Affiliations: Department of Electronic and Information System
Engineering, Faculty of Science and Technology, Hirosaki University, Hirosaki
036-8561, Japan | Department of Nano-Material Systems, Graduate School
of Engineering, Gunma University, Kiryu 376-8515, Japan
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
