Table 2.

Collection details and GenBank accession numbers of taxa included in the phylogenetic analyses.

Taxon1	Culture2 and status3	GenBank accession number4					Reference
		ITS	tef1	tub2	cal	his3
Diaporthe sp. 5	CBS 125575	KC343207	KC343933	KC344175	KC343449	KC343691	Gomes et al. (2013)
D. acaciarum	CBS 138862T	KP004460	N/A	KP004509	N/A	KP004504	Crous et al. (2014a)
D. acaciigena	CBS 129521T	KC343005	KC343731	KC343973	KC343247	KC343489	Gomes et al. (2013)
D. acutispora	CGMCC 3.18285T	KX986764	KX999155	KX999195	KX999274	KX999235	Gao et al. (2017)
	LC 6142	KX986762	KX999153	KX999193	KX999272	KX999233	Gao et al. (2017)
D. amygdali	CBS 111811	KC343019	KC343745	KC343987	KC343261	KC343503	Gomes et al. (2013)
	CBS 115620	KC343020	KC343746	KC343988	KC343262	KC343504	Gomes et al. (2013)
	CBS 120840	KC343021	KC343747	KC343989	KC343263	KC343505	Gomes et al. (2013)
	CBS 126679ET	KC343022	KC343748	KC343990	KC343264	KC343506	Gomes et al. (2013)
	CDP 1442	PP577989	PP579314	PP579329	PP579345	N/A	This study
	CDP 1906	PP577990	PP579315	PP579330	PP579346	N/A	This study
	CDP 2029	PP577991	PP579316	PP579331	PP579347	N/A	This study
D. amygdali(syn. D. chongqingensis)	CGMCC 3.19603T	MK626916	MK654866	MK691321	MK691209	MK726257	Guo et al. (2020)
	PSCG 436	MK626917	MK654867	MK691322	MK691208	MK726256	Guo et al. (2020)
D. amygdali(syn. D. fusicola)	CGMCC 3.17087T	KF576281	KF576256	KF576305	KF576233	N/A	Gao et al. (2015)
	CGMCC 3.17088	KF576263	KF576238	KF576287	KF576221	N/A	Gao et al. (2015)
D. amygdali(syn. D. garethjonesii)	MFLUCC 12-0542aT	KT459423	KT459457	KT459441	KT459470	N/A	Hyde et al. (2016)
	MFLUCC 12-0542b	KT459424	KT459458	KT459442	KT459471	N/A	Hyde et al. (2016)
D. amygdali(syn. D. kadsurae)	CFCC 52586T	MH121521	MH121563	MH121600	MH121439	MH121479	Yang et al. (2018)
	CFCC 52587	MH121522	MH121564	MH121601	MH121440	MH121480	Yang et al. (2018)
D. amygdali(syn. D. mediterranea)	CBS 146754T	MT007489	MT006989	MT006686	MT006761	MT007095	León et al. (2020)
	DAL-6	MT007486	MT006986	MT006683	MT006758	MT007092	León et al. (2020)
D. amygdali(syn. D. nannuoshanensis)	SAUCC 194.86PT	MT822614	MT855926	MT855811	MT855693	MT855582	Huang et al. (2021a)
	SAUCC 194.91T	MT822619	MT855931	MT855816	MT855698	MT855587	Huang et al. (2021a)
D. amygdali(syn. D. ovoidea)	CGMCC 3.17092T	KF576264	KF576239	KF576288	KF576222	N/A	Gao et al. (2015)
	CGMCC 3.17093	KF576265	KF576240	KF576289	KF576223	N/A	Gao et al. (2015)
D. amygdali(syn. D. sinensis)	JZB 320167T	MW010224	MW205235	MW056016	MW205220	N/A	Manawasinghe et al. (2021)
	JZB 320168PT	MW010225	MW205236	MW056017	MW205221	N/A	Manawasinghe et al. (2021)
	JZB 320169PT	MW010226	MW205237	MW056018	MW205222	N/A	Manawasinghe et al. (2021)
D. amygdali(syn. D. sterilis)	CBS 136969T	KJ160579	KJ160611	KJ160528	KJ160548	MF418350	Lombard et al. (2014)
	CBS 136970	KJ160580	KJ160612	KJ160529	KJ160549	N/A	Lombard et al. (2014)
	CPC 20575	KJ160581	KJ160613	KJ160530	KJ160550	N/A	Lombard et al. (2014)
	MFLUCC 17-1011	KY964211	KY964167	KY964095	KY964126	N/A	Dissanayake et al. (2017)
D. amygdali(syn. Phomopsis ternstroemiae)	CGMCC 3.15183T	KC153098	KC153089	N/A	N/A	N/A	Gao et al. (2014)
	CGMCC 3.15184	KC153099	KC153090	N/A	N/A	N/A	Gao et al. (2014)
D. aseana	MFLUCC 12-0299aT	KT459414	KT459448	KT459432	KT459464	N/A	Hyde et al. (2016)
	MFLUCC 12-0299b	KT459415	KT459449	KT459433	KT459465	N/A	Hyde et al. (2016)
	MFLUCC 12-0299c	KT459416	KT459450	KT459434	KT459466	N/A	Hyde et al. (2016)
