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Table 3 SNPs of Salmonella Enteritidis that disrupt open-reading-frames (ORFs) and comparison of translated genes to NCBI reference sequences of Salmonella enterica

From: Single nucleotide polymorphisms that differentiate two subpopulations of Salmonella enteritidis within phage type

Salmonella Enteritidis gene with SNP Type of SNP as referenced to S. Enteritidis PT4 Location of SNP in S. Enteritidis PT4 genome Salmonella Enteritidisa Other Salmonella enterica subsp. I serotypesb,c Outlier microbes
       O-antigen serotype    
    D1 D1 D1 D1 D1 D1 D1 A D1 B B B B B B C1 C1 C2 C2 C3 na na na
    PT 13a 21046 PT13a 21027 PT4 22079 (same as reference) Gallinarum Dublin Typhi Paratyphi A Javiana Typhimurium LT2 Typhimurium DT104 Typhimurium 4,[5],12:i:- Saintpaul Schwarzengrund Heidelberg Agona Choleraesuis Infantis Hadar Newport Kentucky Salmonella enterica subsp. arizonae Salmonella bongori E. coli 0157:H7 Sakai
A) Polymorphisms that distinguish PT13a 21046 from PT13a 21027 and S. Enteritidis PT4
fhuA (SEN0196) substitution: ORF termination 226922 - + + + (78) + (78) - (23) - (23) + (78) + (78) + (78) + (78) + (78) + (78) + (99) + (100) + (78) + (78) + (78) + (78) + (99) + (97) + (99) + (93)
mocR (SEN3898) deletion: 92 bp 4189388-4189479 - + + + (100) + (99) + (98) + (98) nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd
DGC (SEN4316) deletion: 80 bp of 5' end + 135 bp upstream 4642252-4642331 - + + + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (90) + (90) - nd
B) Polymorphisms that distinguish PT13a 21027 from PT13a 21046 and S. Enteritidis PT4
foxA (SEN0347) deletion: 1 bp 393529 + - + - (99) + (99) + (98) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (98) + (99) + (99) - nd - nd - nd
putP (SEN0989) substitution: ORF termination 1095448 + - + + (99) + (100) - nd + (100) + (100) + (99) + (99) + (99) + (99) + (99) + (100) - nd - (44) + (100) + (99) + (100) - (nd) + (99) - nd - nd
kdgM (SEN0992) deletion: 1 bp 1099079 + - + + (99) + (99) + (97) + (99) + (98) + (99) + (99) + (99) + (99) + (98) + (99) - nd + (99) + (99) + (99) + (99) - nd + (96) - nd - nd
ydcZ (SEN1464) deletion: 6 bp 1554930 + - + + (100) + (99) + (99) + (98) + (99) + (99) + (99) + (99) + (100) + (100) + (98) + (99) + (99) + (98) + (99) + (99) + (99) + (95) - nd - nd
ydjN (SEN1723) substitution: ORF termination 1828544 + - + + (99) + (99) + (99) + (99) + (99) + (100) + (100) + (100) + (100) + (99) + (100) + (99) + (99) + (100) + (100) + (99) + (100) + (99) + (99) + (96)
ytcJ-like (SEN1576) substitution: ORF termination 1681327 + - + + (99) + (99) + (99) + (98) + (98) + (99) + (99) na + (98) + (98) + (99) + (99) + (98) + (99) + (99) + (99) + (99) - nd + (96) - nd
pgk (SEN2751) deletion: 12 bp in-frame 2939833-2939844 + - + + (99) + (97) + (98) + (97) + (99) + (98) + (98) + (98) + (98) + (99) + (98) + (97) - (80) + (97) + (98) + (98) + (97) + (99) + (85) - nd
cysN (SEN2773) substitution: ORF termination 2957802 + - + + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (92) + (87)
dsdA (SEN3619) deletion: 10 bp 3880104-3880113 + - + + (100) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (99) + (100) + (99) + (99) + (99) + (99) + (100) + (99) + (97) - nd - nd
lrgB (SEN4042) deletion: 12 bp in-frame 4368126-4368137 + - + + (100) + (99) + (99) + + (100) + (100) + (100) + (100) + (100) + (100) + (100) + (100) + (100) + (100) + (100) + (100) + (100) + (99) + (97) - nd
yjfK (SEN4139) shared deletion: fusion of yjfK and yjfL; ribosomal binding site of yjfL removed 4472579-4472589 + - + + (99) + (99) + (99) + (99) + (99) + (99) + (100) + (100) + (100) + (99) + (100) + (99) + (99) + (100) + (100) + (100) + (99) - nd - (89) - nd
yjfL (SEN4140)    + - + - nd + (100) + (99) + (100) + (99) + (100) + (100) + (99) + (100) + (99) + (100) + (99) + (99) + (100) + (100) + (100) + (99) - (nd) + (98) - (nd)
sefD (SEN4250) deletion: single bp 4574262 + - + - (99) + (100) - (99) - (99) - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd - nd
a Abbreviations and symbols: na, possible error in contig assembly or database or otherwise not applicable; nd, no similar gene detected; nucleotide sequence similarity rather than amino acid sequence similarity is included for genes that are pseudogenes, which are recorded by a "-" even if percent nucleotide similarity is high.
