Identification and characterization of repetitive extragenic palindromes (REP)-associated tyrosine transposases: implications for REP evolution and dynamics in bacterial genomes

Table 2 Correlation between REP numbers and presence or absence of their cognate RAYTs in different bacterial strains

	REP symbol
Host strain	Pput1	Pput2	Pput3	Pput4	Pflu1	Pflu2	Pflu3	Xaxo	Xcam	Smal1	Smal2	Smal3	Smal4	S_sp1	S_sp2
Pseudomonas putida KT2440	62 35	4 3	21 27	0 0	0	0	0 0	0 0	0	0	0	0	0	0	0
Pseudomonas putida F1	70 30	4 4	56 78	0 0	0	0	0 0	0 0	0	0	0	0	0	0	0
Pseudomonas putida GB-1	16 4	62 14	4 23	6 63	0	0	0 0	0 0	0	0	0	0	0	0	0
Pseudomonas putida W619	0 0	1 1	0 0	24 77	0	0	0 0	0 0	0	0	0	0	0	0	0
Pseudomonas fluorescens SBW25	0 0	0 0	0 0	0 0	387	104	83 119	0 0	0	0	0	0	0	0	0
Pseudomonas fluorescens Pf0-1	0 0	0 0	0 0	0 0	0	0	0 0	0 0	0	0	0	0	0	0	0
Pseudomonas fluorescens Pf-5	0 0	0 0	0 0	0 0	0	1	0 0	0 0	0	0	0	0	0	0	0
Xanthomonas axonopodis pv. citri str. 306	0 0	0 0	0 0	0 0	0	0	0 0	9 23	0	0	0	0	0	0	0
Xanthomonas. campestris pv. vesicatoria str. 85-10	0 0	0 0	0 0	0 0	0	0	0 0	7 11	1	0	0	0	0	0	0
Xanthomonas campestris pv. campestris str. 8004	0 0	0 0	0 0	0 0	0	0	0 0	0 3	43	0	0	0	0	0	0
Xanthomonas. campestris pv. campestris str. ATCC 33913	0 0	0 0	0 0	0 0	0	0	0 0	1 3	48	0	0	0	0	0	0
Xanthomonas campestris pv. campestris str. B100	0 0	0 0	0 0	0 0	0	0	0 0	2 4	49	0	0	0	0	0	0
Stenotrophomonas maltophilia R551-3	0 0	0 0	0 0	0 0	0	0	0 0	0 0	0	49	259	39	266	25	4
Stenotrophomonas maltophilia K279a	0 0	0 0	0 0	0 0	0	0	0 0	0 0	0	7	13	52	427	47	16
Stenotrophomonas sp. SKA14	0 0	0 0	0 0	0 0	0	0	0 0	0 0	0	3	7	7	323	69	37

The values represent the numbers of exact copies of REP sequences, flanking identified rayt genes (as denoted in Table 1), in bacterial genomes. For dimorphic REPs, the upper value corresponds to the number of upper REP sequences from Table 1 and vice versa. In cases where the cognate rayt gene or its close homolog (flanked by the same REPs) is actually present in the given genome, the numbers are written in bold and underlined.

ISSN: 1471-2164