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.
Kang
Cheol-Hee
CH
Department of Microbiology and Biotechnology Research Institute, Chungbuk National University, Cheongju 361-763, Korea.
Nam
Young-Do
YD
Chung
Won-Hyong
WH
Quan
Zhe-Xue
ZX
Park
Yong-Ha
YH
Park
Soo-Je
SJ
Desmone
Racheal
R
Wan
Xiu-Feng
XF
Rhee
Sung-Keun
SK
D004269:DNA, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D009154:Mutation; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis
D004269:DNA, Bacterial