Table 1.

List of genome sequences used in this study^a

Species	Reference collection/Isolate number	Assembly Size (Mbp)	Number of gene models	Genome accession number	Reference
Dothideomycetes
Botryosphaeriales
Botryosphaeria kuwatsukai	LW030101	47.39	11,278	MDSR01000000	[35, 51]
Botryosphaeria dothidea	CMW8000	43.50	11,368	http://genome.jgi.doe.gov/Botdo1_1/Botdo1_1.home.html	[36]
Diplodia corticola	CBS112549	34.99	9376	MNUE01000001	[30]
Diplodia sapinea	CBS117911	36.05	9589	AXCF00000000	[52]
	CBS138184	35.24	9386	JHUM00000000	[52]
Diplodia scrobiculata	CBS139796	34.93	9204	LAEG00000000	[53]
Diplodia seriata	UCDDS831	37.12	9759	MSZU00000000	[32]
	F98.1	37.27	9832	LAQI00000000	[37]
Eutiarosporella darliae	2G6	27.27	7904	GFXH01000000	[27]
Eutiarosporella pseudodarliae	V4B6	26.74	7846	GFXI01000000	[27]
Eutiarosporella tritici-australis	153	26.59	7783	GFXG01000000	[27]
Lasiodiplodia gonubiensis	CBS115812	41.14	10,649	RHKH00000000	Present study
Lasiodiplodia pseudotheobromae	CBS116459	43.01	10,964	RHKG00000000	Present study
Lasiodiplodia theobromae	CBS164.96	42.97	10,961	RHKF00000000	Present study
	CSS01	43.28	11,017	RHKB00000000	[49]
Macrophomina phaseolina	MS6	48.88	10,799	AHHD00000000	[34]
Neofusicoccum cordaticola	CBS123634	45.71	12,822	RHKC00000000	Present study
	CBS123638	43.56	12,630	RHKD00000000	Present study
Neofusicoccum kwambonambiense	CBS123639	44.17	12,839	RHKE00000000	Present study
	CBS123642	44.21	12,904	RKSS00000000	Present study
Neofusicoccum parvum	CMW9080	41.41	12,870	RHJX00000000	Present study
	CBS123649	42.16	12,453	RHJY00000000	Present study
	UCRNP2	42.52	12,691	AORE00000000	[33]
Neofusicoccum ribis	CBS115475	43.18	12,708	RHJZ00000000	Present study
	CBS121.26	43.12	12,733	RHKA00000000	Present study
Neofusicoccum umdonicola	CBS123644	42.29	12,816	RHKB00000000	Present study
Capnodiales
Acidomyces richmondensis	meta	26.82	10,338	JOOL00000000	[54]
Baudoinia panamericana	UAMH 10762	21.88	10,508	AEIF00000000	[4]
Cercospora berteroae	CBS538.71	33.89	11,903	PNEN00000000	[55]
Cercospora beticola	09–40	37.06	12,463	LKMD00000000	[55]
Cercospora zeina	CMW25467	40.76	10,193	MVDW00000000	[56]
Dothistroma septosporum	NZE10	30.21	12,415	AIEN00000000	[4]
Pseudocercospora eumusae	CBS 114824	47.12	12,632	LFZN01000000	[57]
Pseudocercospora fijiensis	CIRAD86	29.98	13,066	AIHZ00000000	[4]
Pseudocercospora musae	CBS 116634	60.44	13,129	LFZO00000000	[57]
Ramularia collo-cygni	URUG2	32.25	11,612	FJUY00000000	[58]
Sphaerulina musiva	SO2202	29.35	10,233	AEFD00000000	[4]
Zymoseptoria tritici	IPO323	39.69	10,963	ACPE00000000	[59]
Dothideales
Aureobasidium namibiae	CBS 147.97	25.43	10,259	AYEM00000000	[60]
Aureobasidium subglaciale	EXF-2481	25.80	10,792	AYYB00000000	[60]
Hysteriales
Hysterium pulicare	CBS 123377	38.43	12,352	AJFK00000000	[4]
Rhytidhysteron rufulum	CBS 306.38	40.18	12,117	AJFL00000000	[4]
Myriangiales
Elsinoe australis	NL1	23.34	9223	NHZQ00000000	[7]
Mytilinidiales
Lepidopterella palustris	CBS 459.81	45.67	13,861	LKAR00000000	[61]
Pleosporales
Alternaria alternata	SRC1lrK2f	32.99	13,466	LXPP00000000	[62]
Ascochyta rabiei	ArDII	34.66	10,596	JYNV00000000	[63]
Bipolaris maydis	ATCC 48331	32.93	12,705	AIHU00000000	[4]
Bipolaris oryzae	ATCC 44560	31.36	12,002	AMCO00000000	[64]
Bipolaris sorokiniana	ATCC 44560	34.41	12,214	AEIN00000000	[64]
Bipolaris victoriae	FI3	32.83	12,882	AMCY00000000	[64]
Bipolaris zeicola	26-R− 13	31.27	12,853	AMCN00000000	[64]
Clohesyomyces aquaticus	CBS 115471	49.68	15,811	MCFA00000000	[65]
Corynespora cassiicola	CCP	44.85	17,158	NSJI00000000	[66]
Epicoccum nigrum	ICMP 19927	34.74	12,025	NCTX00000000	[67]
Exserohilum turcicum	Et28A	43.01	11,698	AIHT00000000	[4]
Leptosphaeria maculans	JN3	45.12	12,469	FP929064:FP929139	[12]
Paraphaeosphaeria sporulosa	AP3s5-JAC2a	38.46	14,734	LXPO00000000	[62]
Parastagonospora nodorum	SN15	37.21	15,994	AAGI00000000	[68]
Periconia macrospinosa	DSE2036	54.99	18,735	PCYO00000000	[69]
Pyrenophora tritici-repentis	Pt-1C-BFP	38.00	12,169	AAXI00000000	[70]
Stemphylium lycopersici	CIDEFI 216	35.17	8997	LGLR00000000	[71]
Venturiales
Verruconis gallopava	CBS 43764	31.78	11,357	JYBX00000000	[72]
incertae sedis
Cenococcum geophilum	1.58	177.56	14,709	LKKR00000000	[61]
Coniosporium apollinis	CBS 100218	28.65	9308	AJKL00000000	[72]
Glonium stellatum	CBS 207.34	40.52	14,277	LKAO00000000	[61]
Eurotiomycetes
Eurotiales
Aspergillus nidulans	FGSC A4	30.28	9556	AACD00000000	[73]

^aEntries in boldface represent genomes that were sequenced as part of the present study