Pan-genome analysis of the emerging foodborne pathogen Cronobacterspp. suggests a species-level bidirectional divergence driven by niche adaptation

Grim, Christopher J; Kotewicz, Michael L; Power, Karen A; Gopinath, Gopal; Franco, Augusto A; Jarvis, Karen G; Yan, Qiong Q; Jackson, Scott A; Sathyamoorthy, Venugopal; Hu, Lan; Pagotto, Franco; Iversen, Carol; Lehner, Angelika; Stephan, Roger; Fanning, Séamus; Tall, Ben D

doi:10.1186/1471-2164-14-366

Table 3 Non-core and unique genomic regions (GRs) identified in eight Cronobacter genomes

From: Pan-genome analysis of the emerging foodborne pathogen Cronobacterspp. suggests a species-level bidirectional divergence driven by niche adaptation

GR#	Feature(s) or putative feature(s) ^a	Cdubdub	Cdublac	Cdublau	Cmuy	Ctur	Cuni	Cmal	Csak	Shared locus
1	Acyl reductase-transketolase	-	+	+	+	+	+	+	+
2	Taurine metabolism	-	+	+	+	+	+	+	+
3	Environmental persistence capsule, yih	-	+	+	+	+	+	+	+
4	Filamentous hemagglutinin outer membrane protein	+	+	+	-	+	+	+	+
5	ybh transporter, putative antibiotic resistance efflux pump	+	+	+	-	+	+	+	+
6	γ₄ fimbriae	+	+	+	-	+	+	+	+
7	Phospho-alpha-glucosidase (α-methyl D-glucoside)	+	+	+	-	+	+	+	+
8	DMSO, urea (urt), biotin utilization, MAR (4-aminobutyrate)	+	+	+	+	+	-	+	+
9	π fimbriae	+	+	+	+	+	+	+	-
10	Hydrolase	+	+	+	+	+	+	+	-
11	Transporter and Rhodanese-related sulfurtransferases	+	+	+	+	+	+	+	-	l
12	Lysozyme, virulence regulator	+	+	+	+	+	+	+	-
13	LPS/core OS 2 gene pair	+	+	+	+	+	+	+	-
14	MFS transporter, regulator and dehydrogenase	+	-	-	+	+	+	+	+	f
15	Membrane hydrolase	+	+	-	+	-	+	+	+
16	Large repetitive hemolysin	+	+	-	+	+	+	+	-
17	Putative ABC transporter and DMT permease	+	+	+	-	+	+	+	-	d
18	Beta-glucosidase	+	+	+	+	-	-	+	+
19	Hypothetical proteins	+	+	+	+	-	+	+	-
20	Fatty acid desaturase	+	+	+	+	+	-	-	+
21	OM autotransporter barrel	+	+	+	+	+	+	-	-	a
22	NO reductase	+	+	+	+	+	+	-	-
23	Oxidoreductase	+	+	+	+	+	+	-	-
24	Spermidine-preferential uptake system	+	+	+	+	+	+	-	-
25	Glucuronyl hydrolase, sucrose permease	+	+	+	+	+	+	-	-
26	Hypothetical proteins	+	+	+	-	+	+	-	-
27	Hypothetical proteins	+	-	+	-	+	+	+	-
28	CRISPR	+	+	-	-	+	-	+	+
29	Inositol	+	+	-	+	+	+	-	-
30	Non-heme chloroperoxidase, MxcK	-	-	-	+	+	+	+	+	g
31	Acetyltransferase	-	-	-	+	+	+	+	+
32	Hypothetical proteins	-	+	+	+	-	+	+	-
33	Putative membrane protein and regulator	+	+	+	+	-	+	-	-	h
34	Malonate	+	-	-	+	+	+	+	-
35	Formate dehydrogenase	+	-	-	-	+	+	+	+
36	Phenolic sulfur ester	+	+	+	+	-	-	-	-
37	Deoxyguanosinetriphosphate triphosphohydrolase	+	+	+	+	-	-	-	-
38	Ferrichrome iron receptor	+	+	+	+	-	-	-	-
39	Putative membrane and hypothetical proteins	+	+	+	+	-	-	-	-	i
40	Arylsulfatase	+	+	+	+	-	-	-	-	j
41	Redundant methionine transporter	+	+	+	+	-	-	-	-
42	Ethanolamine permease and deaminase	+	+	+	+	-	-	-	-
43	Ferrichrome-iron receptor	+	+	+	+	-	-	-	-
44	Hypothetical proteins	+	+	+	+	-	-	-	-
45	Ornithine monooxygenase, BtrH	+	+	+	+	-	-	-	-
46	Transmembrane tRNA/peptide synthetase	+	+	+	+	-	-	-	-
47	Indole	+	+	+	+	-	-	-	-
48	Putative LPS modification operon	-	-	-	-	+	+	+	+	i
49	Toxin-antitoxin pair	-	-	-	-	+	+	+	+
50	Exported protein	-	-	-	-	+	+	+	+
51	CynX	+	+	+	-	-	-	+	-
52	γ₄ fimbriae	+	+	+	-	+	-	-	-	l
53	Acyl enzymes	+	+	+	-	+	-	-	-
54	Membrane protein	-	+	+	-	+	-	-	+
55	Curli	+	-	-	-	+	+	+	-
56	Methyl-accepting chemotaxis and/or hypothetical protein	+	+	-	-	+	+	-	-	n
57	Macrophage infectivity potentiator-related protein and regulator	-	-	-	+	+	-	+	+
58	Putative monooxygenase and transcriptional regulators	+	+	+	-	-	-	-	-	d
59	Oligopeptide transport system	+	+	+	-	-	-	-	-
60	Hypothetical proteins	+	+	+	-	-	-	-	-
61	Methyl-accepting chemotaxis and/or hypothetical proteins	+	+	+	-	-	-	-	-
