Table 3.

List of OTUs and accession numbers of sequences.

Name	18S rRNA	ITS1-5.8S  rRNA	28S rRNA	%, SSU-ITS1-  5.8S-LSU/D3	Reference	Family by [8]
Chambersiellidae∗
Fescia grossa	KC242218	—	DQ145636 DQ145684	87.1/—	[54] [55]	Chambersiellidae
Geraldius sp. SAN-2010a	—	—	GU062821	17.8/—	[56]	Chambersiellidae
Cephalobidae
Acrobeloides maximus	EU196016	JX026706	EU195987	94.8/—	[57] [58] [57]	Cephalobidae
Cephalobus cubaensis	AF202161	AF202161	EU253570	89.8/—	[59] [57]
Panagrolobus sp. SN-2010	—	—	HM439771	51.9/—	[60]
Cephalobidae Gen. sp. MHMH-2008	FJ040406	—	—		Holterman et al., 2008, unpublished.
Zeldia punctata	—	DQ146426	EU195988	96.6/—	[61] [57]
Zeldia sp.	AY284675	—	—
Aphelenchidae
Aphelenchus avenae	JQ348399	AF119048	—	96.9/—	[62] [63]	Aphelenchidae
Aphelenchus sp.	—	—	DQ145664 DQ145714		[55]
Paraphelenchus acontioides	—	—	HQ218322	45.5/—	[64]
Paraphelenchus sp.	AY284642	—	—		[18]
Hexatylina + “Anguinata (part)”: Iotonchioidae
Allantonema mirable	—	—	JX291132	10.6/85.8	[39]	Allantonematidae
Bradynema listronoti	DQ915805		DQ915804	45.6/96.8	[65]
Bradynema rigidum			DQ328730	10.4/86.3	[20]
Contortylenchus sp.	—	—	DQ328731	—/85.4	[20]
Deladenus durus	JQ957898	—	—	34.0/—	[66]	Neotylenchidae
Deladenus proximus	JF304744	JF304744	—	35.2/—	[67]
Deladenus siricidicola isolate 354	AY633447		AY633444	45.8/98.1	[68]
Deladenus siricidicola isolate 466	FJ004890	FJ004890	—	41.7/—	[69]
Deladenus siricidicola isolate 1093	FJ004889	FJ004889	—	42.0/—	[69]
Fergusobia camaldulensae	AY589294	—	AY589346	45.7/98.0	[68]
Fergusobia sp. 444	EF011667	—	EF011675	45.7/97.3	[68]
Fergusobia sp. SBG	FJ393270	—	FJ386996	45.7/98.3	[70]
cf. Gymnotylenchus sp. TSH-2005	AY912040	—	—	12.9/—	Powers et al., unpublished.
Howardula aoronymphium	AY589304	AY589304	AY589395	49.7/96.1	[68]	Allantonematidae
Howardula dominicki	AF519234	AF519234	—	37.4/—	[71]
Howardula neocosmis	AF519226	AF519226	—	38.2/—	[71]
Howardula phyllotretae	JX291137	—	DQ328728	41.9/86.1	[39] [20]
Howardula sp. CD353	—	—	JX291131	—/93.9	[39]
Howardula sp. SP-A	AF519232	AF519232	—	37.7/—	[71]
Howardula sp. SP-F	AF519222	AF519222	—	38.2/—	[71]
Howardula sp. SP-MA	AF519233	AF519233	—	38.1/—	[71]
Howardula sp. SP-PS	AF519231	AF519231	—	38.1/—	[71]
Parasitylenchus  bifurcatus	KC875397	—		44.0/85.3	[72]
Parasitylenchus sp.	—	—	DQ328729		[20]
Psyllotylenchus sp. ex Frontopsylla semura	KF373734	—	KF373739	27.1/93.7	This study	Parasitylenchidae
