- Article -
| In Silico Biology 6, 0014 (2006); ©2006, Bioinformation Systems e.V. |
Analysis of tandem repeats found in 44 prokaryotic genomes
Satoshi Mizuta1, Hikaru Munakata1, Abulimiti Aimaiti1, Ichitaro Oya1, Kenji Oosawa2 and Toshio Shimizu1 *
1 Department of Electronic and Information System Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki 036-8561, Japan
2 Department of Nano-Material Systems, Graduate School of Engineering, Gunma University, Kiryu 376-8515, Japan
* Corresponding author
Email: slsimi@si.hirosaki-u.ac.jp
Edited by E. Wingender; received October 07, 2005; revised February 16 and 27, 2006; accepted February 27, 2006; published March 10, 2006
Abstract
Genomes contain various types of repetitive sequences. They may be used as probes for seeking genome rearrangements because they are rather free from the natural selection if they are located in the intergenic regions. In this study, we searched for tandem repeats (TRs) in 44 prokaryotic genomes by the color-coding method and sought the signs of genome rearrangements by detailed analysis of the detected TRs. We found 13,542 tandem repeats from 44 prokaryotic genomes in total ranging from several tens to one thousand per genome. The results of statistical analysis show that TRs tend to exist on high base composition bias regions in some genomes. Moreover, we recognized the characteristic distribution patterns of equivalent TR-pairs in 12 genomes, which are expected to indicate the occurrence of whole-genome duplication (WGD) on the genomes. It is demonstrated that TRs could indeed be used for seeking genome rearrangements. Although it has not been made clear at this time whether or not WGD had occurred in prokaryotic genomes, the results of the analyses of equivalent TR-pairs in this study are thought to be evidences of WGD in these genomes.
Keywords: tandem repeats, color-coding, genome rearrangement, prokaryotes