunkeei YH15, whereas strain LAdo contained a single polymorphism, and strains LAko and LAnu shared another polymorphism. Strain Fhon13 showed 98.8% sequence identity (17 polymorphisms) in the 16 S rRNA gene to L. kunkeei YH-15. An rRNA-based maximum-likelihood phylogeny showed that L. kunkeei and L. apinorum Fhon13 were related to Lactobacillus ozensis, Lactobacillus lindneri, Lactobacillus sanfranciscensis, and Lactobacillus fructivorans (fig. 1a). For the purpose of this discussion, we have considered L. apinorum Fhon13 to be a member of the L. kunkeei species complex.Fig. 1.—

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
Related in: MedlinePlus