D. aseana(“D. hongkongensis”)	SM42	MN651488	MT077103	MT077085	N/A	N/A	Azuddin et al. (2021)
D. aseana(syn. D. tectonigena)	LC 6512	KX986782	KX999174	KX999215	KX999284	KX999254	Gao et al. (2017)
	MFLUCC 12-0767T	KU712429	KU749371	KU743976	KU749358	N/A	Gao et al. (2017)
D. asheicola	CBS 136967T	KJ160562	KJ160594	KJ160518	KJ160542	N/A	Lombardet al. (2014)
	CBS 136968	KJ160563	KJ160595	KJ160519	KJ160543	N/A	Lombardet al. (2014)
D. australafricana	CBS 111886T	KC343038	KC343764	KC344006	KC343280	KC343522	Gomes et al. (2013)
	CBS 113487	KC343039	KC343765	KC344007	KC343281	KC343523	Gomes et al. (2013)
D. batatas	CBS 122.21ET	KC343040	KC343766	KC344008	KC343282	KC343524	Gomes et al. (2013)
D. beckhausii	CBS 138.27	KC343041	KC343767	KC344009	KC343283	KC343525	Gomes et al. (2013)
D. beilharziae	BRIP 54792IT	JX862529	JX862535	KF170921	N/A	N/A	Tan et al. (2013)
D. brasiliensis	CBS 133183T	KC343042	KC343768	KC344010	KC343284	KC343526	Gomes et al. (2013)
	LGMF 926	KC343043	KC343769	KC344011	KC343285	KC343527	Gomes et al. (2013)
D. breyniae	CBS 148910T	ON400846	ON409188	ON409186	ON409189	ON409187	Matio Kemkuignou et al. (2022)
D. caatingaensis	CBS 141542T	KY085926	KY115603	KY115600	KY115597	KY115605	Crous et al. (2016a)
	URM 7483	KY085925	N/A	N/A	N/A	N/A	Crous et al. (2016a)
	URM 7484	KY085928	N/A	KY115602	KY115599	KY115606	Crous et al. (2016a)
	URM 7485	KY085927	KY115604	KY115601	KY115598	N/A	Crous et al. (2016a)
D. celticola	CFCC 53074T	MK573948	MK574623	MK574643	MK574587	MK574603	Cao et al. (2022)
	CFCC 53075	MK573949	MK574624	MK574644	MK574588	MK574604	Cao et al. (2022)
D. celtidis	MFLUCC 20-0180T	MW114346	MW192209	MW148266	N/A	N/A	Tennakoon et al. (2021)
	NCYUCC 19-0331PT	MW114347	MW192210	MW148267	N/A	N/A	Tennakoon et al. (2021)
D. cf.heveae1	CBS 852.97	KC343116	KC343842	KC344084	KC343358	KC343600	Gomes et al. (2013)
D. cha	SAUCC 1497PT	OM090761	OM131209	OM131210	OM131207	OM131208	Mu et al. (2022)
	SAUCC 1562T	MT199863	MT376682	MT376652	MT366912	MT376714	Mu et al. (2022)
D. cinerascens	CBS 719.96	KC343050	KC343776	KC344018	KC343292	KC343534	Gomes et al. (2013)
D. crousii	CAA 820	MK792300	MK828072	MK837923	MK883828	MK871441	Hilário et al. (2020)
	MUM 19.29T	MK792311	MK828081	MK837932	MK883835	MK871450	Hilário et al. (2020)
D. cynaroidis	CBS 122676T	KC343058	KC343784	KC344026	KC343300	KC343542	Marincowitz et al. (2008)
D. cynaroidis(syn. D. salicicola)	VPRI 32789T	JX862531	JX862537	KF170923	N/A	N/A	Tan et al. (2013)
D. cynaroidis(syn. D. subcylindrospora)	KUMCC 17-0151T	MG746629	MG746630	MG746631	N/A	N/A	Hyde et al. (2018)
D. cytosporella	AR 5148	KC843308	KC843117	KC843222	KC843142	N/A	Udayanga et al. (2014b)
	AR 5149	KC843309	KC843118	KC843223	KC843143	N/A	Udayanga et al. (2014b)
	CBS 137020ET	KC843307	KC843116	KC843221	KC843141	MF418283	Udayanga et al. (2014b)
D. cytosporella(“D. chamaeropis”)	CBS 454.81	KC343048	KC343774	KC344016	KC343290	KC343532	Gomes et al. (2013)
	CBS 753.70	KC343049	KC343775	KC344017	KC343291	KC343533	Gomes et al. (2013)
D. cytosporella(syn. D. pimpinellae)	JZB 320131T	MK874656	MT373074	MT373072	N/A	MT373073	Yuan et al. (2020)
D. diospyricola	CBS 136552T	KF777156	N/A	N/A	N/A	N/A	Crous et al. (2013)
D. elaeagni-glabrae	CGMCC 3.18287T	KX986779	KX999171	KX999212	KX999281	KX999251	Gao et al. (2017)
	LC 4806	KX986780	KX999172	KX999213	KX999282	KX999252	Gao et al. (2017)
D. eucommiae	SCHM 0020H	AY601921	N/A	N/A	N/A	N/A	Cao & Chi (1990)
