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Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees.

Tamarit, Daniel; Ellegaard, Kirsten M; Wikander, Johan; Olofsson, Tobias LU ; Vasquez, Alejandra LU and Andersson, Siv G E (2015) In Genome Biology and Evolution 7(6). p.1455-1473
Abstract
Lactobacillus kunkeei is the most abundant bacterial species in the honey crop and food products of honeybees. The 16S rRNA genes of strains isolated from different bee species are nearly identical in sequence and therefore inadequate as markers for studies of co-evolutionary 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... (More)
Lactobacillus kunkeei is the most abundant bacterial species in the honey crop and food products of honeybees. The 16S rRNA genes of strains isolated from different bee species are nearly identical in sequence and therefore inadequate as markers for studies of co-evolutionary 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 micro-cluster have recombined frequently across the host species barriers, arguing against co-diversification. 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. (Less)
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organization
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Contribution to journal
publication status
published
subject
in
Genome Biology and Evolution
volume
7
issue
6
pages
1455 - 1473
publisher
Oxford University Press
external identifiers
  • pmid:25953738
  • wos:000358800100005
  • scopus:84979862576
ISSN
1759-6653
DOI
10.1093/gbe/evv079
language
English
LU publication?
yes
id
c1b8f790-c7ec-47ee-9be2-057d587eb4b7 (old id 5456579)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/25953738?dopt=Abstract
date added to LUP
2015-06-04 14:51:41
date last changed
2017-09-17 06:11:59
@article{c1b8f790-c7ec-47ee-9be2-057d587eb4b7,
  abstract     = {Lactobacillus kunkeei is the most abundant bacterial species in the honey crop and food products of honeybees. The 16S rRNA genes of strains isolated from different bee species are nearly identical in sequence and therefore inadequate as markers for studies of co-evolutionary 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 micro-cluster have recombined frequently across the host species barriers, arguing against co-diversification. 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.},
  author       = {Tamarit, Daniel and Ellegaard, Kirsten M and Wikander, Johan and Olofsson, Tobias and Vasquez, Alejandra and Andersson, Siv G E},
  issn         = {1759-6653},
  language     = {eng},
  month        = {05},
  number       = {6},
  pages        = {1455--1473},
  publisher    = {Oxford University Press},
  series       = {Genome Biology and Evolution},
  title        = {Functionally Structured Genomes in Lactobacillus kunkeei Colonizing the Honey Crop and Food Products of Honeybees and Stingless Bees.},
  url          = {http://dx.doi.org/10.1093/gbe/evv079},
  volume       = {7},
  year         = {2015},
}