Nucleic Acids Research, 2002, Vol. 30, No. 10 e42
© 2002 Oxford University Press
Commonly conserved genetic fragments revealed by genome profiling can serve as tracers of evolution
Department of Functional Materials Science, Faculty of Engineering, Saitama University, 255 Shimo-Okubo, Saitama, Saitama 338-8570, Japan and 1Saitama Institute of Public Health, Kami-Okubo, Saitama, Saitama 338-0824, Japan
We developed a method to produce, identify and analyze DNA fragments for the purpose of taxonomic classification. Genome profiling (GP) is a strategy that identifies genomic DNA fragments common to closely related species without prior knowledge of the DNA sequence. Random PCR, one of the key technologies of GP, is used to produce fragments and may be used even when there are mutations at the priming site. These fragments can then be distinguished based on the information of mobility and melting pattern when subjected to temperature gradient gel electrophoresis (TGGE). Corresponding fragments among several species, designated as commonly conserved genetic fragments (CCGFs), likely have the same genetic origin or correspond to the same gene. The criteria for identification of CCGFs has been defined and presented here. To assess this prediction, some of the fragments were sequenced and were confirmed to be CCGFs. We show that genome profiles bearing evolutionarily conserved CCGFs can be used to classify organisms and trace evolutionary pathways, among other profound applications.
* To whom correspondence should be addressed. Tel: +81 48 858 3533; Fax: +81 48 858 3533; Email: koichi{at}fms.saitama-u.ac.jp