D. eucommiae(syn. D. araliae-chinensis)	GUCC 412.17	OP581220	OP688525	OP688550	N/A	N/A	Hyde et al. (2023)
	GUCC 412.7T	OP581218	OP688523	OP688548	N/A	N/A	Hyde et al. (2023)
	GUCC 412.71	OP581219	OP688524	OP688549	N/A	N/A	Hyde et al. (2023)
D. eucommiae(syn. D. australiana)	BRIP 66145T	MN708222	MN696522	MN696530	N/A	N/A	Wrona et al. (2020)
	BRIP 66149	MN708225	MN696524	MN696533	N/A	N/A	Wrona et al. (2020)
D. eucommiae(syn. D. eucalyptorum)	CBS 132525T	JX069862	N/A	N/A	N/A	N/A	Crous et al. (2012)
	ZHKUCC 22-0044	ON322873	ON315035	ON315063	N/A	N/A	Luo et al. (2022)
	ZHKUCC 22-0045	ON322874	ON315036	ON315064	N/A	ON315006	Luo et al. (2022)
D. eucommiae(syn. D. fujianensis)	JZB 320149PT	MW010212	MW205231	MW056008	MW205212	N/A	Manawasinghe et al. (2021)
	JZB 320150T	MW010213	MW205232	MW056009	MW205213	N/A	Manawasinghe et al. (2021)
	JZB 320152PT	MW010215	MW205233	MW056011	MW205215	N/A	Manawasinghe et al. (2021)
D. eucommiae(syn. D. fusiformis)	JZB 320154T	MW010216	N/A	MW056012	MW205216	N/A	Manawasinghe et al. (2021)
	JZB 320156PT	MW010218	MW205234	MW056014	MW205218	N/A	Manawasinghe et al. (2021)
D. eucommiae(syn. D. globoostiolata)	MFLUCC 23-0025T	OQ600200	OQ603503	OQ678280	N/A	N/A	Monkai et al. (2023)
D. eucommiae(syn. D. hongkongensis)	CBS 115448T	KC343119	KC343845	KC344087	KC343361	KC343603	Gomes et al. (2013)
	LC 3079	KP267851	KP267925	KP293431	N/A	KP293505	Gomes et al. (2013)
D. eucommiae(syn. D. lagerstroemiae)	SCHM 3608H	AY622994	N/A	N/A	N/A	N/A	Chang et al. (2005a)
D. eucommiae(syn. D. lithocarpi)	CGMCC 3.15175T	KC153104	KC153095	KF576311	KF576236	N/A	Gao et al. (2014)
	CGMCC 3.17098	KF576276	KF576251	KF576300	KF576228	N/A	Gao et al. (2014)
D. eucommiae(syn. D. rhodomyrti)	CFCC 53101T	MK432643	MK578119	MK578046	MK442965	MK442990	Cao et al. (2022)
	CFCC 53102	MK432644	MK578120	MK578047	MK442966	MK442991	Cao et al. (2022)
D. eucommiae(syn. D. theobromatis)	SAUCC 102221T	MT199837	MT376656	MT376626	MT366885	MT376687	Dong et al. (2020)
D. eucommiae(syn. D. tuyouyouiae)	BRIP 75017aH	OQ917074	OQ889558	OQ889559	N/A	N/A	Tan & Shivas (2023)
D. eucommiae (syn. D. xylocarpi)	MFLU 17-2592	MN047099	MN077074	N/A	N/A	N/A	Dayarathne et al. 2020
	MFLUCC 17-0413T	MN047098	MN077073	N/A	N/A	N/A	Dayarathne et al. 2020
D. foeniculina	CBS 111553ET	KC843295	KC843104	KC843209	KC843129	KC343585	Udayanga et al. (2014b)
	CBS 111554	KC843296	KC843105	KC843210	KC843130	KC343586	Udayanga et al. (2014b)
	CBS 142547	MF418402	MF418481	MF418562	MF418236	MF418322	Guarnaccia & Crous (2017)
	CDP 0022	MT000992	MN990208	MN990209	N/A	N/A	Boonmee et al. (2021)
	CDP 0209	MT004913	MT011071	MT011077	N/A	N/A	Boonmee et al. (2021)
	CDP 0315	MT004914	MT011072	MT011078	N/A	N/A	Boonmee et al. (2021)
	CDP 1321	PP577994	PP579319	PP579334	N/A	N/A	This study
	CDP 1322	PP577995	N/A	N/A	N/A	N/A	This study
	CDP 1369	PP577996	N/A	N/A	N/A	N/A	This study
	CDP 1371	PP577997	N/A	N/A	N/A	N/A	This study
	CDP 1575	PP577998	PP579320	PP579335	N/A	N/A	This study
	CDP 1816	PP577999	N/A	N/A	N/A	N/A	This study
	CDP 1817	PP578000	PP579321	PP579336	N/A	N/A	This study
	CDP 1818	PP578001	N/A	N/A	N/A	N/A	This study
	CDP 1908	PP578002	PP579322	PP579337	N/A	N/A	This study
	CDP 1947	PP578003	PP579323	PP579338	N/A	N/A	This study
	CDP 2028	PP578004	N/A	N/A	N/A	N/A	This study
	CDP 2056	PP578005	PP579324	PP579339	N/A	N/A	This study
D. foeniculina(syn. D. baccae)	CBS 136972T	KJ160565	KJ160597	MF418509	MG281695	MF418264	Lombard et al. (2014)
	CBS 142546	MF418358	MF418437	MF418517	MF418192	MF418272	Lombard et al. (2014)
