Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements

Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2011) Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements. Journal of Bacteriology, 193 15: 3964-3977. doi:10.1128/JB.01524-10

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Author Chan, Cheong Xin
Beiko, Robert G.
Ragan, Mark A.
Title Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements
Formatted title
Lateral transfer of genes and gene fragments in Staphylococcus extends beyond mobile elements
Journal name Journal of Bacteriology   Check publisher's open access policy
ISSN 0021-9193
1098-5530
1067-8832
Publication date 2011-08-01
Year available 2011
Sub-type Article (original research)
DOI 10.1128/JB.01524-10
Open Access Status File (Publisher version)
Volume 193
Issue 15
Start page 3964
End page 3977
Total pages 14
Place of publication Washington, DC, United States
Publisher American Society for Microbiology
Language eng
Formatted abstract
The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed in part to lateral genetic transfer (LGT), but little is known about the broader extent of LGT within this genus. Here we report the first systematic study of the modularity of genetic transfer among 13 Staphylococcus genomes covering four distinct named species. Using a topology-based phylogenetic approach, we found, among 1,354 sets of homologous genes examined, strong evidence of LGT in 368 (27.1%) gene sets, and weaker evidence in another 259 (19.1%). Within-gene and whole-gene transfer contribute almost equally to the topological discordance of these gene sets against a reference phylogeny. Comparing genetic transfer in single-copy and in multicopy gene sets, we observed a higher frequency of LGT in the latter, and a substantial functional bias in cases of whole-gene transfer (little such bias was observed in cases of fragmentary genetic transfer). We found evidence that lateral transfer, particularly of entire genes, impacts not only functions related to antibiotic, drug, and heavy-metal resistance, as well as membrane transport, but also core informational and metabolic functions not associated with mobile elements. Although patterns of sequence similarity support the cohesion of recognized species, LGT within S. aureus appears frequently to disrupt clonal complexes. Our results demonstrate that LGT and gene duplication play important parts in functional innovation in staphylococcal genomes.
Keyword Multiple sequence alignment
Antibiotic-resistance
Phylogenetic inference
Genome sequence
Nucleotide-sequences
Epidermidis strain
Protein families
Virulence genes
High-throughput
Fitness cost
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID CE0348221
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2012 Collection
Institute for Molecular Bioscience - Publications
 
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