Supplementary table 1

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Table 1: Contingency table for the distribution of replication-related effects on the GC-skew and AT-skew in Bacteria and Archaea. The columns of the table indicate the sign of the nucleotide skews on the leading strand, induced by the replication mechanism. For instance, G > C means that the leading strand is enriched in G over C, thus the sign of the GC-skew on the leading strand is positive, while G = C means that no significant effect of replication on the GC-skew could be detected. The cells of the table contain the number of chromosomes that we found to present the respective GC-skew and AT-skew signs on the leading strand.

Table 1
	G>C A>T	G>C A=T	G>C A<T	G=C A>T	G=C A=T	G=C A<T	G<C A>T	G<C A=T	G<C A<T
All Bacteria	33	73	205	1	33	13	1	1	0
Acidobacteria	0	0	0	0	1	0	0	0	0
Actinobacteria	0	2	12	1	2	3	1	1	0
Aquificales	0	0	0	0	1	0	0	0	0
Bacteroidetes	0	2	4	0	0	0	0	0	0
Chlorobi	0	0	3	0	0	0	0	0	0
Chlamydiae	1	2	8	0	0	0	0	0	0
Chloroflexi	0	0	2	0	0	0	0	0	0
Cyanobacteria	0	0	9	0	7	1	0	0	0
Deinococcus Thermus	0	0	1	0	1	3	0	0	0
Firmicutes Bacilli	27	27	4	0	0	0	0	0	0
Firmicutes Clostridia	3	2	2	0	0	0	0	0	0
Firmicutes Mollicutes	0	3	1	0	10	2	0	0	0
Fusobacteria	1	0	0	0	0	0	0	0	0
Nitrospirae	0	0	0	0	0	0	0	0	0
Planctomycetes	0	0	1	0	0	0	0	0	0
α Proteobacteria	0	6	42	0	5	2	0	0	0
β Proteobacteria	0	1	36	0	0	0	0	0	0
δ Proteobacteria	0	1	10	0	0	0	0	0	0
є Proteobacteria	0	3	6	0	0	0	0	0	0
γ Proteobacteria	1	22	57	0	6	2	0	0	0
Spirochaetes	0	1	7	0	0	0	0	0	0
Thermotogae	0	1	0	0	0	0	0	0	0
All Archaea	0	4	6	0	11	6	0	1	1
Crenarchaeota Thermoprotei	0	0	0	0	5	0	0	0	0
Euryarchaeota Archaeoglobi	0	0	0	0	1	0	0	0	0
Euryarchaeota Halobacteria	0	0	0	0	2	1	0	1	1
Euryarchaeota Methanobacteria	0	1	0	0	1	0	0	0	0
Euryarchaeota Methanomicrobia	0	0	3	0	0	2	0	0	0
Euryarchaeota Methanococci	0	1	1	0	0	0	0	0	0
Euryarchaeota Methanopyri	0	0	0	0	0	1	0	0	0
Euryarchaeota Thermoplasmata	0	1	1	0	1	0	0	0	0
Euryarchaeota Thermococci	0	1	1	0	0	2	0	0	0
Nanoarchaeota Nanoarchaeum	0	0	0	0	1	0	0	0	0

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Supplementary table 2

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Table 2: Comparison between our approach and the methods proposed by Tillier and Collins, 2000 and Lobry and Sueoka, 2002, for 173 chromosomes for which we have performed significance computations. Cases where the p-values are not available for these two methods correspond to chromosomes where the origin and terminus could not be determined with certainty.