D. foeniculina(syn. D. neotheicola)	CBS 123208T	KC343104	KC343830	KC344072	KC343346	KC343588	Gomes et al. (2013)
	CBS 123209T	KC343105	KC343831	KC344073	KC343347	KC343589	Gomes et al. (2013)
D. foeniculina(syn. D. nigra)	JZB 320170T	MN653009	MN892277	MN887113	N/A	N/A	Hyde et al. (2020a)
D. foeniculina(syn. D. ravennica)	MFLUCC 15-0479T	KU900335	KX365197	KX432254	N/A	N/A	Thambugala et al. (2016)
	MFLUCC 17-1029	KY964191	KY964147	KY964075	N/A	N/A	Thambugala et al. (2016)
D. foeniculina(syn. D. rhoicola)	CBS 129528T	JF951146	KC843100	KC843205	KC843124	N/A	Crous et al. (2011a)
D. foeniculina(syn. D. rumicicola)	MFLUCC 18-0739	MH846233	MK049554	MK049555	N/A	N/A	Hyde et al. (2019)
	MFLUCC 18-1566T	MK066126	MK078545	MK078546	N/A	N/A	Hyde et al. (2019)
D. foeniculina(syn. D. theicola)	CBS 187.27ET/IT	KC343107	KC343833	KC344075	KC343349	KC343591	Gomes et al. (2013)
D. foeniculina(syn. D. zaobaisu)	CGMCC 3.19598T	MK626922	MK654855	MK691245	N/A	MK726207	Guo et al. (2020)
	PSCG 032	MK626923	MK654856	MK691246	N/A	MK726208	Guo et al. (2020)
D. foeniculina(syn. P californica)	CBS 135430ET	KC843301	KC843110	KC843215	KC843135	MF418284	Udayanga et al. (2014b)
D. forlicesenica	MFLUCC 17-1015T	KY964215	KY964171	KY964099	N/A	N/A	Dissanayake et al. (2017)
	MFLUCC 21-0011	MW677455	MW680161	MW680159	N/A	MW680160	Dissanayake et al. (2017)
D. ganjae	CBS 180.91T	KC343112	KC343838	KC344080	KC343354	KC343596	Gomes et al. (2013)
	PSCG 489	MK626955	MK654897	MK691287	MK691202	MK726204	Guo et al. (2020)
D. glabrae	SCHM 3622H	AY601918	N/A	N/A	N/A	N/A	Chang et al. (2005b)
D. glabrae(syn. D. alangii)	CFCC 52556T	MH121491	MH121533	MH121573	MH121415	MH121451	Yang et al. (2018)
	CFCC 52559	MH121494	MH121536	MH121576	MH121418	MH121454	Yang et al. (2018)
D. glabrae(syn. D. conferta)	SAUCC 194.16PT	MT822544	MT855858	MT855741	MT855629	MT855513	Dong et al. (2021a)
	SAUCC 194.9T	MT822537	MT855851	MT855734	MT855622	MT855506	Dong et al. (2021a)
D. glabrae(syn. D. hubeiensis)	JZB 320123T	MK335809	MK523570	MK500147	MK500235	N/A	Manawasinghe et al. (2019)
	JZB 320128	MK335814	MK523573	MK500152	MK500240	N/A	Manawasinghe et al. (2019)
D. glabrae(syn. D. tectonae)	MFLUCC 12-0777T	NR147590	KU749359	KU743977	KU749345	N/A	Doilom et al. (2016)
	MFLUCC 14-1139	KU712438	KU749366	KU743985	KU749353	N/A	Doilom et al. (2016)
	SM62	MN651493	MT077104	MT077086	N/A	N/A	Azuddin et al. (2021)
	SM63	MN651494	MT077105	MT077087	N/A	N/A	Azuddin et al. (2021)
D. glabrae(“D. tulliensis”)	NTUCC 18-154-1	MZ268412	MZ268475	MZ268433	MZ268454	MZ268496	Ariyawansa et al. (2021)
D. glabrae(syn. D. xishuangbannaensis)	SAUCC 194.29PT	MT822557	MT855870	MT855754	MT855641	MT855526	Dong et al. (2021a)
	SAUCC 194.30T	MT822558	MT855871	MT855755	MT855642	MT855527	Dong et al. (2021a)
D. hsinchuensis	NTUPPMCC 18-153-1T	MZ268409	MZ268472	MZ268430	MZ268451	MZ268493	Ariyawansa et al. (2021)
	NTUPPMCC 18-153-2	MZ268410	MZ268473	MZ268431	MZ268452	MZ268494	Ariyawansa et al. (2021)
	NTUPPMCC 18-153-3	MZ268411	MZ268474	MZ268432	MZ268453	MZ268495	Ariyawansa et al. (2021)
D. iberica	CECT 21218T	ON159902	ON398841	ON364049	ON398819	ON398819	Toghueo et al. (2023)
	S32	ON159892	ON398830	ON364039	ON364018	ON398809	Toghueo et al. (2023)
D. inconspicua	MFLUCC 10-0588	JQ619900	JX275417	JX275461	JX197452	N/A	Udayanga et al. (2012b)
	CBS 133813T	KC343123	KC343849	KC344091	KC343365	KC343607	Gomes et al. (2013)
	LGMF 922	KC343124	KC343850	KC344092	KC343366	KC343608	Gomes et al. (2013)
