title: Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees.
abstract: Lactobacillus kunkeei is the most abundant bacterial species in the honey crop and food products of honeybees. The 16 S rRNA genes of strains isolated from different bee species are nearly identical in sequence and therefore inadequate as markers for studies of coevolutionary patterns. Here, we have compared the 1.5 Mb genomes of ten L. kunkeei strains isolated from all recognized Apis species and another two strains from Meliponini species. A gene flux analysis, including previously sequenced Lactobacillus species as outgroups, indicated the influence of reductive evolution. The genome architecture is unique in that vertically inherited core genes are located near the terminus of replication, whereas genes for secreted proteins and putative host-adaptive traits are located near the origin of replication. 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 phylogenetic analyses showed that the bacterial topology was incongruent with the host topology, and that strains of the same microcluster have recombined frequently across the host species barriers, arguing against codiversification. Multiple genotypes were recovered in the individual hosts and transfers of mobile elements could be demonstrated for strains isolated from the same host species. Unlike other bacteria with small genomes, short generation times and multiple rRNA operons suggest that L. kunkeei evolves under selection for rapid growth in its natural growth habitat. The results provide an extended framework for reductive genome evolution and functional genome organization in bacteria.
authors.affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden.
authors.forename: Daniel
authors.initials: D
authors.lastname: Tamarit
authors.affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden.
authors.forename: Kirsten M
authors.initials: KM
authors.lastname: Ellegaard
authors.affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Wikander
authors.affiliation: Medical Microbiology, Department of Laboratory Medicine, Lund University, Sweden.
authors.forename: Tobias
authors.initials: T
authors.lastname: Olofsson
authors.affiliation: Medical Microbiology, Department of Laboratory Medicine, Lund University, Sweden.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Vásquez
authors.affiliation: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden siv.andersson@icm.uu.se.
authors.forename: Siv G E
authors.initials: SG
authors.lastname: Andersson
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics; D001516:Bees / Q000382:microbiology*; D022761:Gene Transfer, Horizontal; D059646:Genome Size; D016680:Genome, Bacterial; D007778:Lactobacillus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D011995:Recombination, Genetic
chemical_list: D001426:Bacterial Proteins
keywords: Lactobacillus kunkeei; genome organization; genome reduction; honeybee; recombination