Psyllotylenchus sp. ex Neopsylla setosa	KF373733	—	KF373738	27.1/93.7	This study
Rubzovinema sp. ex Amphipsylla rossica	KF155281	KF155281	KF155281	90.0/100.0	This study	Neotylenchidae
Rubzovinema sp. ex Ctenophthalmus cecundus	KF155282	KF155282	KF155282	89.8/100.0	This study
Rubzovinema sp. ex Citellophilus tesquorum	KF155283	KF155283	KF155283	93.2/100.0	This study
Rubzovinema sp. ex Frontopsylla semura	KF373732	—	KF373737	27.1/93.7	This study
Rubzovinema sp. ex Neopsylla setosa	KF373731	—	KF373736	27.1/93.7	This study
Skarbilovinema laumondi	—	—	JX291136	10.9/91.0	[39]	Iotonchioidea
Skarbilovinema lyoni	JX291138	—	DQ328733	41.8/86.3	[39] [20]
Spilotylenchus sp. ex Mesopsylla hebes	KF373735	—	KF373740	27.1/93.4	This study	Parasitylenchidae
cf. Sychnotylenchus sp. CSP1-09	DQ080531	—	—	12.9/—	Powers et al., unpublished.	Sychnotylenchidae
Wachekitylenchus bovieni	—	—	DQ328732	—/85.9	[20]	Parasitylenchidae
Unidentified Allantonematidae HaMW	JQ941710	—	—	18.5/—	Rhule, unpublished.	Allantonematidae
Unidentified Allantonematidae NK2011_2	AB663183	—	—	12.0/—	[73]
Unidentified Allantonematidae NK2011_3	AB663184	—	—	12.0/—	[73]
Unidentified nematode 804U-025	EU880149	—	—	12.0/—	[74]
Unidentified nematode CD289	—	—	JX291133	—/84.1	[39]
Unidentified nematode RGD591T12	AB455970	—	—	12.0/—	[73]
Unidentified nematode WY2009_BAR-1	—	—	FJ661075	—/96.3	[75]
Unidentified parasite ex Chrysobothris affinis	—	—	DQ202658	—/51.0	Hunt et al., unpublished.
Hexatylina + “Anguinata (part)”: Sphaerularioidea
Deladenus sp. PDL-2005	AJ966481	—	—	35.0/—	[16]	Neotylenchidae
cf. Helionema sp. MHMH-2008	EU669913	—	—	34.0/—	[19]	Parasitylenchidae (genera dubia in Hexatylina)
cf. Hexatylus sp. Westplace	AY912050	—	—	12.9/—	Powers et al., unpublished.	Neotylenchidae
Nothotylenchus acris	AY593914	—	—	34.0/—	[76]	Anguinidae
Sphaerularia bombi	AB250212	—	DQ328726	56.7/100.0	Takahashi, unpublished. [20]	Sphaerulariidae
Sphaerularia vespae	AB300595	AB300595	AB300596	54.7/100.0	[77]
Unidentified nematode 801L-022	EU880129	—	—	12.1/—	[74]
Anguinata
Anguina tritici	AY593913	JF826515	HO058555 DQ328723	57.6/92.9	Holterman et al., unpublished. Rao and Rao, unpublished. Rao et al., unpublished. [20]	Anguinidae
Ditylenchus adasi	EU669909	—	—	34.6/—	[19]
Ditylenchus angustus	AJ966483	—	—	34.6/—	[16]
Ditylenchus destructor		JX162205		50.0/99.5	[78]
Ditylenchus dipsaci	AY593911	AY593911	JF327759	60.9/100.0	[76] Zhao 2011, unpublished.
