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Nucleic Acids Research, 2000, Vol. 28, No. 3 706-709
© 2000 Oxford University Press

Structural analysis of DNA sequence: evidence for lateral gene transfer in Thermotoga maritima

Peder Worning, Lars J. Jensen, Karen E. Nelson1, Søren Brunak and David W. Ussery*

Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark and 1The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

The recently published complete DNA sequence of the bacterium Thermotoga maritima provides evidence, based on protein sequence conservation, for lateral gene transfer between Archaea and Bacteria. We introduce a new method of periodicity analysis of DNA sequences, based on structural parameters, which brings independent evidence for the lateral gene transfer in the genome of T.maritima. The structural analysis relates the Archaea-like DNA sequences to the genome of Pyrococcus horikoshii. Analysis of 24 complete genomic DNA sequences shows different periodicity patterns for organisms of different origin. The typical genomic periodicity for Bacteria is 11 bp whilst it is 10 bp for Archaea. Eukaryotes have more complex spectra but the dominant period in the yeast Saccharomyces cerevisiae is 10.2 bp. These periodicities are most likely reflective of differences in chromatin structure.

* To whom correspondence should be addressed. Tel: +45 4525 2488; Fax: +45 4593 1585; Email: dave@cbs.dtu.dk


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