TABLE 3.

Identification of CDC regions in the A. alternata apple pathotype reference genome.

FERA 1166 contig	Length (bp)	A. gaisen	A. tenuissima								A. arborescens
		Pear	Apple				–				–
		FERA	FERA	FERA	FERA	FERA	FERA	FERA	FERA	FERA	FERA	RGR	RGR
		650	1166	635	743	1177	648	1082	1164	24350	675	97.0013	97.0016
1	3902980	32	49	26	40	60	53	21	28	36	34	35	26
2	3781932	31	49	26	40	58	51	20	29	35	33	34	26
3	3000390	33	50	26	40	59	53	21	28	36	34	35	26
4	2851745	32	49	27	41	59	53	21	28	36	34	36	27
5	2693844	33	49	27	40	60	53	21	29	36	34	36	27
6	2583941	33	50	27	40	60	53	21	29	36	34	36	27
7	2502671	33	49	26	40	59	52	21	28	36	34	35	26
8	2455819	32	49	27	40	60	52	21	29	35	33	35	26
9	2451092	32	49	26	40	59	52	20	28	35	33	35	26
10	2402550	31	49	26	40	58	51	21	28	35	32	34	25
11	2194253	32	49	26	40	59	52	21	28	35	34	35	26
12	1303685	33	49	27	40	59	53	21	28	36	34	36	27
13	767820	23	48	24	36	47	44	17	25	29	25	26	20
14 (CDC)	549494	0	81	29	79	115	0	23	33	0	0	0	0
15 (CDC)	435297	62	90	51	79	407	0	0	0	0	0	0	0
16	433285	23	48	26	40	53	51	18	28	33	26	27	20
17	391795	26	48	20	33	56	51	19	27	29	30	30	23
18 (CDC)	368761	0	49	22	40	32	0	0	0	0	0	0	0
19 (CDC)	225742	0	48	22	61	72	0	18	31	0	0	0	0
20 (CDC)	154051	0	69	20	45	214	0	0	0	0	0	0	0
21 (CDC)	143777	0	49	20	36	219	0	0	0	0	0	0	0
22	109256	25	50	20	30	50	35	14	22	30	26	27	22

Read depth is shown from illumina reads against each contig, by isolate. Contigs showing reductions in coverage from non-pathotype isolates were identified as regions of conditionally dispensable chromosomes (CDCs).