Figure 3

Schematic diagram of the modular structure of RGP99_XN in the X. nematophila ATCC19061 (Xn) genome and of some RGP99_XN module counterparts in the P. luminescens TT01 (Pl), P. asymbiotica ATCC43949 (Pa), X. bovienii SS-2004 (Xb) genomes. A. RGP99_XN can be divided into four subregions or modules, which are distinguished by letters a, b, c, d. G + C is indicated above the modules. B. The T6SS (RGP99_XN_b) and XhlA/B (RGP99_XN_c) module counterparts in P. luminescens TT01 (RGP9_PL), P. asymbiotica ATCC43949 (RGP8_PA) and X. bovienii Sj- 2004 (GI7_XB). The boxes represent modules, corresponding to blocks of genes specific to the strain or blocks of syntenic genes, (i.e. with a conserved genomic organization in at least two genomes of the Entero set). The putative biological functions of modules are defined by the specific colors of the box (see the legend below the figure). Yellow squares indicate modules conserved in at least two genomes of the Entero set. Others are modules specific to the strain. The thin vertical black arrows indicate RGP integration sites. The conserved modules in the four genomes are linked by dotted lines. Modules are conserved if they have more than 80% of syntenic genes in common (syntenic genes between two genomes are colocalized genes that shared at least 30% of identity on 80% of the shortest sequence by BlastP). For example, the two modules RGP99_XN_b (T6SS) and RGP99_XN_c (xhl AB) are conserved between the four genomes. RGP99_XN_b is composed of 16 genes potentially encoding a type six secretion system (T6SS). The 16 genes display colocalized orthologous genes in XB, PA and PL (identity between orthologs of XN and XB modules: 75% to 97%; identity between orthologs of XN, PL and PA modules: 58% to 91%). RGP99_XN_c is composed of 3 genes, two of them encode an hemolysin belonging to the two partner secretion system family and display colocalized orthologs in XB (73 to 90% of identity), PA (52 to 75% of identity) and PL (51 to 77% of identity).