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doi:10.1534/genetics.105.046466
A more recent version of this article appeared on February 1, 2006.
REGULAR RESEARCH PAPERS |
Adaptation of multilocus sequencing to study variation within a major clone: evolutionary relationships of Salmonella enterica serovar Typhimurium
Honghua Hu 1, Ruiting Lan 1 and Peter R. Reeves 1*
1 The University of Sydney
* To whom correspondence should be addressed. E-mail: reeves{at}angis.usyd.edu.au.
Submitted on June 3, 2005
Revised on September 21, 2005
Accepted on 21 September 2005
Serovar Typhimurium of Salmonella enterica is a model organism for studies of pathogenesis, that exhibits phage type variation and variation in host range and virulence, but in a recent study showed no sequence variation in four genes, indicating the clonal nature of this serovar. We determined the relationships of 46 Typhimurium isolates of nine phage types using mutational changes detected either by matching AFLP (amplified-fragment length polymorphism) fragments to computer modeled LT2 AFLP fragments; or by sequencing intergenic regions. 51 polymorphic sites were detected, which gave a single phylogenetic tree. Comparison with genome sequences of five other serovars, Typhi, Paratyphi A, Gallinarum, Enteritidis and Pullorum, enabled determination of the root of the tree. Only two parallel events were observed, giving high confidence in the tree branching order. The mutation-based tree provided a high level of consistency and a clear lineage for the Typhimurium isolates studied. This enabled us to show that for seven of the nine phage types used, the isolates studied have a single origin, but that two phage types clearly have more than one independent origin. We found that sequencing intergenic regions provides a good strategy for detection of mutational polymorphisms and study of phylogenetic relationships of closely related isolates and would be applicable to many other species.
Key Words: Typhimurium, intergenic regions (IGs), mutational changes, phylogenetic relationships, single nucleotide polymorphisms (SNPs)
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