Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus

Table 1 Number and size of regions of genomic plasticity (RGPs) in the P. luminescens TT01, P. asymbiotica ATCC43949, X. nematophila ATCC19061 and X. bovienii SS-2004 genomes, according to the set of bacterial genomes used to search for synteny ruptures in the core genome

	Genome	Number of predicted RGPs (% of the whole genome), when compared with the
	size (bp)	"Genus" set¹*	"Photo + Xeno" set²*	"Entero" set³*	"Entero" set after cleaning**
P. luminescens TT01	5688987	111 (32.8%)	122 (58.2%)	113 (69%)	96 (61.5%)
P. asymbiotica ATCC43949	5064808	85 (25.68%)	118 (56.4%)	107 (67.4%)	92 (59.1%)
X. nematophila ATCC19061	4432590	96 (36.2%)	95 (49.5%)	97 (62.9%)	83 (54.1%)
X. bovienii SS-2004	4225498	81 (33.1%)	80 (45.8%)	88 (59.6%)	71 (52.6%)

* RGPs before manual inspection
** RGPs after manual inspection (see Materials and Methods)
¹P. luminescens TT01 and P. asymbiotica ATCC 43949 for Photorhabdus strains; X. bovienii SS-2004 and X. nematophila ATCC19061 for Xenorhabdus strains.
²P. luminescens TT01, P. asymbiotica ATCC 43949, X. bovienii SS-2004, X. nematophila ATCC19061
³P. luminescens TT01, P. asymbiotica ATCC43949, X. nematophila ATCC19061, X. bovienii SS-2004, Yersinia pestis CO92 (accession number NC_003143); Salmonella enterica subsp. enterica Typhi (accession number NC_003198), Erwinia carotovora SCRI1043 (accession number NC_004547) and E. coli K12 (accession number NC_000913).

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