REP code: defining bacterial identity in extragenic space.
Through the analysis of 57 bacterial genomes we have detected repetitive extragenic palindromic DNA sequences (REPs) in 11 species. For a sequence to be considered as REP, the following criteria should be met: (i) It should be extragenic, (ii) palindromic, (iii) of a length between 21 and 65 bases and (iv) should constitute more than 0.5% of the total extragenic space. Species-specific REPs have been found in human pathogens such as Escherichia coli, Salmonella enterica, Neisseria meningitidis, Mycobacterium tuberculosis, Rickettsia conorii and Pseudomonas aeruginosa, the plant pathogen Agrobacterium tumefaciens and the soil bacteria Deinococcus radiodurans, Pseudomonas putida and Sinorhizobium meliloti.
Tobes
Raquel
R
Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín. Department of Plant Biochemistry and Molecular and Cellular Biology. Profesor Albareda number 1, E-18008 Granada, Spain.
Ramos
Juan-Luis
JL
D016960:Agrobacterium tumefaciens / Q000235:genetics; D001419:Bacteria / Q000235:genetics*; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics*; D034301:Deinococcus / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000235:genetics; D009345:Neisseria meningitidis / Q000235:genetics; D011550:Pseudomonas aeruginosa / Q000235:genetics; D016958:Pseudomonas putida / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D020114:Rickettsia conorii / Q000235:genetics; D019779:Salmonella enterica / Q000235:genetics; D016962:Sinorhizobium meliloti / Q000235:genetics
D004269:DNA, Bacterial; D021901:DNA, Intergenic