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Table 3 Impacts of translation and function of proteins encoded by genes presenting GO-terms highly impacted by intragenic and non-homoplastic fixed variants in Salmonella enterica subsp. enterica serovars Pullorum and Gallinarum

From: First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts

GO

Position

Genes

Reference genotype

Genotype in Gallinarum

Genotype in Pullorum

Protein translation

impact in Gallinarum

Protein translation impact in Pullorum

Impact on protein function

GO:0006428

54,044

SEN_RS00235

G

G

T

Null

Missense variant

Modification in Pullorum

GO:0006428

54,289

SEN_RS00235

T

T

C

Null

Synonymous variant

Potential modification

GO:0006428

54,658

SEN_RS00235

C

C

T

Null

Synonymous variant

Potential modification

GO:0006428

55,063

SEN_RS00235

G

G

A

Null

Synonymous variant

Potential modification

GO:0006522

1,313,705

SEN_RS06395

C

C

T

Null

Stop gained

Partial lost in Pullorum

GO:0006522

1,313,706

SEN_RS06395

A

A

G

Null

Missense variant

Modification in Pullorum

GO:0004822

54,044

SEN_RS00235

G

G

T

Null

Missense variant

Modification in Pullorum

GO:0004822

54,289

SEN_RS00235

T

T

C

Null

Synonymous variant

Potential modification

GO:0004822

54,658

SEN_RS00235

C

C

T

Null

Synonymous variant

Potential modification

GO:0004822

55,063

SEN_RS00235

G

G

A

Null

Synonymous variant

Potential modification

GO:0015079

99,941

SEN_RS00445

C

CGCTGGG

C

Disruptive inframe insertion

NULL

Partial lost in Gallinarum

GO:0015079

3,489,575

SEN_RS17095

C

CG

C

Frameshift variant

NULL

Modification in Gallinarum

GO:0003747

1,343,057

SEN_RS06530

C

C

A

Null

Synonymous variant

Potential modification

GO:0003747

1,343,237

SEN_RS06530

A

A

G

Null

Synonymous1 variant

Potential modification

GO:0003747

339,779

SEN_RS01530

G

G

T

Null

Missense variant

Modification in Pullorum

  1. The identification of variants, detection of fixed variants, assignment of GO-terms to variants, and gene-ontology enrichment analysis were performed with the scripts ‘VARCall’, ‘phyloFixedVar’, ‘GetGOxML’, and ‘EveryGO’, respectively. The variant annotation was performed with SnpEff against reference genome S. Enteritidis (strain P125109, accession NC_011294.1). The p-values of hypergeometric tests were adjusted by Bonferroni correction. The lowest corrected p-values representing GO-terms highly impacted by fixed variants (i.e. < 5.0×10-2), the highest GO-levels presenting the most accurate GO-terms (i.e. ≥ 5), and the highest number of hits representing relevant GO-terms quantitatively (i.e. ≥ 4) are presented