Table 2 Identification of core (C), lineage specific (LS) and pathogen specific (PS) regions in the Fusarium oxysporum f. sp. cepae (Foc) isolate Fus2 genome, through alignment of Foc, F. oxysporum (Fo) and f. sp. lyccopersici (Fol) assemblies. The percentage of non-masked bp covered by aligned sequence is shown for each reference contig.

Alignment to Fus2 contig	Specificity	Foc	Foc	Foc	Fo	Fo	Fo	Fo	Fo	Fol
Alignment to Fus2 contig	Specificity	Fus2	125	A23	A13	A28	CB3	PG	Fo47	4287
1	C	100	99	99	96	98	97	98	98	90
2	C	100	99	99	92	97	96	97	98	93
3	C	100	98	99	95	93	96	94	95	92
4	C	99	98	98	91	95	93	78	93	88
5	C	100	99	99	92	94	94	96	94	92
6	C	100	98	98	94	97	97	97	96	92
7	C	100	98	99	89	95	94	93	93	85
8	C	100	98	99	93	93	93	97	96	93
9	C	99	97	97	89	93	94	95	90	85
10	LS + PS	99	88	87	15	12	11	9	6	24
11	C	99	93	95	80	92	89	88	82	63
12	C	100	98	99	85	89	88	96	94	83
13	C	100	96	97	88	92	91	92	91	88
14	LS	99	84	86	81	80	29	57	48	30
15	C	100	99	99	91	98	95	96	96	89
16	LS + PS	93	68	67	15	11	11	12	10	11
17	C	99	97	96	86	86	91	92	91	81
18	LS*	99	93	89	60	63	50	51	57	39
19	LS + PS	93	53	57	19	15	11	12	12	11
20	LS	98	86	88	87	85	15	10	9	9
21	LS + PS	91	61	60	9	9	6	4	6	7
22	LS	100	86	87	80	77	29	46	67	54

*Contig 18 was identified as non-PS LS, but later analysis showed synteny to FOL chromosome 12 and alignment of Fo raw sequencing reads across this region.

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