62	Beta-lactamase	-	-	-	-	-	+	+	+	j
63	Peptide chain release factor	-	-	-	-	+	+	+	-
64	Chemotaxis	-	-	-	+	-	+	+	-	e
65	Helicase	-	+	+	+	-	-	-	-
66	Hypothetical proteins	-	-	+	-	-	+	-	+
67	Dulcitol	-	-	-	+	+	+	-	-
68	Short-chain dehydrogenase and regulator	+	-	+	-	-	-	-	-	d
69	Type I RMS	-	+	+	-	-	-	-	-	c
70	Pyroxidine/pyroxidal metabolism	-	+	+	-	-	-	-	-	e
71	qseBC, ompV	-	+	+	-	-	-	-	-	f
72	Maltose phosphate PTS and glucosidase	-	+	-	+	-	-	-	-
73	Cellulose degradation	-	+	-	+	-	-	-	-
74	Transporter and secreted pair	-	-	-	+	-	-	-	+
75	Hypothetical proteins	-	-	-	+	-	-	-	+
76	β fimbriae	-	+	-	-	-	-	-	+
77	Periplasmic or lipo-protein	-	-	-	-	+	-	-	+
78	α-mannosidase	-	-	-	-	+	-	-	+
79	Regulator and hypothetical protein	-	-	-	-	+	+	-	-
80	Short chain dehydrogenase	-	-	-	-	+	+	-	-
81	Membrane protein	-	-	-	-	-	-	+	+
82	γ₁ fimbriae	-	-	-	-	-	-	+	+
83	(+/−) putative membrane and (+/−) hypothetical proteins; variable	+	+	+	+	-	+	+	-
84	Arsenic resistance; MFS transporter, regulator and hypothetical proteins	+	-	-	-	-	-	-	-	i
85	Putative monoamine oxidase, carboxymuconolactone decarboxylase and hypothetical proteins	+	-	-	-	-	-	-	-	l
86	Hypothetical proteins	-	+	-	-	-	-	-	-
87	Putative monoamine oxidase, carboxymuconolactone decarboxylase and hypotheticals; homologous to GR85	-	+	-	-	-	-	-	-	i
88	Putative sulfatase and hypothetical proteins	-	-	+	-	-	-	-	-	a
89	LysE Superfamily exporter	-	-	+	-	-	-	-	-	d
90	Hypothetical proteins	-	-	+	-	-	-	-	-
91	Radical SAM and ABC ATPase proteins	-	-	+	-	-	-	-	-
92	Mannanase	-	-	+	-	-	-	-	-	g
93	Putative reductases and hypothetical proteins	-	-	+	-	-	-	-	-	i
94	Membrane protein	-	-	+	-	-	-	-	-	k
95	D-glucarate permease, transketolase, homologous to GR117	-	-	-	+	-	-	-	-	c
96	Type I RMS	-	-	-	+	-	-	-	-	d
97	Modulator of drug activity B (mdaB), MFS transporter and regulator	-	-	-	+	-	-	-	-	n
98	Hypothetical proteins	-	-	-	+	-	-	-	-
99	Hypothetical proteins	-	-	-	+	-	-	-	-	h
100	Hypothetical proteins	-	-	-	+	-	-	-	-
101	FHA	-	-	-	+	-	-	-	-
102	L-rhamnose ABC transporter	-	-	-	+	-	-	-	-
103	Urea carboxylase	-	-	-	+	-	-	-	-
104	Heteropolysaccharide degradation	-	-	-	-	+	-	-	-	b
105	qseBC, ompV	-	-	-	-	+	-	-	-	d
106	Sigma factor, catalase	-	-	-	-	+	-	-	-	k
107	Beta-glucosidase, cellobiose	-	-	-	-	+	-	-	-
108	Short chain dehydrogenase	-	-	-	-	+	-	-	-
109	Paralogous enzyme island	-	-	-	-	+	-	-	-
110	DND operon	-	-	-	-	+	-	-	-
111	Xanthosine utilization	-	-	-	-	+	-	-	-
112	κ fimbriae	-	-	-	-	-	+	-	-
113	Putative epoxide hydrolase	-	-	-	-	-	+	-	-	b
114	Cupin superfamily homologues	-	-	-	-	-	+	-	-	d
115	Hypothetical proteins	-	-	-	-	-	+	-	-
116	Hypothetical proteins	-	-	-	-	-	+	-	-	i
117	D-glucarate permease, transketolase	-	-	-	-	-	+	-	-
118	Large exoproteins involved in heme utilization or adhesion	-	-	-	-	+	-	+	+
119	MipA homologue and signal transduction pair	-	-	-	-	-	-	+	-	i
120	Hemolysin, activator and secretion	+	-	+	-	-	-	-	-
121	Membrane spanning and hypothetical proteins	-	-	-	-	-	-	-	+	a
122	Hypothetical proteins	-	-	-	-	-	-	-	+
123	Csak invasin locus	-	-	-	-	-	-	-	+
124	Unique transporter	-	-	-	-	-	-	-	+	e
125	Nucleoside-sugar efflux	-	-	-	-	-	-	-	+
126	γ₁ fimbriae	-	-	-	-	-	-	-	+
127	nanC, sugar isomerase, hydrolase	-	-	-	-	-	-	-	+
128	Paralogous enzyme island	-	-	-	-	-	-	-	+
129	Sialic acid	-	-	-	-	-	-	-	+

^aFeature(s), or putative feature(s), were assigned based on BLASTp homology of encoded ORFs to known proteins. Shared chromosomal loci of genomic regions are indicated by matching letters. Features in bold are biochemical traits, used previously to biotype Cronobacter isolates.

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