	LGMF 931	KC343125	KC343851	KC344093	KC343367	KC343609	Gomes et al. (2013)
	URM 7776	MG696772	MG710414	MG710395	MG710391	MG710410	Bezerra et al. (2018)
D. inconspicua(syn. D. lutescens)	SAUCC 194.36T	MT822564	MT855877	MT855761	MT855647	MT855533	Sun et al. (2021)
D. inconspicua(syn. D. pseudoinconspicua)	URM 7873	MH122535	MH122530	MH122521	MH122525	MH122518	Crous et al. (2018)
	URM 7874T	MH122538	MH122533	MH122524	MH122528	MH122517	Crous et al. (2018)
D. inconspicua(“D. pterocarpi”)	MFLUCC 10-0571ET	JQ619899	JX275416	JX275460	JX197451	N/A	Udayanga et al. (2012b)
	MFLUCC 10-0588	JQ619900	JX275417	JX275461	JX197452	N/A	Udayanga et al. (2012b)
D. inconspicua(syn. D. samaneae)	SDBR-CMU470T	OQ600197	OQ603500	OQ678277	OQ646880	OQ646884	Monkai et al. (2023)
D. infertilis	CBS 199.39	KC343051	KC343777	KC344019	KC343293	KC343535	Gomes et al.(2013)
	CBS 230.52T	KC343052	KC343778	KC344020	KC343294	KC343536	Gomes et al.(2013)
	CPC 20322	KC343053	KC343779	KC344021	KC343295	KC343537	Gomes et al.(2013)
D. isoberliniae	STMA 18245	OR348653	OR468813	OR468823	OR468833	OR468803	Lambert et al. (2023)
	STMA 18291	OR348654	OR468812	OR468822	OR468832	OR468802	Lambert et al. (2023)
D. isoberliniae(syn. D. pungensis)	SAUCC 194.112T	MT822640	MT855952	MT855837	MT855719	MT855607	Sun et al. (2021)
	SAUCC 194.89	MT822617	MT855929	MT855814	MT855696	MT855585	Sun et al. (2021)
D. lenispora	CGMCC 3.20101T	MT385952	MT424687	MT424707	MW022472	MW022493	Dissanayake et al. (2020)
	GZCC 19-0343PT	MT797182	MT793025	MT793036	MW022473	MW022494	Dissanayake et al. (2020)
D. leucospermi	CBS 111980T	JN712460	KY435632	KY435673	KY435663	KY435653	Crous et al. (2011b)
	CDP 0052	MT002843	MT011070	MT011076	MT011066	N/A	Boonmee et al. (2021)
	CDP 1211	PP578006	N/A	PP579340	PP579350	N/A	This study
	CDP 1251	PP578007	PP579325	PP579341	PP579351	N/A	This study
	CDP 2055	PP578008	PP579326	PP579342	N/A	N/A	This study
D. leucospermi(syn. D. infecunda)	CBS 133812T	KC343126	KC343852	KC344094	KC343368	KC343610	Gomes et al. (2013)
	CPC 20293	KC343129	KC343855	KC344097	KC343371	KC343613	Gomes et al. (2013)
	CPC 20309	KC343132	KC343858	KC344100	KC343374	KC343616	Gomes et al. (2013)
D. leucospermi(syn. D. pyracanthae)	CAA 487	KY435636	KY435626	KY435667	KY435657	KY435647	Santos et al. (2017b)
	CBS 142384T	KY435635	KY435625	KY435666	KY435656	KY435646	Santos et al. (2017b)
D. leucospermi (syn. D. rossmaniae)	CAA 763	MK792291	MK828064	MK837915	MK883823	MK871433	Hilário et al. (2020)
	MUM 19.30T	MK792290	MK828063	MK837914	MK883822	MK871432	Hilário et al. (2020)
D. longicolla	ATCC 60325T	KJ590728	KJ590767	KJ610883	KJ612124	KJ659188	Udayanga et al. (2015)
	CBS 116023	KC343198	KC343924	KC344166	KC343440	KC343682	Gomes et al. (2013)
	CBS 127267	KC343199	KC343925	KC344167	KC343441	KC343683	Gomes et al. (2013)
	CBS 659.78	KC343201	KC343927	KC344169	KC343443	KC343685	Gomes et al. (2013)
D. longicolla(syn. D. megabiguttulata)	ZHKUCC 22-0067T	ON322895	N/A	ON315085	ON315001	ON315025	Luo et al. (2022)
	ZHKUCC 22-0068PT	ON322896	ON315053	ON315086	N/A	ON315026	Luo et al. (2022)
D. longicolla(syn. D. unshiuensis)	CGMCC 3.17566T	KJ490584	KJ490463	KJ490405	N/A	KJ490526	Huang et al. (2015)
	PSCG 339	MK626928	MK654879	MK691300	MK691181	MK726188	Huang et al. (2015)
D. lusitanicae	CBS 123212	KC343136	KC343862	KC344104	KC343378	KC343620	Gomes et al. (2013)
	CBS 123213T	MH863280	KC343863	KC344105	KC343379	KC343621	Gomes et al. (2013)