	species	accession	AT	T&C, 2000	L&S, 2002	GC	T&C, 2000	L& S, 2002
1	A. bacterium El	NC_008009	0	1	1	0	1	1
2	A. sp ADP1	NC_005966	0	1	1	1	1	1
3	A. pernix	NC_000854	0	NA	NA	0	NA	NA
4	A. tumefaciens	NC_003062	1	1	1	1	1	1
5	A. tumefaciens	NC_003063	1	1	1	1	1	1
6	A. variabilis A	NC_007413	0	0	0	0	0	0
7	A. dehalogenans	NC_007760	0	0	0	1	0	1
8	A. marginale St	NC_004842	1	1	1	1	1	1
9	A. aeolicus	NC_000918	0	0	0	0	0	0
10	A. fulgidus	NC_000917	0	NA	NA	0	NA	NA
11	A. yellows witc	NC_007716	1	1	1	1	1	1
12	A. sp EbN1	NC_006513	1	1	1	1	1	1
13	B. anthracis Am	NC_003997	1	1	1	1	1	1
14	B. fragilis NCT	NC_003228	1	1	1	1	1	1
15	B. henselae Hou	NC_005956	1	1	1	1	1	1
16	B. cicadellinic	NC_007984	0	NA	NA	0	NA	NA
17	B. bacteriovoru	NC_005363	1	1	1	1	1	1
18	B. longum	NC_004307	0	1	1	0	1	1
19	B. bronchisepti	NC_002927	1	1	1	1	1	1
20	B. burgdorferi	NC_001318	1	1	1	1	1	1
21	B. japonicum	NC_004463	1	1	1	1	1	1
22	B. abortus 9-94	NC_006932	1	1	1	1	1	1
23	B. abortus 9-94	NC_006933	1	1	1	1	1	1
24	B. aphidicola	NC_004545	1	1	1	1	1	1
25	B. 383	NC_007509	1	1	1	1	1	1
26	B. 383	NC_007510	1	1	1	1	1	1
27	B. 383	NC_007511	1	1	1	1	1	1
28	C. jejuni	NC_002163	1	1	1	1	1	1
29	C. Blochmannia	NC_005061	1	1	1	1	1	1
30	C. hydrogenofor	NC_007503	0	0	0	1	0	1
31	C. crescentus	NC_002696	1	1	1	1	1	1
32	C. muridarum	NC_002620	1	1	1	1	1	1
33	C. abortus S26	NC_004552	1	1	1	1	1	1
34	C. chlorochroma	NC_007514	1	1	1	1	1	1
35	C. violaceum	NC_005085	1	1	1	1	1	1
36	C. salexigens D	NC_007963	1	1	1	1	1	1
37	C. acetobutylic	NC_003030	1	1	1	1	1	1
38	C. psychrerythr	NC_003910	1	1	1	1	1	1
39	C. diphtheriae	NC_002935	1	1	1	1	1	1
40	C. burnetii	NC_002971	0	1	1	1	1	1
41	C. bacterium Ye	NC_007775	0	0	0	0	0	0
42	D. aromatica RC	NC_007298	1	1	1	1	1	1
43	D. CBDB1	NC_007356	1	1	1	1	1	1
44	D. geothermalis	NC_008025	1	1	1	1	1	1
45	D. hafniense Y5	NC_007907	0	0	0	1	0	1
46	D. psychrophila	NC_006138	1	1	1	1	1	1
47	D. desulfurican	NC_007519	1	1	1	1	1	1
48	E. canis Jake	NC_007354	1	1	1	1	1	1
49	E. faecalis V58	NC_004668	1	1	1	1	1	1
50	E. carotovora a	NC_004547	1	1	1	1	1	1
51	E. litoralis HT	NC_007722	1	1	1	1	1	1
52	E. coli 536	NC_008253	0	1	1	1	1	1
53	F. tularensis h	NC_007880	1	1	1	1	1	1
54	F. CcI3	NC_007777	1	1	1	1	1	1
55	F. nucleatum	NC_003454	1	1	1	1	1	1
56	G. kaustophilus	NC_006510	1	1	1	1	1	1
57	G. metallireduc	NC_007517	1	1	1	1	1	1
58	G. violaceus	NC_005125	0	NA	NA	0	NA	NA
59	G. oxydans 621H	NC_006677	1	1	1	1	1	1
60	H. ducreyi 3500	NC_002940	1	1	1	1	1	1
61	H. chejuensis K	NC_007645	1	1	1	1	1	1
62	H. marismortui	NC_006396	1	1	1	0	1	1
63	H. marismortui	NC_006397	0	NA	NA	0	NA	NA
64	H. sp	NC_002607	0	NA	NA	1	NA	NA
65	H. walsbyi	NC_008212	0	NA	NA	0	NA	NA
66	H. acinonychis	NC_008229	0	0	1	1	0	1
67	I. loihiensis L	NC_006512	0	1	1	1	1	1
68	J. CCS1	NC_007802	1	1	1	1	1	1
69	L. acidophilus	NC_006814	0	0	0	1	0	1
70	C. hutchinsonii	NC_008255	0	1	0	1	1	1
71	L. lactis	NC_002662	1	1	1	1	1	1
72	L. intracellula	NC_008011	1	1	1	1	1	1
73	L. pneumophila	NC_006369	1	1	1	1	1	1
74	L. xyli xyli CT	NC_006087	1	1	1	1	1	1
75	L. interrogans	NC_005823	1	1	1	1	1	1
76	L. interrogans	NC_005824	0	1	1	1	1	1
77	L. innocua	NC_003212	1	1	1	1	1	1
78	M. magneticum A	NC_007626	1	1	1	1	1	1
79	M. succinicipro	NC_006300	1	1	1	1	1	1
80	M. florum L1	NC_006055	0	1	1	0	1	0
81	M. BNC1	NC_008254	1	1	1	0	1	1
82	M. thermoautotr	NC_000916	0	1	1	0	1	1
83	M. burtonii DSM	NC_007955	1	1	1	1	1	1
84	M. jannaschii	NC_000909	0	0	0	1	0	0
85	M. kandleri	NC_003551	1	1	1	0	1	0
86	M. acetivorans	NC_003552	1	1	1	1	1	1
87	M. stadtmanae	NC_007681	0	0	1	1	0	1
88	M. hungatei JF-	NC_007796	1	1	1	1	1	1
