Limits...
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.

Show MeSH

Related in: MedlinePlus

Flux of protein families in L. kunkeei and related species. The flux of protein families has been mapped onto the species phylogeny shown in supplementary figure S5, Supplementary Material online. The number of gains of protein families is shown to the left and losses to the right above each branch. The total number of protein families is indicated below each branch. The numbers at the terminal branches include singletons. Lactobacillus sanfranciscensis (LbSf), L. brevis (LbBr), L. buchneri (LbBu) and L. plantarum (LbPl). Abbreviations of strain names are defined in table 1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4494060&req=5

evv079-F2: Flux of protein families in L. kunkeei and related species. The flux of protein families has been mapped onto the species phylogeny shown in supplementary figure S5, Supplementary Material online. The number of gains of protein families is shown to the left and losses to the right above each branch. The total number of protein families is indicated below each branch. The numbers at the terminal branches include singletons. Lactobacillus sanfranciscensis (LbSf), L. brevis (LbBr), L. buchneri (LbBu) and L. plantarum (LbPl). Abbreviations of strain names are defined in table 1.

Mentions: To learn more about the evolutionary history of L. kunkeei, we performed an ancestral reconstruction, that is, an inference of the most likely branches at which protein families have been lost and gained. To this end, we first clustered the proteomes of all species within the Lactobacillaceae and Leuconostocaceae and three additional outgroups into 2,397 protein families. Based on these, we inferred a phylogeny for the L. kunkeei species complex and its closest relatives (supplementary fig. S5, Supplementary Material online), onto which we mapped the gains and losses of protein families using generalized parsimony with a penalty for gains of two times the penalty for losses (fig. 2). This analysis allows independent gains of protein families at unrelated nodes or branches in the tree by horizontal gene transfer. Protein families may also be lost and regained.Fig. 2.—


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)

Flux of protein families in L. kunkeei and related species. The flux of protein families has been mapped onto the species phylogeny shown in supplementary figure S5, Supplementary Material online. The number of gains of protein families is shown to the left and losses to the right above each branch. The total number of protein families is indicated below each branch. The numbers at the terminal branches include singletons. Lactobacillus sanfranciscensis (LbSf), L. brevis (LbBr), L. buchneri (LbBu) and L. plantarum (LbPl). 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-F2: Flux of protein families in L. kunkeei and related species. The flux of protein families has been mapped onto the species phylogeny shown in supplementary figure S5, Supplementary Material online. The number of gains of protein families is shown to the left and losses to the right above each branch. The total number of protein families is indicated below each branch. The numbers at the terminal branches include singletons. Lactobacillus sanfranciscensis (LbSf), L. brevis (LbBr), L. buchneri (LbBu) and L. plantarum (LbPl). Abbreviations of strain names are defined in table 1.
Mentions: To learn more about the evolutionary history of L. kunkeei, we performed an ancestral reconstruction, that is, an inference of the most likely branches at which protein families have been lost and gained. To this end, we first clustered the proteomes of all species within the Lactobacillaceae and Leuconostocaceae and three additional outgroups into 2,397 protein families. Based on these, we inferred a phylogeny for the L. kunkeei species complex and its closest relatives (supplementary fig. S5, Supplementary Material online), onto which we mapped the gains and losses of protein families using generalized parsimony with a penalty for gains of two times the penalty for losses (fig. 2). This analysis allows independent gains of protein families at unrelated nodes or branches in the tree by horizontal gene transfer. Protein families may also be lost and regained.Fig. 2.—

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