D. melonis	CBS 507.78IT	KC343142	KC343868	KC344110	KC343384	KC343626	Gomes et al. (2013)
	FAU 640	KJ590702	KJ590741	KJ610858	KJ612099	KJ659184	Udayanga et al. (2015)
D. micheliae	SCHM 3603H	AY620820	N/A	N/A	N/A	N/A	Chang et al. (2005b)
D. micheliae (syn. D. australpacifica)	BRIP 60163dH	OM918688	OM960597	OM960615	N/A	N/A	Tan & Shivas (2022)
D. micheliae (syn. D. chimonanthi)	SCHM 3614H	AY622993	N/A	N/A	N/A	N/A	Chang et al. (2005a)
D. micheliae (syn. D. middletonii)	BRIP 54884eT	KJ197286	KJ197248	KJ197266	N/A	N/A	Thompson et al. (2015)
	BRIP 57329	KJ197285	KJ197247	KJ197265	N/A	N/A	Thompson et al. (2015)
	SAUCC 194.27	MT822555	MT855868	MT855752	MT855639	MT855524	Huang et al. (2021b)
D. morinendophytica	ZHKUCC 22-0069T	ON322897	ON315054	ON315087	N/A	ON315027	Luo et al. (2022)
	ZHKUCC 22-0070PT	ON322898	ON315055	ON315088	N/A	ON315028	Luo et al. (2022)
	ZHKUCC 22-0071PT	ON322899	ON315056	ON315089	ON315002	ON315029	Luo et al. (2022)
D. myracrodruonis	URM 7972T	MK205289	MK213408	MK205291	MK205290	N/A	da Silva et al. (2019)
D. parva	CGMCC 3.19599T	MK626919	MK654858	MK691248	N/A	MK726210	Guo et al. (2020)
	PSCG 035	MK626920	MK654859	MK691249	MK691169	MK726211	Guo et al. (2020)
D. patagonica	CBS 145291T	MN509717	MN509739	MN509728	MN974279	N/A	Zapata et al. (2020)
	CBS 145755	MN509718	MN509740	MN509729	N/A	N/A	Zapata et al. (2020)
D. pustulata	CBS 109742	KC343185	KC343911	KC344153	KC343427	KC343669	Gomes et al. (2013)
	CBS 109784	KC343187	KC343913	KC344155	KC343429	KC343671	Gomes et al. (2013)
D. pygmaeae	CDP 1370T	PP577992	PP579317	PP579332	PP579348	N/A	This study
	CDP 2030	PP577993	PP579318	PP579333	PP579349	N/A	This study
D. raonikayaporum	CBS 133182T	KC343188	KC343914	KC344156	KC343430	KC343672	Gomes et al. (2013)
D. rizhaoensis	CFCC 57562T	OP955930	OP959767	OP959773	OP959782	OP959785	Zhu et al. (2023)
	CFCC 57563	OP955931	OP959766	OP959772	OP959781	OP959784	Zhu et al. (2023)
D. rudis	CBS 109768	KC843329	KC843088	KC843175	KC843144	KC343717	Udayanga et al. (2014b)
	CBS 114436	KC343232	KC343958	KC344200	KC343474	KC343716	Gomes et al. (2013)
	CBS 135434	KC843338	KC843098	KC843185	KC843154	N/A	Udayanga et al. (2014b)
	CBS 135435	KC843332	KC843091	KC843178	KC843147	N/A	Udayanga et al. (2014b)
	CBS 135437	KC843336	KC843095	KC843182	KC843151	N/A	Udayanga et al. (2014b)
	CDP 1323	PP578009	PP579327	PP579343	PP579352	N/A	This study
	CDP 1861	PP578010	PP579328	PP579344	PP579353	N/A	This study
D. rudis(syn. D. italiana)	MFLUCC 18-0090T	MH846237	MH853686	MH853688	MH853690	N/A	Hyde et al. (2019)
	MFLUCC 18-0091IT	MH846238	MH853687	MH853689	MH853691	N/A	Hyde et al. (2019)
D. rudis(syn. D. medusaea)	CBS 109292ET	KC843331	KC843090	KC843177	KC843146	N/A	Udayanga et al. (2014b)
D. rudis(syn. D. viticola)	CBS 113201ET	KC343234	KC343960	KC344202	KC343476	KC343718	Gomes et al. (2023)
D. sackstonii	BRIP 54669bT	KJ197287	KJ197249	KJ197267	N/A	N/A	Thompson et al. (2015)
	GZCC 19-0129	MT385962	MT424697	MT424716	MT424727	OP150786	Dissanayake et al. (2020)
D. sackstonii(syn. D. caryae)	CFCC 52563T	MH121498	MH121540	MH121580	MH121422	MH121458	Yang et al. (2018)
	CFCC 52564	MH121499	MH121541	MH121581	MH121423	MH121459	Yang et al. (2018)
D. sackstonii(syn. D. juglandigena)	GUCC 422.161	OP581230	OP688535	OP688560	N/A	N/A	Wang et al. (2022)
	GUCC 422.16T	OP581229	OP688534	OP688559	N/A	N/A	Wang et al. (2022)
D. sackstonii(syn. D. machili)	SAUCC 194.111T	MT822639	MT855951	MT855836	MT855718	MT855606	Huang et al. (2021b)
