The pangenome of the wheat pathogen Pyrenophora tritici-repentis reveals novel transposons associated with necrotrophic effectors ToxA and ToxB

Gourlie, Ryan; McDonald, Megan; Hafez, Mohamed; Ortega-Polo, Rodrigo; Low, Kristin E.; Abbott, D. Wade; Strelkov, Stephen E.; Daayf, Fouad; Aboukhaddour, Reem

doi:10.1186/s12915-022-01433-w

Table 1 Summary statistics for 40 isolates of Pyrenophora tritici-repentis sequenced with Illumina HiSeq X and assembled with Shovill/SPAdes, and two isolates sequenced with PacBio and assembled with Flye/Pilon (table is sorted by race then isolate name)

From: The pangenome of the wheat pathogen Pyrenophora tritici-repentis reveals novel transposons associated with necrotrophic effectors ToxA and ToxB

Isolate	Race	NE	Year	Location^a	Host	Size (MB)	Contigs	GC	TE	N50	Genes	BUSCO	Accessory
Isolate	Race	NE	Year	Location^a	Host	Size (MB)	Contigs	(%)	(%)	(kbp)	Genes	(%)	(%)
ASC1	1	AC	1985	Manitoba	T. aestivum	34.78	6495	50.9	6.9	65.5	13,124	99.3	22.5
I-33–1	1	AC	2001	Azerbaijan	T. aestivum	35.06	6850	50.9	6.9	75.2	13,055	99.5	22.1
L3-1	1	AC	2016	Alberta	T. durum	34.93	6666	50.9	6.9	77.2	13,115	99.4	22.4
L4-1	1	AC	2016	Alberta	T. durum	34.74	6361	50.9	6.9	72.4	13,063	99.6	22.1
SW20-7	1	AC	2016	Saskatchewan	T. durum	35	6568	50.9	7.2	76.2	13,116	99.4	22.5
SW2-1	1	AC	2016	Saskatchewan	T. durum	35.11	6789	50.9	6.9	74.3	13,116	99.7	21.3
SW21-1	1	AC	2016	Saskatchewan	T. durum	34.62	6282	50.9	6.8	74.3	12,965	99.4	21.6
SW21-7	1	AC	2016	Saskatchewan	T. durum	34.97	6741	50.9	7	74.7	13,126	99.4	22.5
SW21-8	1	AC	2016	Saskatchewan	T. durum	34.96	6631	50.9	6.9	75	13,073	99.4	22.2
SW7-5	1	AC	2016	Saskatchewan	T. durum	35.65	6701	50.8	6.9	73.7	13,490	99.6	24.6
86–124	2	A	1986	Manitoba	T. aestivum	34.9	6832	50.9	6.9	60.7	13,209	99.2	23
AB88-2	2	A	2010	Alberta	T. aestivum	34.83	6465	50.9	6.9	75.3	13,126	99.5	22.5
L2-1	2	A	2016	Alberta	T. durum	34.96	6923	50.9	7.1	72.9	13,130	99.4	22.5
SW1-2	2	A	2016	Saskatchewan	T. durum	35.08	6599	50.9	7.1	71.2	13,365	99.4	24
SW15-1	2	A	2016	Saskatchewan	T. durum	34.83	6272	50.9	6.6	78.8	13,201	99.7	22.9
T132-2	2	A	2017	Tunisia	T. durum	34.41	6472	50.9	6.8	57.1	12,935	99.4	21.3
331–2	3	C	1985	Manitoba	Triticum sp.	34.44	6828	51	6.9	55.6	12,909	99.5	21.2
D308	3	C	1985	Manitoba	T. aestivum	34.33	6809	51	6.8	58.5	12,826	99.1	N/A^c
D308^b	3	C	1985	Manitoba	T. aestivum	39.6	70	50.8	18.6	3667	12,501	99.6	18.7
I-72–1	3	C	2001	Syria	Triticum sp.	34.35	6734	51	6.8	58.6	13,011	99.5	21.8
I-72–7	3	C	2001	Syria	Triticum sp.	34.35	6696	51	7	58.9	12,901	99.4	21.2
SC29-1	3	C	1999	Saskatchewan	T. durum	34.19	6464	51	6.8	59	12,951	99.5	21.5
SW21-5	3	C	2016	Saskatchewan	T. durum	34.66	6619	51	7.2	63.5	13,029	99.5	22
90–2	4	Absent	1990	Canada	T. aestivum	35.22	3818	50.8	7.2	225.9	12,909	99.5	21.3
G9-4	4	Absent	2016	Alberta	wild grass	36.97	8035	50.7	9.8	78.2	13,148	98.7	23
T126-1	4	Absent	2017	Tunisia	T. durum	34.15	6373	51	6.5	62.4	12,837	99.6	20.6
92-171R5	5	B	1992	Saskatchewan	T. aestivum	36.81	14,647	51.1	10.2	45.1	13,393	99.3	24.1
Alg3-24	5	B	1993	Algeria	T. durum	34.3	6098	50.9	6.6	73.6	12,900	99.6	21.1
Alg4x-1	5	B	1993	Algeria	T. durum	35.71	8072	50.9	7.5	71	13,193	99.4	22.9
I-17–2	5	B	2001	Azerbaijan	T. durum	34.25	6555	51	7	62.5	12,820	99.6	20.7
I-34–5	5	B	2001	Azerbaijan	Triticum sp.	34.29	6315	51	6.8	61.9	12,841	99.6	20.8
I-35–56	5	B	2001	Azerbaijan	T. durum	34.24	6516	51	6.9	62.6	12,918	99.5	21.3
I-36–1	5	B	2001	Azerbaijan	T. durum	34.36	6467	50.9	6.7	62.4	12,881	99.5	21
AlgH1	6	BC	1993	Algeria	T. durum	34.74	6902	51	6.9	61.7	13,159	99.3	22.7
AZ35-5	7	AB	2001	Azerbaijan	T. durum	35.3	7165	50.9	7.1	72.1	13,239	99.5	23.2
T176-2	7	AB	2017	Tunisia	T. aestivum	34.7	6896	50.9	7.3	57.1	13,141	99.5	22.6
T181-1	7	AB	2017	Tunisia	T. durum	34.78	6718	51.2	6.5	57.5	13,583	99.4	25.1
I-34–1	8	ABC	2001	Azerbaijan	T. durum	34.38	6405	50.9	6.6	64.5	13,036	99.5	22
I-35–18	8	ABC	2001	Azerbaijan	T. durum	34.85	6698	50.9	7	65.3	13,071	99.4	22.9
I-73–1	8	ABC	2001	Syria	T. aestivum	34.62	6619	50.9	6.8	63.4	12,941	99.5	N/A^c
I-73–1^b	8	ABC	2001	Syria	T. aestivum	39.9	39	50.8	18.3	3647	12,744	99.6	20
T128-1	Atypical	B	2017	Tunisia	T. durum	34.12	6095	51	6.4	59.1	13,002	99.6	21.7

NE Necrotrophic effector
^aAlberta, Saskatchewan, and Manitoba are provinces within Canada
^bLong-read assemblies
^cNot included in pangenome

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