Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori

Saunders, Nigel J; Boonmee, Prawit; Peden, John F; Jarvis, Stephen A

doi:10.1186/1471-2164-6-9

Table 6 Top 50 most divergent genes by HNS in H. pylori strain 26695 plus those additional genes > 2 SD greater than the mean by DNS and the 50 most divergent by HNS

From: Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori

HNS order	annotation	HP#	J99 #	DNS order	TNS order
1	cag pathogenicity island protein (cag7)	HP0527	JHP0476	1	1
2	hypothetical protein	HP0119	NAH	17	7
3	vacuolating cytotoxin (vacA) paralog	HP0922	JHP0856	6	5
4	vacuolating cytotoxin (vacA) paralog	HP0289	JHP0274	2	2
5	poly E-rich hypothetical protein	HP0322	JHP0305	3	8
6	hypothetical protein	HP1142	JHP1070	91	19
7	cag island protein (cagA)	HP0547	JHP0495	31	15
8	hypothetical protein	HP0205	JHP0191	57	78
9	hypothetical protein	HP0609	JHP0556*	4	6
10	hypothetical protein	HP0453	NAH	75	58
11	adenine specific DNA methyltransferase (mod)	HP1522	JHP1411	363	207
12	hypothetical protein	HP0488	JHP0440	7	10
13	hypothetical protein	HP1116	JHP1044	8	11
14	type IIS restriction enzyme R and M protein (ECO57IR)	HP1517	NAH	28	42
15	hypothetical protein	HP0513	JHP0462	122	28
16	hypothetical protein	HP0906	JHP0842	42	22
17	vacuolating cytotoxin (vacA) paralog	HP0610	JHP0556*	13	12
18	type III restriction enzyme R protein (res)	HP1521	JHP1410	195	210
19	DNA-directed RNA polymerase, beta subunit (rpoB)	HP1198	JHP1121	84	23
20	adenine/cytosine DNA methyltransferase	HP0054	NAH	109	120
21	type I restriction enzyme R protein (hsdR)	HP1402	JHP1424	103	86
22	DNA transfer protein (cagE)	HP0441	JHP0492	29	51
23	type III restriction enzyme R protein	HP1371	JHP1285	52	119
24	DNA topoisomerase I (topA)	HP0440	NAH	63	149
25	outer membrane protein (omp26)	HP1157	JHP1084	34	27
26	type I restriction enzyme R protein (hsdR)	HP0464	NAH	36	90
27	cag pathogenicity island protein (cag8)	HP0528	JHP0477	74	50
28	virB4 homolog (virB4)	HP0459	NAH	53	49
29	hypothetical protein	HP0586	JHP0534	631	163
30	multidrug resistance protein (spaB)	HP0600	JHP0547	97	41
31	RNA polymerase sigma-70 factor (rpoD)	HP0088	JHP0081	56	55
32	hypothetical protein	HP0731	JHP0668	132	80
33	hypothetical protein	HP1520	NAH	167	20
34	vacuolating cytotoxin	HP0887	JHP0819	18	25
35	type III restriction enzyme R protein (res)	HP0592	NAH	16	30
36	hypothetical protein	HP0118	JHP0110	179	27
37	type I restriction enzyme R protein (hsdR)	HP0846	JHP0784	342	101
38	hypothetical protein	HP1187	JHP1113	142	31
39	hypothetical protein	HP0030	JHP0026	45	24
40	HP0478	JHP0430	1080	220
41	hypothetical protein	HP1143	JHP1071	58	29
42	hypothetical protein	HP0669	JHP0613	69	60
43	N-methylhydantoinase	HP0696	JHP0632	19	35
44	type I restriction enzyme M protein (hsdM)	HP1403	JHP1423	125	340
45	translation initiation factor IF-2 (infB)	HP1048	JHP0377	291	332
46	hypothetical protein	HP0996	JHP0942	5	14
47	DNA polymerase III alpha-subunit (dnaE)	HP1460	JHP1353	297	219
48	hypothetical protein	HP0733	JHP0670	224	222
49	preprotein translocase subunit (secA)	HP0786	JHP0723	119	176
50	hypothetical protein	HP0120	NAH	283	44
53	hypothetical protein	HP0058	JHP0051	121	16
54	DNA polymerase I (polA)	HP1470	JHP1363	30	77
59	hypothetical protein	HP1089	JHP0336	12	67
64	DNA mismatch repair protein (MutS)	HP0621	JHP0565	22	137
68	2',3'-cyclic-nucleotide 2'-phosphodiesterase (cpdB)	HP0104	JHP0096	54	73
75	fucosyltransferase	HP0651	JHP0596	48	43
77	hypothetical protein	HP0508	JHP0458	139	32
87	urease beta subunit (urea amidohydrolase) (ureB)	HP0072	JHP0067	21	38
90	cell division protein (ftsK)	HP1090	JHP0335	37	181
99	outer membrane protein (omp3)	HP0079	JHP0073	68	45
100	cag pathogenicity island protein (cag3)	HP0522	JHP0471	11	48
101	outer membrane protein (omp17)	HP0725	JHP0662	209	47
122	hypothetical protein	HP0080	JHP0074	9	18
127	hypothetical protein	HP1479	JHP1372	55	153
129	iron(III) dicitrate transport protein (fecA)	HP1400	JHP1426	32	99
142	outer membrane protein	HP0486	JHP0438	26	147
160	virulence associated protein homolog (vacB)	HP1248	JHP1169	50	164
166	translation elongation factor EF-Tu (tufB)	HP1205	JHP1128	49	64
168	cytochrome oxidase (cbb3 type) (fixN)	HP0144	JHP0132	27	102
170	hypothetical protein	HP1003	NAH	38	61
180	flagellin A (flaA)	HP0601	JHP0548	33	40
207	DNA repair protein (recN)	HP1393	JHP1434	35	154
256	hypothetical protein	HP0788	JHP0725	41	72
276	hypothetical protein	HP0186	JHP0174	47	130
277	hypothetical protein	HP1106	JHP1033	59	272
296	hypothetical protein	HP1333	JHP1253	40	53
320	hypothetical protein	HP0059	JHP0052	43	21
448	integrase/recombinase (xerD)	HP0995	JHP0941	25	39
449	hypothetical protein	HP0449	NAH	51	81
451	GMP reductase (guaC)	HP0854	JHP0790	44	169
582	hypothetical protein	HP0489	JHP0441	10	36
693	cag island protein (cagT)	HP0532	JHP0481	23	87
737	hypothetical protein	HP0427	JHP0952	14	3
738	hypothetical protein	HP1408	JHP1300	15	4
866	hypothetical protein	HP1115	JHP1042	20	33
1021	cag pathogenicity island protein (cag13)	HP0534	JHP0482	60	225
1090	hypothetical protein	HP1516	NAH	593	34
1129	hypothetical protein	HP0611	JHP0299	230	37
1256	secreted protein involved in flagellar motility	HP1192	JHP1117	410	13
1338	hypothetical protein	HP0345	NAH	249	46
1432	histidine and glutamine-rich metal-binding protein	HP1432	JHP1321	46	9
1449	histidine-rich, metal binding polypeptide (hpn)	HP1427	NAH	39	26
1548	hypothetical protein	HP0756	JHP0693	24	71

* probably frame shifted components of the same vacA related gene
Genes with > 2 SD divergence in each analysis are indicated in bold
NAH indicates No Annotated Homologue in the other sequence

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ISSN: 1471-2164

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