	SAUCC 194.69	MT822597	MT855909	MT855794	MT855677	MT855565	Huang et al. (2021b)
D. sackstonii(syn. D. orixae)	GZCC 21–1085PT	OL889852	OL944724	OL944726	N/A	N/A	Lu et al. (2022)
	KUNCC 21–10714T	OK283041	OK432279	OK432278	OK484485	OK484486	Lu et al. (2022)
D. scobina	CBS 251.38	KC343195	KC343921	KC344163	KC343437	KC343679	Gomes et al. (2013)
D. serafiniae	BRIP 54136	KJ197273	KJ197235	KJ197253	N/A	N/A	Thompson et al. (2015)
	BRIP 55665bT	KJ197274	KJ197236	KJ197254	N/A	N/A	Thompson et al. (2015)
D. silvicola	CFCC 54191T	MZ727041	MZ816347	MZ753491	MZ753472	MZ753481	Jiang et al. (2021)
	M79	MZ727042	MZ816348	MZ753492	MZ753473	MZ753482	Jiang et al. (2021)
D. stictica	CBS 370.54	KC343212	KC343938	KC344180	KC343454	KC343696	Gomes et al. (2013)
D. tectonendophytica	LC 8115	KY491550	KY491560	KY491570	N/A	N/A	Gao et al. (2017)
	MFLUCC 13-0471T	KU712439	KU749367	KU743986	KU749354	N/A	Gao et al. (2017)
D. trevorrowii	BRIP 70737aT	OM918703	OM960612	OM960630	N/A	N/A	Tan & Shivas (2022)
D. tulliensis	BRIP 62248aT	KR936130	KR936133	KR936132	N/A	N/A	Crous et al. (2015)
D. tulliensis(syn. D. etinsideae)	BRIP 64096aH	OM918692	OM960601	OM960619	N/A	N/A	Tan & Shivas (2022)
D. ueckeri	CBS 119639	KC343202	KC343928	KC344170	KC343444	KC343686	Gomes et al. (2013)
	CBS 139283T	KJ590726	KJ590747	KJ610881	KJ612122	KJ659215	Udayanga et al. (2015)
	CGMCC 3.17534	KP267897	KP267971	KP293477	N/A	KP293547	Gao et al.(2016)
	FAU660	KJ590723	KJ590744	KJ610878	KJ612121	KJ659212	Udayanga et al. (2015)
	LC 3564	KP267912	KP267986	KP293492	N/A	KP293559	Gao et al.(2016)
	HNQH01	MN424521	MN424563	MN424535	MN424577	MN424549	From GenBank (unpublished)
	HNQH04	MN424527	MN424569	MN424541	MN424583	MN424555	From GenBank (unpublished)
	HNWC03	MN424519	MN424561	MN424533	MN424575	MN424547	From GenBank (unpublished)
	HNWN01	MN424522	MN424564	MN424536	MN424578	MN424550	From GenBank (unpublished)
	HNWN02	MN424523	MN424565	MN424537	MN424579	MN424551	From GenBank (unpublished)
D. ueckeri(syn. D. durionigena)	VTCC 930005T	MN453530	MT276157	MT276159	N/A	N/A	Crous et al. (2020)
	KCSR 1906.7	MN453531	MT276158	MT276160	N/A	N/A
D. ueckeri(syn. D. miriciae)	BRIP 54736jT	KJ197282	KJ197244	KJ197262	N/A	N/A	Thompson et al. (2015)
	BRIP 55662c	KJ197283	KJ197245	KJ197263	N/A	N/A	Thompson et al. (2015)
	CGMHD 1023	MH268404	MH368012	MH368009	MH368011	MH368010	From GenBank (unpublished)
D. ueckeri(syn. D. passifloricola)	CBS 141329T	KX228292	N/A	KX228387	N/A	KX228367	Crous et al. (2016b)
	NFIF-3-11	MG786598	MG925401	MG925398	MK238995	MK238998	Chaisiri et al. (2021a)
	ZHKUCC 20-0017	MT355687	MT409341	MT409295	MT409317	N/A	Dong et al. (2021b)
D. ueckeri(syn. D. rosae)	MFLUCC 17-2574	MG906793	MG968954	MG968952	N/A	N/A	Wanasinghe et al. (2018)
	MFLUCC 17-2658T	MG828894	N/A	MG843878	MG829273	N/A	Wanasinghe et al. (2018)
	MFLUCC 18-0354	MG906792	MG968953	MG968951	N/A	N/A	Wanasinghe et al. (2018)
D. ueckeri(syn. D. thunbergiicola)	MFLUCC 12-0033T	KP715097	KP715098	N/A	N/A	N/A	Liu et al. (2015)
D. ueckeri (syn. D. vochysiae)	LGMF 1583T	MG976391	MK007526	MK007527	MK007528	MK033323	Noriler et al. (2019)
D. xishuangbanica	CGMCC 3.18282	KX986783	KX999175	KX999216	N/A	KX999216	Gao et al. (2017)
	CGMCC 3.18283T	KX986784	KX999176	KX999217	N/A	N/A	Gao et al. (2017)

¹ Taxon or strain previous name is noted in brackets if different from current name for taxa that have been synonymised (indicated by syn.) or resolved in the present study or in previous studies.

² Acronyms of culture collections, AR, FAU: isolates in culture collection of Systematic Mycology and Microbiology Laboratory, USDA-ARS, Beltsville, Maryland, USA; ATCC: American Type Culture Collection, Virginia, USA; BRIP: Plant Pathology Herbarium, Department of Primary Industries, Dutton Park, Queensland, Australia; CAA: Collection of Artur Alves housed at Department of Biology, University of Aveiro, Portugal; CBS: CBS-KNAW Fungal Bio-diversity Centre, Utrecht, The Netherlands; CDP: culture collection of D.S. Pereira, housed at the Lab Bugworkers | M&B-BioISI | Tec Labs – Innovation Centre, Faculty of Sciences, University of Lisbon, Lisbon, Portugal; CECT: Spanish Type Culture Collection at University of Valencia, Valencia, Spain; CFCC: China Forestry Culture Collection Center, Beijing, China; CGMCC: China General Microbiological Culture Collection Center, China; CGMHD: Chang Gung Memorial Hospital, Taiwan; CPC: working collection of P.W. Crous, housed at CBS; DAL: strains deposited in fungal collection of the Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Valencia, Spain; GUCC: Guizhou University Culture Collection; GZCC: Guizhou Academy of Agricultural Sciences Culture Collection, Guizhou, China; JZB: culture collection of Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; KUMCC: Culture Collection of Kunming Institute of Botany, Kunming, China; KUNCC: Kunming Institute of Botany Culture Collection, Chinese Academy of Sciences, Kunming, China; LC: working collection of Lei Cai, housed at Laboratory State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, China; LGMF: Culture Collection of Laboratório de Genética de Microrganismos (LabGeM), Universidade Federal do Paraná, Curitiba, Brazil; MFLU: Herbarium of Mae Fah Luang University, Chiang Rai, Thailand; MFLUCC: Mae Fah Luang University Culture Collection, Chiang Rai, Thailand; MUM: Culture Collection of Micoteca da Universidade do Minho, Braga, Portugal; NCYUCC: National Chiayi University Culture Collection, Taiwan; NTUCC: Department of Plant Pathology and Microbiology, National Taiwan University Culture Collection, Taiwan; NTUPPMCC: Department of Plant Pathology and Microbiology, National Taiwan University Culture Collection; PSCG: personal culture collection of Y.S. Guo, China; SAUCC: Shandong Agricultural University Culture Collection, China; SCHM: Mycological Herbarium of South China Agricultural University, Guangzhou, China; SDBR-CMU: Culture Collection of Sustainable Development of Biological Resources Laboratory at Chiang Mai University, Chiang Mai, Thailand; STMA: culture collection of HZI, Helmholtz Center for Infection Research, Braunschweig, Germany; URM: Culture Collection of Universidade Federal de Pernambuco, Recife, Brazil; VPRI: Victorian Plant Pathology Herbarium, National Collection of Fungi, Knoxfield, Victoria, Australia; VTCC: Vietnam Type Culture Collection, Center of Biotechnology, Vietnam National University, Hanoi, Vietnam; ZHKUCC: University of Agriculture and Engineering Culture Collection, China.

³ Status of the strains or specimens are noted by bold superscript ET (ex-epitype), H (holotype), IT (ex-isotype), PT (ex-paratype) and T (ex-type).

⁴ Newly generated sequences are in bold; n/a: sequences not available; cal: partial calmodulin gene; his3: partial histone H3 gene; ITS: partial cluster of nrRNA genes, including the nuclear 5.8S rRNA gene and its flanking internal transcribed spacer regions ITS1 and ITS2; tef1: partial translation elongation factor 1-alpha gene; tub2: partial beta-tubulin gene.