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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