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

Table 1 Single nucleotide polymorphisms (SNPs) and small insertions/deletions (InDels) fixed at phylogenetic branches where genomes of Salmonella enterica subsp. enterica serovars Enteritidis (n = 33), Pullorum (n = 5), Gallinarum (n = 8) and Dublin (n = 13) diverged

	Serovars	Variants							Total
		Intragenic					Intergenic
		sSNP	nsSNP	nsInDel	rSNP	rInDel	SNP	InDel
Homoplastic	Dublin versus all ^a	0	0	0	0	0	0	0	0
	Enteritidis versus Dublin ^b	0	0	0	3948	93	439	117	4597
	Pullorum + Gallinarum versus Enteritidis ^b	0	0	0	0	0	0	2	2
	Pullorum versus Gallinarum ^a	1	1	5	6	113	4	47	117
	Gallinarum versus Pullorum	0	0	8	236	84	16	38	382
Non-homoplastic	Dublin versus all ^a	3129	819	87	0	0	438	115	4588
	Enteritidis versus Dublin ^b	0	0	0	0	1	0	2	3
	Pullorum + Gallinarum versus Enteritidis ^b	0	0	31	0	0	0	5	36
	Pullorum versus Gallinarum ^a	95	139	81	0	0	15	27	357
	Gallinarum versus Pullorum ^a	5	1	108	0	0	3	38	155

The variant calling analysis was performed with the ‘VARCall’ workflow (i.e. 12,929 SNPs and 1157 small InDels). The fixed non-homoplastic variants are defined by common genotypes across the considered group of genomes, as well as different genotypes in all the others compared genomes. The fixed homoplastic variants are defined by common genotypes across the considered group of genomes and genomes of independent phylogenetic clades, as well as different genotypes in genomes of the compared child-leaves. According to the variant annotation performed with SnpEff against reference genome S. Enteritidis (strain P125109, accession NC_011294.1), the fixed variants presenting reference (r) and alternative (synonymous: s; non-synonymous: ns) genotypes are presented
^aAnalysis performed with the script ‘phyloFixedVar’ (i.e. dependently of the phylogenetic inference)
^bAnalysis performed with the script ‘FixedVar’ (i.e. independently of the phylogenetic inference)

ISSN: 1471-2180