Diverse genome structures of Salmonella paratyphi C.
BACKGROUND
Salmonella paratyphi C, like S. typhi, is adapted to humans and causes typhoid fever. Previously we reported different genome structures between two strains of S. paratyphi C, which suggests that S. paratyphi C might have a plastic genome (large DNA segments being organized in different orders or orientations on the genome). As many but not all host-adapted Salmonella pathogens have large genomic insertions as well as the supposedly resultant genomic rearrangements, bacterial genome plasticity presents an extraordinary evolutionary phenomenon. Events contributing to genomic plasticity, especially large insertions, may be associated with the formation of particular Salmonella pathogens.


RESULTS
We constructed a high resolution genome map in S. paratyphi C strain RKS4594 and located four insertions totaling 176 kb (including the 90 kb SPI7) and seven deletions totaling 165 kb relative to S. typhimurium LT2. Two rearrangements were revealed, including an inversion of 1602 kb covering the ter region and the translocation of the 43 kb I-CeuI F fragment. The 23 wild type strains analyzed in this study exhibited diverse genome structures, mostly as a result of recombination between rrn genes. In at least two cases, the rearrangements involved recombination between genomic sites other than the rrn genes, possibly homologous genes in prophages. Two strains had a 20 kb deletion between rrlA and rrlB, which is a highly conservative region and no deletion has been reported in this region in any other Salmonella lineages.


CONCLUSIONS
S. paratyphi C has diverse genome structures among different isolates, possibly as a result of large genomic insertions, e.g., SPI7. Although the Salmonella typhoid agents may not be more closely related among them than each of them to other Salmonella lineages, they may have evolved in similar ways, i.e., acquiring typhoid-associated genes followed by genome structure rearrangements. Comparison of multiple Salmonella typhoid agents at both single sequenced genome and population levels will facilitate the studies on the evolutionary process of typhoid pathogenesis, especially the identification of typhoid-associated genes.
Liu
Wei-Qiao
WQ
Microbiology, Peking University Health Science Center, Beijing, China. wqliu@ucalgary.ca
Liu
Gui-Rong
GR
Li
Jun-Qian
JQ
Xu
Guo-Min
GM
Qi
Danni
D
He
Xiao-Yan
XY
Deng
Juan
J
Zhang
Feng-Min
FM
Johnston
Randal N
RN
Liu
Shu-Lin
SL
D000220:Adaptation, Biological / Q000235:genetics; D004251:DNA Transposable Elements; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D004706:Endodeoxyribonucleases / Q000378:metabolism; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D016254:Mutagenesis, Insertional; D015183:Restriction Mapping; D012479:Salmonella paratyphi C / Q000235:genetics*
D004251:DNA Transposable Elements; D004706:Endodeoxyribonucleases; C071132:endodeoxyribonuclease I-CeuI; C025580:endodeoxyribonuclease XBAI; C064053:CCTAGG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific
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