clone NTS_28S_061A_2_b4			KC558346		[79]
Ditylenchus drepanocercus	JQ429768	JQ429774	JQ429772	48.7/89.3	[80]
Ditylenchus halictus	AY589297			52.8/97.3	[68]
Ficotylus congestae	EU018049			45.6/97.5	[81]
Halenchus fucicola	EU669912	—	—	34.6/—	[19]
Pseudhalenchus minutus	AY284638			34.6/—	[19]
Unidentified entomoparasitic nematode SAS-2006 “Neotylenchus” sp.	—	—	DQ328725	—/85.6	[20]
“Tylenchina”: Tylenchidae
Aglenchus agricola	FJ969113	—	—	46.0/—	van Megen et al., unpublished.	Tylenchidae
Aglenchus sp.	—	—	JQ004996		[82]
Coslenchus costatus	AY284581	—	—	45.5/—	[18]
Coslenchus sp.	—	—	JQ005007		[82]
Filenchus annulatus	JQ814880	—	JQ005017	46.4/—	[82]
Tylenchus davainei	AY284588	—	—	33.9/—	[18]
“Tylenchina”: Tylodoridae
Eutylenchus excretorius	EU915487	EU915500	EU915490	35.8/—	[83]	Atylenchidae
Cephalenchus hexalineatus	AY284594	—	—	44.1/—	[18]	Tylodoridae
“Tylenchina”: Boleodoridae
Basiria gracilis	EU130839	—	DQ328717	44.6/—	[84] [20]	Tylenchidae
Basiria sp. 3 TJP-2012	—	—	JQ004998	12.0/—	[82]
Boleodorus thylactus	AY993976	—	—	46.7/—	[16]
Boleodorus sp.	—	—	JQ005001		[18]
Neopsilenchus magnidens	AY284585	—	—	45.6/—	[18]
Neopsilenchus sp. 3 TJP-2012	—	—	JQ005020		[82]
Neopsilenchus sp. 1 TJP-2012	—	—	JQ005018	11.9/—	[82]
“Hoplolaimina”: Merliniidae
Nagelus leptus	—	—	DQ328715	45.2/—	[20]	Telotylenchidae
Nagelus obscurus	EU306350	—	—		[17]
Pratylenchoides ritteri	AJ966497	—	JX261964	48.7/—	[16] [85]	Pratylenchidae
Psilenchus cf. hilarulus	AY284593	—	EU915489	44.1/—	[18] [83]	Psilenchidae
Scutylenchus quadrifer	AY284599	—	—	41.5/—	[18]	Telotylenchidae
Scutylenchus sp.	—	JQ069956	—		[86]
“Tylenchina”: Ecphyadophoridae
Ecphyadophora sp. JH-2004	AY593917	—	—	33.7/—	[76]	Ecphyadophoridae
“Ditylenchus” brevicauda	AY284635	—	—	33.9/—	[18]	Anguinidae
Malenchus andrassyi	AY284587	—	—	32.3/—	[18]	Tylenchidae
Ottolenchus discrepans	AY284590	—	—	33.7/—	[18]
Criconematina
Hemicriconemoides gaddi	—	KC520471	KC520470	55.6/—	[87]	Criconematidae
Hemicriconemoides pseudobrachyurus	AY284622	—	—		[18]
Hemicycliophora lutosa	—	GQ406237	GQ406240	53.2/—	[88]	Hemicycliophoridae
Hemicycliophora thienemanni	AY284628	—	—		[18]
Meloidoderita kirjanovae	—	DQ768427	DQ768428	50.8/—	[89]	Sphaeronematidae
Sphaeronema alni	FJ969127	—	—		van Megen, unpublished.
Meloidoderita sp.	GU253916	GU253917	JQ771954	50.8/—	[90] Cudejkova and Cermak, unpublished.
