title: Remarkable sequence signatures in archaeal genomes.
abstract: Complete archaeal genomes were probed for the presence of long (> or = 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.
authors.affiliation: The Center for Applied Genomics, Hospital for Sick Children, Toronto, Ontario M5G 1Z8, Canada. afadiel@yale.edu
authors.forename: Ahmed
authors.initials: A
authors.lastname: Fadiel
authors.forename: Stuart
authors.initials: S
authors.lastname: Lithwick
authors.forename: Gopi
authors.initials: G
authors.lastname: Ganji
authors.forename: Stephen W
authors.initials: SW
authors.lastname: Scherer
mesh_terms: D001483:Base Sequence; D004249:DNA Damage; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D005816:Genetic Complementation Test; D020745:Genome, Archaeal; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D019641:DNA, Archaeal; D009707:Nucleosomes