Table 4 Functionally annotated mutations (i.e. excluding genes coding hypothetical proteins) of Salmonella enterica subsp. enterica serovars (i.e. SNPs, InDels and genes) associated by microbial GWAS with animal sources (i.e. avian bovine, swine and fish). The accessory genes and coregenome variants (i.e. SNPs and InDels) were annotated with Prokka (1.12) and SNPeff (4.1 g), respectively. After exclusion of variants from recombination events based on iVARCall2 and ClonalFrameML, the workflow ‘microbial-GWAS’ corrects the population structure based on Linear Mixed Model (LMM), then perform associations with Wald tests implemented in GEMMA. The associated mutations (i.e. Wald tests) refer to polygenicity with regard to Quantile-Quantile (QQ) plots from microbial GWAS (i.e. p < 1 × 10^− 2) and present high (i.e. > 5%) and low (i.e. < 5‰) frequencies of presence (i.e. genes and alternative variants) in the studied and compared genomes, respectively. The genes with undefined names are assigned to STM identifiers with regard to the reference genome of Salmonella Typhimurium LT2 (NCBI NC_003197.1). HGVS stands for Human Genome Variation Society. N/A and ND stand for not applicable and not determined. N/A refers to intergenic regions. The term ‘gene’ refers to the gene presence

Avian

Gene

1.2 × 10^− 8

zntR2

HTH-type transcriptional regulator ZntR

N/A

N/A

N/A

P0ACS5

Avian

Gene

1.2 × 10⁻⁸

cph2_2

Phytochrome-like protein cph2

N/A

N/A

N/A

Q55434

Avian

Gene

1.2 × 10⁻⁸

merP2

Mercuric transport protein periplasmic component

N/A

N/A

N/A

P13113

Avian

Gene

1.2 × 10⁻⁸

merP1

Mercuric transport protein periplasmic component

N/A

N/A

N/A

P13113

Avian

Gene

1.7 × 10⁻⁵

recD2

ATP-dependent RecD-like DNA helicase

N/A

N/A

N/A

Q9RT63

Avian

Gene

4.6 × 10⁻³

dcuA

Anaerobic C4-dicarboxylate transporter DcuA

N/A

N/A

N/A

P0ABN5

Avian

SNP

8.8 × 10⁻⁷

sinH

Intimin-like inverse autotransporter protein SinH

2,650,403

c.399C > T

p.Pro133Pro

E8XGK6

Avian

SNP

8.8 × 10⁻⁷

ilvY

HTH-type transcriptional activator IlvY

4,116,598

c.616G > A

p.Glu206Lys

P0A2Q2

Avian

SNP

8.8 × 10⁻⁷

ilvC

Ketol-acid reductoisomerase (NADP(+))

4,117,833

c.457C > T

p.Ala153Ser

P05989

Avian

SNP

8.8 × 10⁻⁷

N/A

N/A

4,217,302

N/A

N/A

N/A

Bovine

Gene

8.6 × 10⁻⁵

repE

Replication initiation protein

N/A

N/A

N/A

P03856

Bovine

Gene

2.8 × 10⁻³

hicB

Antitoxin HicB

N/A

N/A

N/A

P67697

Bovine

Gene

3.7 × 10⁻³

eptC

Phosphoethanolamine transferase EptC

N/A

N/A

N/A

P0CB40

Bovine

SNP

1.6 × 10⁻³

N/A

N/A

294,951

N/A

N/A

N/A

Bovine

SNP

6.5 × 10⁻⁶

arnD

4-deoxy-4-formamido-L-arabinose phosphoundecaprenol deformylase ArnD

2,408,955

c.884A > C

p.Ala295Ala

O52326

Bovine

SNP

6.5 × 10⁻⁶

srmB

ATP-dependent RNA helicase SrmB

2,783,562

c.660 T > C

p.Lys220Asn

Q8ZMX7

Bovine

SNP

6.5 × 10⁻⁶

aspA

Aspartate ammonia-lyase

4,572,050

c.332C > T

p.Asn111Ile

Q7CPA1

Swine

Indel

3.3 × 10⁻³

N/A

N/A

4,816,900

N/A

N/A

N/A

Swine

SNP

4.8 × 10⁻⁷

pepE

Dipeptidase E

4,414,198

c.488G > T

p.Pro163Leu

P36936

Swine

SNP

1.7 × 10⁻¹¹

iroN

TonB-dependent siderophore receptor protein

2,924,248

c.1516G > C

p.Gly506Arg

Q8ZMN0

Swine

SNP

1.7 × 10⁻¹¹

priA

Primosomal protein N

4,304,871

c.689 T > C

p.Lys230Thr

Q8ZKN8

Swine

SNP

6.9 × 10⁻⁰⁵

ybeK or rihA

Pyrimidine-specific ribonucleoside hydrolase RihA

725,582

c.912A > G

p.Ala304Ala

Q8ZQY4

Swine

SNP

2.3 × 10⁻¹⁵

ilvY

HTH-type transcriptional activator IlvY

4,116,897

c.317C > A

p.Leu106Gln

P0A2Q2

Fish

Gene

2.3 × 10⁻⁸

dapH

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase

N/A

N/A

N/A

Q7A2S0

Fish

Gene

3.3 × 10⁻³

cgkA

Kappa-carrageenase

N/A

N/A

N/A

P43478