Tylenchulus semipenetrans	AJ966511	FJ588909	FJ969710	57.5/—	[16]  [91]  [92]	Tylenchulidae
“Hoplolaimina”: Belonolaimidae
Belonolaimus longicaudatus	AY633449	DQ672366	GQ896548	55.8/—	[68] [93] [94]	Belonolaimidae
Ibipora lolii	JQ771535	—	—	30.9/—	[95]
“Hoplolaimina”: Hoplolaimidae
Carphodorus sp.	JQ771538	—	JQ771550	41.3/—	[95]
Globodera pallida	EU855119	EU85511	BM415342 BM415248 CV577211 CV577977 CV579301E U85511	93.6/—	Nowaczyk et al., unpublished. Opperman, unpublished  [96].	Heteroderidae
Heterodera glycines	AF216579 BI704127 BI748392 CA940548 CB379240 CB379263 CB379850 CB380242 CB825296 CB825409 CB825970 CB935610 CK348871 CK348904 CK349175 CK352112	AF216579	AF133304 AF216579 BI704144 BI704144 BI749520 CA940190 CA940212 CA940243 CA940406 CA940424 CA940429 CA940589 CB238697 CB279977 CB299455 CB373844 CB373981 CB379125 CB379140 CB379219 CB379312 CB379439 CB379505  CB379696 CB379707 CB379996 CB380091 CB380241 CB824788 CB824878 CB825995 CB934877 CB934931 CB934950 CB934954 CK348525 CO036619 HM560850 JN684906	98.3/—	[97]  [96]. [98]  Yan and Davis, unpublished. [99] Ye et al., unpublished. Wei et al., unpublished.
Morulaimus sp.	JQ771540	—	—	31.5/—	[95]	Belonolaimidae
Radopholus similis	AJ966502 AY912509 EF384224 EY190988 EY191076 EY191697 EY191883 EY192786 EY192788 EY193123 EY193253 EY194340 EY194464 EY194646 EY195472 FJ040398	AY912509  EF384224	EU555409 EY189839 EY190550 EY190620 EY190961 EY191066 EY191073 EY191135 EY191160 EY191173 EY191237 EY192021 EY192028 EY192080 EY192091 EY192247 EY192381 EY192472 EY192501 EY192526 EY192892 EY192907 EY193005 EY193037 EY193249 EY193314 EY193798 EY193897 EY193971 EY194395 EY194454 EY194530 EY195146 EY195204	97.5/—	[16] [100] Long et al., unpublished. [101]  Holterman et al., unpublished. [102]  [100] Zhao unpublished. [86]	Pratylenchidae
			EY195406
			EY195408 EY195580 EY195889 EY195943 GQ281471 JN091962 JQ782249
Rotylenchulus reniformis	JX406356	FJ374686	HM131884 FJ906072	59.4/—	[103] Rahman et al., unpublished. [104]	Rotylenchulidae
“Hoplolaimina”: Pratylenchidae
Dolichodorus sp. WY-2006	DQ912918	—	—	33.9/—	[105]	Dolichodoridae
Hirschmanniella loofi	EU306353	EU620472	EU620469	51.6/—	[17] [106]	Pratylenchidae
Macrotrophurus arbusticola	AY284595	—		33.9/—	[18]	Telotylenchidae
Meloidogyne arenaria	U42342	U42342	U42342 AF023855 AF023856	99.2/—	Georgi and Abbott, unpublished.	Meloidogynidae
Meloidogyne artiellia	AF248477	AF248477	AF248477	99.2/—	[107]
Nacobbus aberrans	AJ966494	DQ017473	U47557	49.0/—	[16] [108] [109]	Pratylenchidae
Pratylenchus vulnus	EU669955	JQ966892	BQ580554 CV198923 CV198995 CV199233 CV199349 CV199490 CV200136 CV200423 CV200464 CV200467 CV200471 CV200530 CV200687 CV200896 CV201004 CV201135 EL887566 EL887705 EL888035 EL888060 EL888174 EL888269 EL888739 EL888778 EL889241 EL889472 EL889797 EL889934 EL889934 EL889977 EL889994 EL890380 EL890701 JQ003993 JQ003994 JX047008	100.0/—	[19] [110]  [96]  [96] [111] Zhao, unpublished. [112]
Tylenchorhynchus dubius	EU306352	—	DQ328707	53.2/—	[17] [20]	Telotylenchidae
Tylenchorhynchus zeae	—	EF519711	—		[113]

*Clades of the tree, marked by boldface.