89	M. flagellatus	NC_007947	1	1	1	1	1	1
90	M. capsulatus B	NC_002977	1	1	1	1	1	1
91	M. thermoacetic	NC_007644	1	0	1	1	0	1
92	M. MCS	NC_008146	1	1	1	1	1	1
93	M. capricolum A	NC_007633	0	0	0	0	0	1
94	M. xanthus DK 1	NC_008095	1	1	1	1	1	1
95	N. equitans	NC_005213	0	NA	NA	0	NA	NA
96	N. pharaonis	NC_007426	1	1	1	1	1	1
97	N. gonorrhoeae	NC_002946	1	1	1	1	1	1
98	N. sennetsu Miy	NC_007798	1	1	1	1	1	1
99	N. hamburgensis	NC_007964	1	1	1	1	1	1
100	N. oceani ATCC	NC_007484	1	1	1	1	1	1
101	N. europaea	NC_004757	1	1	1	1	1	1
102	N. multiformis	NC_007614	1	1	1	1	1	1
103	N. farcinica IF	NC_006361	0	NA	NA	0	NA	NA
104	N. sp	NC_003272	0	0	0	0	0	0
105	N. aromaticivor	NC_007794	1	1	1	1	1	1
106	O. iheyensis	NC_004193	1	1	1	1	1	1
107	O. yellows phyt	NC_005303	1	1	1	0	1	1
108	P. sp UWE25	NC_005861	1	1	1	1	1	1
109	P. multocida	NC_002663	1	1	1	1	1	1
110	P. carbinolicus	NC_007498	1	1	1	1	1	1
111	P. luteolum DSM	NC_007512	1	1	1	1	1	1
112	P. profundum SS	NC_006370	1	1	1	1	1	1
113	P. profundum SS	NC_006371	1	1	1	1	1	1
114	P. luminescens	NC_005126	1	1	1	1	1	1
115	P. torridus DSM	NC_005877	0	NA	NA	0	NA	NA
116	P. sp	NC_005027	1	1	1	1	1	1
117	P. JS666	NC_007948	1	1	1	1	1	1
118	P. gingivalis W	NC_002950	1	1	1	1	1	1
119	P. marinus CCMP	NC_005042	1	1	1	1	1	1
120	P. acnes KPA171	NC_006085	1	1	1	1	1	1
121	P. atlantica T6	NC_008228	1	1	1	1	1	1
122	P. aeruginosa	NC_002516	1	1	1	1	1	1
123	P. arcticum 273	NC_007204	0	0	1	1	0	1
124	P. aerophilum	NC_003364	0	NA	NA	0	NA	NA
125	P. abyssi	NC_000868	1	1	1	1	1	1
126	R. eutropha JMP	NC_007347	1	1	1	1	1	1
127	R. eutropha JMP	NC_007348	1	1	1	1	1	1
128	R. etli CFN 42	NC_007761	0	NA	NA	0	NA	NA
129	R. sphaeroides	NC_007493	0	1	1	1	1	1
130	R. sphaeroides	NC_007494	0	NA	NA	0	NA	NA
131	R. ferrireducen	NC_007908	1	1	1	1	1	1
132	R. palustris Bi	NC_007925	1	1	1	1	1	1
133	R. rubrum ATCC	NC_007643	1	1	1	1	1	1
134	R. bellii RML36	NC_007940	0	1	0	1	1	1
135	R. denitrifican	NC_008209	1	1	1	1	1	1
136	R. xylanophilus	NC_008148	1	1	1	1	1	1
137	S. degradans 2-	NC_007912	1	1	1	1	1	1
138	S. ruber DSM 13	NC_007677	0	0	1	1	0	1
139	S. enterica Cho	NC_006905	0	1	1	1	1	1
140	S. denitrifican	NC_007954	1	1	1	1	1	1
141	S. boydii Sb227	NC_007613	0	1	0	0	1	1
142	S. TM1040	NC_008044	1	1	1	1	1	1
143	S. meliloti	NC_003047	1	1	1	1	1	1
144	S. glossinidius	NC_007712	1	1	1	1	1	1
145	S. alaskensis R	NC_008048	1	1	1	1	1	1
146	S. aureus COL	NC_002951	1	1	1	1	1	1
147	S. agalactiae 2	NC_004116	0	0	0	1	0	1
148	S. avermitilis	NC_003155	1	1	0	0	1	1
149	S. acidocaldari	NC_007181	0	NA	NA	0	NA	NA
150	S. thermophilum	NC_006177	1	1	1	1	1	1
151	S. CC9605	NC_007516	1	1	1	1	1	1
152	S. PCC6803	NC_000911	0	0	0	0	0	0
153	S. aciditrophic	NC_007759	1	1	1	1	1	1
154	T. tengcongensi	NC_003869	1	1	1	1	1	1
155	T. fusca YX	NC_007333	1	1	1	1	1	1
156	T. kodakaraensi	NC_006624	1	1	1	0	1	0
157	T. acidophilum	NC_002578	0	1	1	1	1	1
158	T. elongatus	NC_004113	0	0	0	0	0	1
159	T. maritima	NC_000853	0	1	1	1	1	1
160	T. thermophilus	NC_005835	1	1	1	0	1	1
161	T. denitrifican	NC_007404	1	1	1	1	1	1
162	T. crunogena XC	NC_007520	1	1	1	1	1	1
163	T. denticola AT	NC_002967	1	1	1	1	1	1
164	T. whipplei TW0	NC_004551	1	1	1	0	1	0
165	U. urealyticum	NC_002162	0	0	0	1	0	1
166	V. cholerae	NC_002505	1	1	1	1	1	1
167	V. cholerae	NC_002506	1	1	1	1	1	1
168	W. brevipalpis	NC_004344	0	NA	NA	0	NA	NA
169	W. endosymbiont	NC_006833	0	NA	NA	0	NA	NA
170	W. succinogenes	NC_005090	1	1	1	1	1	1
171	X. campestris	NC_003902	1	1	1	1	1	1
172	X. fastidiosa	NC_002488	1	1	1	1	1	1
173	Y. pestis Antiq	NC_008150	1	1	1	1	1	1
174	Z. mobilis ZM4	NC_006526	0	1	1	0	1	1

