Table 4. Summary of gene classes that are over-represented in repeat regions (i.e., the 2000 bp flanking predicted transposable elements).

	TE repeat content (%)	Over-representation of gene classes in repeat regions
		Small secreted proteins	All secreted proteins	Secondary metabolism	Expanded orphan multi-gene families
Alternaria brassicicola	5.58			•
Baudoinia compniacensis	0.4
Cladosporium fulvum	44.24
Cochliobolus heterostrophus C5	7.77	•	•		•
Cochliobolus heterostrophus C4 (*)	0
Cochliobolus sativus	5.44	•		•	•
Dothistroma septosporum	0.67
Hysterium pulicare (*)	0.57
Leptosphaeria maculans	30.93	•	•	•	•
Mycosphaerella fijiensis	38.97		•
Mycosphaerella graminicola	11.66	•			•
Mycosphaerella populicola	20.81			•
Mycosphaerella populorum	3.56	•	•		•
Pyrenophora tritici-repentis	11.44	•	•	•	•
Pyrenophora teres f. teres (*)	1.98				•
Rhytidhysteron rufulum (*)	0.18
Setosphaeria turcica	11.16	•	•	•	•
Stagonospora nodorum	2.37		•		•

See also Table S27 for more information. Genomes labeled with an asterisk (*) have been sequenced exclusively using Illumina technology.