title: Use of subtractive hybridization for comprehensive surveys of prokaryotic genome differences.
abstract: Comparative bacterial genomics shows that even different isolates of the same bacterial species can vary significantly in gene content. An effective means to survey differences across whole genomes would be highly advantageous for understanding this variation. Here we show that suppression subtractive hybridization (SSH) provides high, representative coverage of regions that differ between similar genomes. Using Helicobacter pylori strains 26695 and J99 as a model, SSH identified approximately 95% of the unique open reading frames in each strain, showing that the approach is effective. Furthermore, combining data from parallel SSH experiments using different restriction enzymes significantly increased coverage compared to using a single enzyme. These results suggest a powerful approach for assessing genome differences among closely related strains when one member of the group has been completely sequenced.
authors.affiliation: Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, L-441, 7000 East Avenue, Livermore, CA 94551, USA.
authors.forename: Peter G
authors.initials: PG
authors.lastname: Agron
authors.forename: Madison
authors.initials: M
authors.lastname: Macht
authors.forename: Lyndsay
authors.initials: L
authors.lastname: Radnedge
authors.forename: Evan W
authors.initials: EW
authors.lastname: Skowronski
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.forename: Gary L
authors.initials: GL
authors.lastname: Andersen
mesh_terms: D004262:DNA Restriction Enzymes / Q000737:chemistry; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D016480:Helicobacter pylori / Q000235:genetics; D009154:Mutation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016366:Open Reading Frames; D011387:Prokaryotic Cells / Q000145:classification
chemical_list: D004262:DNA Restriction Enzymes