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Supplementary figure 1

Figure 1:

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Figure 1: Results from simulations where the effect of replication is constant (r=0.1), the standard variation of the nucleotide skews is constant for both groups of genes (sd=0.01), the breakpoint location is constant (fr=0.25), and the coding sequence related effects (m) vary. The y-axis represents the distance between the real and the estimated breakpoints.

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Supplementary figure 2

Figure 2:

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Figure 2: Results from simulations where the coding-sequence related effect is constant (m=0.1), the standard variation of the nucleotide skews is constant for both groups of genes (sd=0.01), the breakpoint location is constant (fr=0.25), and the replication effect (r) varies. The y-axis represents the distance between the real and the estimated breakpoints.

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Supplementary figure 3

Figure 3:

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Figure 3: Results from simulations where the replication and the coding-sequence related effects are constant (m=2.0 and r=0.1), the standard variation of the nucleotide skews is constant for both groups of genes (sd=0.01), but the position of the breakpoint (fr) varies. The y-axis represents the distance between the real and the estimated breakpoints.

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Supplementary figure 4

Figure 4:

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Figure 4: Results from simulations where the effect of replication is constant (r=0.01 for the first graph and r=0.1 for the second graph), the coding sequence related effect is constant (m=2.0), the breakpoint location is constant (fr=0.25) and the standard variation of the nucleotide skews varies. The y-axis represents the distance between the real and the estimated breakpoints.

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