Relationship between genome similarity and DNA-DNA hybridization among closely related bacteria.
DNA-DNA hybridization has been established as an important technology in bacterial species taxonomy and phylogenetic analysis. In this study, we analyzed how the efficiency with which the genomic DNA from one species hybridizes to the genomic DNA of another species (DNA-DNA hybridization) in microarray analysis relates to the similarity between two genomes. We found that the predicted DNA-DNA hybridization based on genome sequence similarity correlated well with the experimentally determined microarray hybridization. Between closely related strains, significant numbers of highly divergent genes (<55% identity) and/or the accumulation of mismatches between conserved genes lowered the DNA-DNA hybridization signal, and this reduced the hybridization signals to below 70% for even bacterial strains with over 97% 16S rRNA gene identity. In addition, our results also suggest that a DNA-DNA hybridization signal intensity of over 40% indicates that two genomes at least shared 30% conserved genes (>60% gene identity). This study may expand our knowledge of DNA-DNA hybridization based on genomic sequence similarity comparison and further provide insights for bacterial phylogeny analyses.
Department of Microbiology and Biotechnology Research Institute, Chungbuk National University, Cheongju 361-763, Korea.
Cheol-Hee
CH
Kang
Young-Do
YD
Nam
Won-Hyong
WH
Chung
Zhe-Xue
ZX
Quan
Yong-Ha
YH
Park
Soo-Je
SJ
Park
Racheal
R
Desmone
Xiu-Feng
XF
Wan
Sung-Keun
SK
Rhee
D004269:DNA, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D009154:Mutation; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis
D004269:DNA, Bacterial