# indicates that the genetic region was previously described as variable among S. Enteritidis isolates [21]. Table 4 Regions (REG) and single genes (SING) absent in the S. Enteritidis PT4 P125109 chromosome and predicted by CGH analysis as present in at least one Enteritidis isolate.   ISOLATE DESIGNATION GENE RANGE HOMOLOGOUSa GENE DESCRIPTION REG 10A 31/88 SDT1842-SDT1843 Z-VAD-FMK mouse No Similar to E coli K12 ymfD, ymfE phage proteins REG 10B 31/88, 8/89, 47/95 (only SDT1860) SDT1846-SDT1860 No Shigella Phage proteins REG 11# 8/89, AF3353, 31/88 (only STY1036) STY1034-STY1036 SL1344, LT2, TY2, DT104 Part of

Gifsy-2 antitermination ninG, dnaJ REG 12A 31/88, 8/89 SL2583-SL2584 SBG Phage related protein REG 12B 31/88, 8/89 SL2588-SL2594 some SBG Phage proteins, putative methyltransferase, unknown REG 12C 31/88, 8/89 SL2599-SL2600 LT2, SDT104 Gifsy-1 integrase, unknown REG 13 AF3353, 8/89 (only STY1013) STY1011-STY1013 TY2, LT2, SL1344, DT104 Phage proteins (integrase, excisionase) REG 14 AF3353, 8/89 (only STY1021) STY1021-STY1024 TY2, LT2, SL1344, DT104 Phage proteins REG 15A# AF3353 STY3674-STY3689

SL1344, LT2, TY2, SPA ST35 phage proteins REG 15B AF3353 STY3696-STY3702 TY2, SPA, LT2, SL1344 ST35 phage proteins REG16A AF3353 STY4600-STY4602 TY2, SPA. LT2, SL1344, SBG (except 4600) Part of S. Typhi phage SopE REG16B AF3353 STY4605-STY4607 TY2, SPA, LT2, SL1344, SBG Part of S. Typhi phage SopE REG16C# AF3353 STY4613-STY4628 TY2, SPA. LT2, SL1344 (except 4619) Part MCC950 of S. Typhi phage SopE REG16D# AF3353 STY4633-STY4635 SL1344, LT2, SPA Part of S. Typhi phage SopE REG16E AF3353 STY4638-STY4639 TY2, SPA, LT2. SL1344 (except 4639) Part of S. Typhi phage SopE REG16F AF3353 STY4641-STY4645 TY2, SPA. LT2 (except 4641) Part of S. Typhi phage SopE SING 10 53/94, 57/94, 47/95,

49/98 SBG0310 No unknown SING 11 31/88 SBG3602 LT2, CT18 Hypothetical protein SING 12 S1400/94 STY0114 TY2, SPA Putative IS transposase SING 13 77/02 STY0480 TY2, SPA Hypothetical protein SING 14 49/98 STY4582 No Exported protein SING 15 31/88 STM0293 SL1344, DT104 unknown SING 16 31/88 SDT2674 SL1344 unknown SING 17 31/88, 8/89 STM2584 DT104, SL1344 gogB, leucine-rich repeat protein SING 18 49/98 STY3619 TY2, SPA, LT2, SL1344 Conserved membrane protein SING 19 AF3353 VAV2 SBG0897 SBG Phage related protein SING 20 AF3353 SDT1865 No unknown SING 21 AF3353 SDT3861 No unknown SING 22 AF3353 STY1073 LT2, TY2 unknown SING 23 AF3353 STY2013 TY2 unknown SING 24 AF3353 STY4600 TY2, SPA Transcriptional regulator SING 25 AF3353 KPT-8602 STY4619 TY2, SPA Putative membrane protein SING 26 AF3353 STY4639 TY2, LT2, SPA Hypothetical protein a indicates when the REG or SING has homologous region described in other sequenced Salmonella serovars (see list of abbreviations). # indicates that the genetic region was previously described as variable among S. Enteritidis isolates [21]. Figure 1 Graphic representation of the chromosomal genes found in this study as part of S . Enteritidis Dispensable Genome (233 genes).