Phylogenetic Analysis of Entomoparasitic Nematodes, Potential Control Agents of Flea Populations in Natural Foci of Plague

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 sp.; MHMH-2008	FJ040406	—	—		Holterman et al., 2008, unpublished.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 TSH-2005	AY912040	—	—	12.9/—	Powers et al., unpublished.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.