Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees.
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.
Affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden.Show MeSH
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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.—
Affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden.