Table 1.

Isolated and reference strains of Diaporthe included in this study. # GenBank accession numbers in bold were newly generated in this study. The taxonomic novelty is indicated in bold italic.

Species	Isolates1	GenBank accession numbers2					References
		ITS	tub2	his3	tef1	cal
Diaportheacaciarum	CBS 138862T	KP004460	KP004509	KP004504	-	-	Crous et al. (2014)
D.acericola	MFLUCC 17-0956T	KY964224	KY964074	-	KY964180	KY964137	Dissanayake et al. (2017)
D.alangii	CFCC 52556T	MH121491	MH121573	MH121451	MH121533	MH121415	Yang et al. (2018)
D.ambigua	CBS 114015T	KC343010	KC343978	KC343494	KC343736	KC343252	Gomes et al. (2013)
D.amygdali	CBS 126679T	KC343022	KC343990	KC343506	KC343748	KC343264	Gomes et al. (2013)
D.angelicae	CBS 111592T	KC343026	KC343994	KC343511	KC343752	KC343268	Gomes et al. (2013)
D.arctii	CBS 136.25	KC343031	KC343999	KC343515	KC343757	KC343273	Gomes et al. (2013)
D.arezzoensis	MFLU 19-2880T	MT185503	MT454055	-	-	-	Li et al. (2020)
D.batatas	CBS 122.21	KC343040	KC344008	KC343524	KC343766	KC343282	Gomes et al. (2013)
D.beilharziae	BRIP 54792T	JX862529	KF170921	-	JX862535	-	Thompson et al. (2015)
D.biguttulata	ICMP 20657T	KJ490582	KJ490403	KJ490524	KJ490461	-	Huang et al. (2015)
D.breyniae	CBS 148910T	ON400846	ON409186	ON409187	ON409188	ON409189	Present study
D.camporesii	JZB 320143T	MN533805	MN561316	-	-	-	Hyde et al. (2020)
D.caryae	CFCC 52563T	MH121498	MH121580	MH121458	MH121540	MH121422	Yang et al. (2018)
D.celtidis	NCYU 19-0357T	MW114346	MW148266	-	MW192209	-	Tennakoon et al. (2021)
D.cerradensis	CMRP 4331T	MN173198	MW751671	MW751663	MT311685	MW751655	Iantas et al. (2021)
D.chimonanthi	SCHM 3614T	AY622993					Chang et al. (2005)
D.chinensis	MFLUCC 19-0101T	MW187324	MW245013	-	MW205017	MW294199	de Silva et al. (2021)
D.chromolaenae	MFLUCC 17-1422T	MH094275	-	-	-	-	Mapook et al. (2020)
D.cichorii	MFLUCC 17-1023T	KY964220	KY964104	-	KY964176	KY964133	Dissanayake et al. (2017)
D.cinnamomi	CFCC 52569T	MH121504	MH121586	MH121464	MH121546	-	Yang et al. (2018)
D.citriasiana	CBS 134240T	JQ954645	KC357459	MF418282	JQ954663	KC357491	Huang et al. (2013)
D.compacta	LC3083T	KP267854	KP293434	KP293508	KP267928	-	Gao et al. (2016)
D.convolvuli	CBS 124654	KC343054	KC344022	KC343538	KC343780	KC343296	Gomes et al. (2013)
D.cucurbitae	DAOM 42078T	KM453210	KP118848	KM453212	KM453211	-	Udayanga et al. (2015)
D.cuppatea	CBS 117499T	AY339322	JX275420	KC343541	AY339354	JX197414	Van Rensburg et al. (2006)
D.discoidispora	ICMP 20662T	KJ490624	KJ490445	KJ490566	KJ490503	-	Huang et al. (2015)
D.durionigena	VTCC 930005T	MN453530	MT276159	-	MT276157	-	Crous et al. (2020)
D.endophytica	CBS 133811T	KC343065	KC344033	KC343549	KC343791	KC343307	Gomes et al. (2013)
D.eres	CBS 138594T	KJ210529	KJ420799	KJ420850	KJ210550	KJ434999	Udayanga et al. (2014)
D.fici-septicae	MFLU 18-2588T	MW114348	MW148268	-	MW192211	-	Tennakoon et al. (2021)
D.fructicola	MAFF 246408T	LC342734	LC342736	LC342737	LC342735	LC342738	Crous et al. (2019)
D.ganjae	CBS 180.91T	KC343112	KC344080	KC343596	KC343838	KC343354	Gomes et al. (2013)
D.glabrae	SCHM 3622T	AY601918	-	-	-	-	Chang et al. (2005)
D.goulteri	BRIP 55657aT	KJ197290	KJ197270	-	KJ197252	-	Thompson et al. (2015)
D.guangdongensis	ZHKUCC20-0014T	MT355684	MT409292	-	MT409338	MT409314	Dong et al. (2021)
D.gulyae	BRIP 54025T	JF431299	KJ197271	-	JN645803	-	Thompson et al. (2015)
D.guttulata	CGMCC 3.20100T	MT385950	MT424705	MW022491	MT424685	MW022470	Dissanayake et al. (2020)
D.helianthi	CBS 592.81T	KC343115	KC344083	KC343599	KC343841	JX197454	Gomes et al. (2013)
D.heterostemmatis	SAUCC 194.85T	MT822613	MT855810	MT855581	MT855925	MT855692	Sun et al. (2021)
D.hordei	CBS 481.92	KC343120	KC344088	KC343604	KC343846	KC343362	Gomes et al. (2013)
D.hubeiensis	JZB 320123T	MK335809	MK500148	-	MK523570	MK500235	Manawasinghe et al. 2019
D.infecunda	CBS 133812T	KC343126	KC344094	KC343610	KC343852	KC343368	Gomes et al. (2013)
D.infertilis	CBS 230.52T	KC343052	KC344020	KC343536	KC343778	KC343294	Guarnaccia and Crous (2017)
D.kochmanii	BRIP 54033T	JF431295	-	-	JN645809	-	Thompson et al. (2011)
D.kongii	BRIP 54031T	JF431301	KJ197272	-	JN645797	-	Thompson et al. (2011)
D.leucospermi	CBS 111980T	JN712460	KY435673	KY435653	KY435632	KY435663	Crous et al. (2011c)
D.longicolla	FAU 599T	KJ590728	KJ610883	KJ659188	KJ590767	KJ612124	Udayanga et al. (2015)
D.longispora	CBS 194.36T	KC343135	KC344103	KC343619	KC343861	KC343377	Gomes et al. (2013)
D.lusitanicae	CBS 123212T	KC343136	KC344104	KC343620	KC343862	KC343378	Gomes et al. (2013)
D.machili	SAUCC 194.111T	MT822639	MT855836	MT855606	MT855951	MT855718	Huang et al. (2021)
D.manihotia	CBS 505.76	KC343138	KC344106	KC343622	KC343864	KC343380	Gomes et al. (2013)
D.masirevicii	BRIP 57892aT	KJ197277	KJ197257	-	KJ197239	-	Thompson et al. (2015)
D.mayteni	CBS 133185T	KC343139	KC344107	KC343623	KC343865	KC343381	Gomes et al. (2013)
D.megalospora	CBS 143.27	KC343140	KC344108	KC343624	KC343866	KC343382	Gomes et al. (2013)
D.melonis	CBS 507.78T	KC343142	KC344110	KC343626	KC343868	KC343384	Gomes et al. (2013)
D.micheliae	SCHM 3603	AY620820	-	-	-	-	Chang et al. (2005)
D.middletonii	BRIP 54884eT	KJ197286	KJ197266	-	KJ197248	-	Thompson et al. (2015)
D.myracrodruonis	URM 7972T	MK205289	MK205291	-	MK213408	MK205290	da Silva et al. (2019)
D.neoarctii	CBS 109490	KC343145	KC344113	KC343629	KC343871	KC343387	Gomes et al. (2013)
D.neoraonikayaporum	MFLUCC 14-1136T	KU712449	KU743988	-	KU749369	KU749356	Doilom et al. (2017)
D.novem	CBS 127271T	KC343157	KC344125	KC343641	KC343883	KC343399	Gomes et al. (2013)
D.ovalispora	ICMP 20659T	KJ490628	KJ490449	KJ490570	KJ490507	-	Huang et al. (2015)
D.pachirae	COAD 2074T	MG559537	MG559541	-	MG559539	MG559535	Milagres et al. (2018)
D.passifloricola	CBS 141329T	KX228292	KX228387	KX228367	-	-	Crous et al. (2016)
D.phaseolorum	CBS 113425	KC343174	KC344142	KC343658	KC343900	KC343416	Gomes et al. (2013)
D.pseudolongicolla	CBS 117165T	DQ286285	-	-	DQ286259	-	Petrović et al. (2018)
D.pyracanthae	CBS142384 T	KY435635	KY435666	KY435645	KY435625	KY435656	Santos et al. (2017)
D.racemosae	CBS 143770T	MG600223	MG600227	MG600221	MG600225	MG600219	Marin-Felix et al. (2019)
D.raonikayaporum	CBS 133182T	KC343188	KC344156	KC343672	KC343914	KC343430	Gomes et al. (2013)
D.rosae	MFLUCC 17-2658T	MG828894	MG843878	-	-	MG829273	Wanasinghe et al. (2018)
D.rosiphthora	COAD 2913T	MT311196	-	-	MT313692	MT313690	Pereira et al. (2021)
D.rossmaniae	CAA 762T	MK792290	MK837914	MK871432	MK828063	MK883822	Hilário et al. (2020)
D.sackstonii	BRIP 54669bT	KJ197287	KJ197267	-	KJ197249	-	Thompson et al. (2015)
D.sambucusii	CFCC 51986T	KY852495	KY852511	KY852503	KY852507	KY852499	Yang et al. (2018)
D.schini	CBS 133181T	KC343191	KC344159	KC343675	KC343917	KC343433	Gomes et al. (2013)
D.schoeni	MFLU 15-1279T	KY964226	KY964109	-	KY964182	KY964139	Dissanayake et al. (2017a)
D.sclerotioides	CBS 296.67T	KC343193	KC344161	KC343677	KC343919	KC343435	Gomes et al. (2013)
D.serafiniae	BRIP 55665aT	KJ197274	KJ197254	-	KJ197236	-	Thompson et al. (2015)
D.siamensis	MFLUCC 10-0573a	JQ619879	JX275429	-	JX275393	-	Udayanga et al. (2012)
D.sinensis	CGMCC 3.19521T	MK637451	MK660447	-	MK660449	-	Feng et al. (2019)
D.sojae	CBS 139282T	KJ590719	KJ610875	KJ659208	KJ590762	KJ612116	Udayanga et al. (2015)
D.stewartii	CBS 193.36	FJ889448	-	-	GQ250324	-	Santos et al. (2010)
D.subellipicola	KUMCC 17-0153T	MG746632	MG746634	-	MG746633	-	Hyde et al. (2018)
D.subordinaria	CBS 101711	KC343213	KC344181	KC343697	KC343939	KC343455	Gomes et al. (2013)
D.tecomae	CBS 100547	KC343215	KC344183	KC343699	KC343941	KC343457	Gomes et al.(2013)
D.tectonae	MFLUCC 12-0777T	KU712430	KU743977	-	KU749359	KU749345	Doilom et al. (2017)
D.tectonendophytica	MFLUCC 13-0471T	KU712439	KU743986	-	KU749367	KU749354	Doilom et al. (2017)
D.terebinthifolii	CBS 133180T	KC343216	KC344184	KC343700	KC343942	KC343458	Gomes et al. (2013)
D.thunbergiicola	MFLUCC 12-0033T	KP715097	-	-	KP715098	-	Liu et al. (2015)
D.tulliensis	BRIP 62248a	KR936130	KR936132	-	KR936133	-	Crous et al. (2015)
D.ueckeri	FAU 656	KJ590726	KJ610881	KJ659215	KJ590747	KJ612122	Huang et al. (2015)
	BRIP 54736j (type of D.miriciae)	KJ197283	KJ197263	-	KJ197245	-	Thompson et al. (2015)
D.unshiuensis	CGMCC 3.17569T	KJ490587	KJ490408	KJ490529	KJ490466	-	Huang et al. (2015)
D.vexans	CBS 127.14	KC343229	KC344197	KC343713	KC343955	KC343471	Gomes et al.(2013)
D.vitimegaspora	STE-U 2675	AF230749	-	-	-	-	Mostert et al. (2001)
D.vochysiae	LGMF 1583T	MG976391	MK007527	MK033323	MK007526	MK007528	Noriler et al. (2019)
D.yunnanensis	CGMCC 3.18289T	KX986796	KX999228	KX999267	KX999188	KX999290	Gao et al. (2017)

¹BRIP: Queensland Plant Pathology Herbarium, Brisbane, Australia; CBS: Westerdijk Fungal Biodiversity Institute, Utrecht, the Netherlands; CGMCC: Chinese General Microbiological Culture Collection Center, Beijing, China; COAD: Culture Collection of Octávio de Almeida Drumond. Universidade Federal de Viçosa, Viçosa, Brasil; FAU: Isolates in culture collection of Systematic Mycology and Microbiology Laboratory; ICMP: International Collection of Micro-organisms from Plants, Auckland, New Zealand; KUMCC: Kumming Institute of Botany, Kumming, China; LGMF, Laboratório de Genética de Microrganismos (LabGeM) culture collection, at the Federal University of Paraná, Brazil; MAFF: Ministry of Agriculture, Forestry and Fisheries, Tokyo, Japan; MFLUCC: Mae Fah Luang University Culture Collection, Chiang Rai, Thailand; SAUCC: Shandong Agricultural University Culture Collection, Shandong, China; STE-U: Department of Plant Pathology, Stellenbosch University, Stellenbosch, South Africa; URM: Culture Collection at the Universidade Federal de Pernambuco, Recife, Brazil; VTCC: Vietnam Type Culture Collection, Center of Biotechnology, Vietnam National University, Hanoi, Vietnam; ZHKUCC: Culture Collection of Zhongkai University of Agriculture and Engineering, Guangzhou, China. ^T indicates type material. ²ITS: internal transcribed spacers and intervening 5.8S nrDNA; tub2: partial β-tubulin gene; his3: partial histone H3 gene; tef1: partial elongation factor 1-alpha gene; cal: partial calmodulin gene.