b Numbers in parentheses indicate % similarty between translated amino acid sequences of S. Enteritidis in comparison to indicated serotype, unless a pseudogene is present and reported as nucleotide similarity.
c Strains and databases referenced are:
Serotype designation Refseq: Genbank accession                   
Salmonella enterica subsp. arizonae serovar 62:z4,z23:--, complete genome NC_010067 CP000880                   
Salmonella enterica subsp. enterica serovar 4,[5],12:i:- str. CVM23701 NZ_ABAO00000000 ABAO00000000                   
Salmonella enterica subsp. enterica serovar Agona str. SL483 NZ_ABEK00000000 ABEK00000000                   
Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 NC_006905 AE017220                   
Salmonella enterica subsp. enterica serovar Dublin str. CT_02021853 NZ_ABAP00000000 ABAP00000000                   
Salmonella enterica subsp. enterica serovar Heidelberg str. SL476 NC_011083 CP001120                   
Salmonella enterica subsp. enterica serovar Heidelberg str. SL486 NZ_ABEL00000000 ABEL00000000                   
Salmonella enterica subsp. enterica serovar Javiana str. GA_MM04042433 NZ_ABEH00000000 ABEH00000000                   
Salmonella enterica subsp. enterica serovar Kentucky str. CDC 191 NZ_ABEI00000000 ABEI00000000                   
Salmonella enterica subsp. enterica serovar Kentucky str. CVM29188 NZ_ABAK00000000 ABAK00000000                   
Salmonella enterica subsp. enterica serovar Newport str. SL254 NC_011080 CP000604                   
Salmonella enterica subsp. enterica serovar Newport str. SL317 NZ_ABEW00000000 ABEW00000000                   
Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 NC_006511 CP000026                   
Salmonella enterica subsp. enterica serovar Saintpaul str. SARA23 NZ_ABAM00000000 ABAM00000000                   
Salmonella enterica subsp. enterica serovar Saintpaul str. SARA29 NZ_ABAN00000000 ABAN00000000                   
Salmonella enterica subsp. enterica serovar Schwarzengrund str. CVM19633 NC_011094 CP001127                   
Salmonella enterica subsp. enterica serovar Schwarzengrund str. SL480 NZ_ABEJ00000000 ABEJ00000000                   
Salmonella enterica subsp. enterica serovar Typhi Ty2 NC_004631 AE014613                   
Salmonella enterica subsp. enterica serovar Typhi str. CT18 NC_003198 AL513382                   
Salmonella typhimurium LT2 NC_003197 AE006468                   
E. coli 0157:H7 Sakai NC_002695 BA000007                   
Sanger Institute databases are available at http://www.sanger.ac.uk/Projects/Salmonella/.
Salmonella bongori 12419 ATCC 43975
Salmonella enterica Enteritidis PT4 NCTC 13349
Salmonella enterica Gallinarum 287/91 NCTC 13346