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Journal of Bacteriology, September 2006, p. 6599-6610, Vol. 188, No. 18
0021-9193/06/$08.00+0     doi:10.1128/JB.00734-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Intraspecific Variability of the Terminal Inverted Repeats of the Linear Chromosome of Streptomyces ambofaciens

Laboratoire de Génétique et Microbiologie, UMR INRA 1128, IFR 110, Université Henri Poincaré Nancy 1, Faculté des Sciences et Techniques, BP239, 54506 Vanduvre-lès-Nancy, France,¹ Génoscope, Centre National de Séquençage, 2 rue Gaston Crémieux CP5706 91057 Evry cedex, France,² Institut de Génétique et Microbiologie, UMR CNRS 8621, Université Paris-Sud 11, Bâtiment 400, 91405 Orsay cedex, France³

Received 22 May 2006/ Accepted 7 July 2006

The sequences of the terminal inverted repeats (TIRs) ending the linear chromosomal DNA of two Streptomyces ambofaciens strains, ATCC23877 and DSM40697 (198 kb and 213 kb, respectively), were determined from two sets of recombinant cosmids. Among the 215 coding DNA sequences (CDSs) predicted in the TIRs of strain DSM40697, 65 are absent in the TIRs of strain ATCC23877. Reciprocally, 45 of the 194 predicted CDSs are specific to the ATCC23877 strain. The strain-specific CDSs are located mainly at the terminal end of the TIRs. Indeed, although TIRs appear almost identical over 150 kb (99% nucleotide identity), large regions of DNA of 60 kb (DSM40697) and 48 kb (ATCC23877), mostly spanning the ends of the chromosome, are strain specific. These regions are rich in plasmid-associated genes, including genes encoding putative conjugal transfer functions. The strain-specific regions also share a G+C content (68%) lower than that of the rest of the genome (from 71% to 73%), a percentage that is more typical of Streptomyces plasmids and mobile elements. These data suggest that exchanges of replicon extremities have occurred, thereby contributing to the terminal variability observed at the intraspecific level. In addition, the terminal regions include many mobile genetic element-related genes, pseudogenes, and genes related to adaptation. The results give insight into the mechanisms of evolution of the TIRs: integration of new information and/or loss of DNA fragments and subsequent homogenization of the two chromosomal extremities.

^# F.C. and A.G. contributed equally to this report.

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