Remarkable sequence signatures in archaeal genomes

Fadiel, Ahmed; Lithwick, Stuart; Ganji, Gopi; Scherer, Stephen W.

doi:https://doi.org/10.1155/2003/458235

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Research Article | Open Access

Volume 1 | Article ID 458235 | https://doi.org/10.1155/2003/458235

Remarkable sequence signatures in archaeal genomes

Ahmed Fadiel,¹Stuart Lithwick,²Gopi Ganji,²and Stephen W. Scherer¹

Received15 Oct 2002

Accepted06 Nov 2002

Abstract

Complete archaeal genomes were probed for the presence of long (≥ 25 bp) oligonucleotide repeats (words). We detected the presence of many words distributed in tandem with narrow ranges of periodicity (i.e., spacer length between repeats). Similar words were not identified in genomes of non-archaeal species, namely Escherichia coli, Bacillus subtilis, Haemophilus influenzae, Mycoplasma genitalium and Mycoplasma pneumoniae. BLAST similarity searches against the GenBank nucleotide sequence database revealed that these words were archaeal species-specific, indicating that they are of a signature character. Sequence analysis and genome viewing tools showed these repeats to be restricted to non-coding regions. Thus, archaea appear to possess a non-coding genomic signature that is absent in bacterial species. The identification of a species-specific genomic signature would be of great value to archaeal genome mapping, evolutionary studies and analyses of genome complexity.

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Copyright © 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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