in the present bacterial taxonomic system , the extremely radioresistant bacteria of the genus deinococcus and the extremely thermophilic bacteria of the genus thermus belong to a common lineage with remarkably different characteristics [ 1 , 2 ] . comparative genomic analyses have shown that after their divergence from a common ancestor , deinococcus species seem to have acquired numerous genes from various other bacteria to survive different kinds of environmental stresses , whereas thermus species have acquired genes from thermophilic archaea and bacteria to adapt to high - temperature environments . for example , the aspartate kinase gene of deinococcus radiodurans has a different evolutionary history from that of thermus thermophilus . in addition , d. radiodurans has several unique protein families   and genomic characters , and there is no genome - wide synteny between d. radiodurans and t. thermophilus . however , phylogenetic analyses based on both orthologous protein sequence comparison and gene content comparison have shown that the genomes of deinococcus and thermus are most closely related with each other [ 3 , 8 ] . the trinucleotide usage correlations have been used to predict the functional similarity between two reca orthologs of bacteria including d. radiodurans and t. thermophilus .   if the genes acquired through horizontal gene transfers are different between deinococcus and thermus , then the genomic base composition ( gc content ) and/or genome signature can be hypothesized to also be different between these 2 genera . however , the gc content of d. radiodurans ( 67% ) is similar to that of t. thermophilus ( 69.4% ) . the genome signature , on the other hand , is a powerful basis for comparing different bacterial genomes [ 1119 ] . phylogenetic analyses based on genome signature comparison have been developed , and these analyses are useful for metagenomics studies . it was reported that comparative study using the frequency of tetranucleotides is a powerful tool for the bacterial genome comparison . in this study , we compared the relative frequencies of tetranucleotides in 89 bacterial genome sequences and determined the phylogenetic positions of d. radiodurans and t. thermophilus . the frequencies of the 89 bacteria were obtained from oligoweb ( oligonucleotide frequency search , http://insilico.ehu.es/oligoweb/ ) . the 89 bacterial species are part of a list that which covers a wide range of bacterial species published in a previous report . the euclidean distance between 2 vectors was calculated using the software package r ( language and environment for statistical computing , http://www.r-project.org ) . on the basis of the distance matrix correspondence analysis , which is a multivariate analysis method for profile data , was performed against the relative frequencies of tetranucleotides in 89 genomes . correspondence analysis summarizes an originally high - dimensional data matrix ( rows ( tetranucleotides ) and columns ( genomes ) ) into a low - dimensional projection ( space ) [ 23 , 24 ] . scores ( coordinates ) in the low - dimensional space are given to each genome . the distance between plots ( genomes ) in a low - dimensional space theoretically depends on the degree of similarity in the relative frequencies of tetranucleotides : a short distance means similar relative frequencies of tetranucleotides between genomes , whereas a long distance means different relative frequencies . thus , distance can be used as an index for similarity among genomes in the relative frequencies of tetranucleotides . distances between all genome pairs were calculated , and then a ranking for distances was obtained . in the neighbor - joining tree ( figure 1 ) , d. radiodurans is located in the high - gc - content cluster , whereas t. thermophilus is grouped with thermanaerovibrio acidaminovorans and their group is located away from the high - gc - content cluster . the neighbor - joining tree ( figure 1 ) was greatly influenced by the genomic gc content bias ; most of the well - defined major taxonomic groups did not form a monophyletic lineage . this result indicates that each constituent of the well - defined major group has diversified by changing its genome signature during evolution . it is consistent with a previous paper indicating that microorganisms with a similar gc content have similar genome signature patterns . thus , bootstrap analysis can not be performed . in this paper , we estimated the similarity between 2 different tetranucleotide frequencies by using correspondence analysis . the correspondence analysis showed that the genome signature of d. radiodurans is most similar to that of pseudomonas aeruginosa ( table 1 ) , whereas the genome signature of t. thermophilus is most similar to that of th . although the d. radiodurans genome signature has similarity to 18 bacterial species within the distance 0.5 , the t. thermophilus genome signature has similarity only to th . these results indicate that t. thermophilus has a different genome signature from those of bacteria included in the high - gc - content cluster ( figure 1 ) . although pearson 's correlation coefficient between the tetranucleotide frequencies of genomes of d. radiodurans and t. thermophilus is 0.630 ( figure 2 ) , that between the tetranucleotide frequencies of genomes of d. radiodurans and pseudomonas aeruginosa is 0.935 ( figure 3 ) and that between the tetranucleotide frequencies of genomes of th . the frequency of horizontal gene transfer between different bacteria may be associated with genome signature similarity . however , the tree topology based on genome signature ( figure 1 ) is different from that based on gene content . this is caused by , among others , an amelioration of the horizontally transferred genes . our findings strongly support the previous report that deinococcus has acquired genes from various other bacteria to survive different kinds of environmental stresses , whereas thermus has acquired genes from thermophilic bacteria to adapt to high - temperature environments .
the extremely radioresistant bacteria of the genus deinococcus and the extremely thermophilic bacteria of the genus thermus belong to a common taxonomic group . considering the distinct living environments of deinococcus and thermus 
 , different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor . 
 their guanine - cytosine ( gc ) contents are similar ; however , we hypothesized that their genomic signatures would be different . 
 our findings indicated that the genomes of deinococcus radiodurans and thermus thermophilus have different tetranucleotide frequencies . 
 this analysis showed that the genome signature of d. radiodurans is most similar to that of pseudomonas aeruginosa , whereas the genome signature of t. thermophilus is most similar to that of thermanaerovibrio acidaminovorans . 
 this difference in genome signatures may be related to the different evolutionary backgrounds of the 2 genera after their divergence from a common ancestor .