ITS sequence of Steinernema cut by 22 Enzymes

    How to identify species of Steinernema: Sequence the ITS region using primers 18S and 26S. Next, using GCG MAP and MAPSORT programs to collect number of cuts and fragment lengths. Sequence length, number of cuts, and fragment lengths can be used to identify nematode species.

TABLE 1: Number of cuts (boldfaced numbers) for each restriction enzyme and fragment arrangement (in descending order)  of ITS sequences of 10 species of  Steinernema cut by 22 enzymes.

Enzyme	bicornutum	carpocapsae	feltiae	glaseri	intermedium	monticolum	neocurtillae	oregonense	scapterisci	sp.
	(1016 bp)	(987 bp)	(980 bp)	(988 bp)	(1061 bp)	(916 bp)	(968 bp)	(973 bp)	(959 bp)	(1022 bp)
AluI	2; 716,177, 123	5; 429, 177,	3; 512, 258,	5; 355, 293,	3; 475, 226,	1; 742, 177	1; 791, 177	4; 509, 177,	5; 269, 215	8; 216, 177,
		150, 120, 66,	177, 33	139, 108, 61,	181, 179			149, 105, 33	177, 163, 71,	175, 162, 116,
		45		32					64	88, 55, 22, 11
ApoI	1; 547, 469	1; 545, 442	4; 318, 213,	1; 545, 443	3; 491, 404,	3; 530, 197,	1; 523, 445	3; 533, 245	1; 513, 446	1; 568, 454
			165, 144, 130		101, 65	98, 94		148, 47
Bcef	2; 735, 156,	1; 731, 256	4; 571, 147,	3; 627, 149,	1; 763, 298	3; 522, 138,	2; 710, 133,	4; 572, 148,	1; 704, 255	3; 638, 149,
	125		125, 88, 49	125, 87		134, 125	125	125, 78, 50		125, 110
BfaI	4; 450, 332,	5; 612, 180,	2; 626, 346, 8	2; 745, 235, 8	2; 918, 135, 8	3; 479, 332,	3; 616, 219,	3; 337, 334,	4; 580, 179,	2; 669, 345, 8
	160, 66, 8	102, 70, 15, 8				97, 11	125, 8	294, 8	122, 70, 8
DdeI	3; 676, 201,	4; 642, 190,	3; 647, 271, 34,	2; 926, 34, 28	3; 726, 284, 28	4; 697, 141, 32,	2; 801, 139,	3;758, 153,	3; 513, 230,	4; 590, 197,
	111, 28	101, 28, 26	28		23	28, 21	28	34, 28	188, 28	173, 34, 28
FokI	0	1; 542, 445	0	0	1; 974, 87	0	1; 881, 87	0	0	1; 708, 314
HhaI	1; 543, 473	2; 541, 240,	1; 880, 100	4; 792, 116,	2; 493, 307,	0	0	2; 762, 107,	2; 533, 221,	1; 954, 68
		206		68, 10, 2	261			104	205
Hin4I	0	0	2; 853, 71, 56	3; 587, 274,	2; 746, 244,	2; 645, 200,	1; 897, 71	2; 846, 71, 56	0	2; 895, 71, 56
				71, 56	71	74
HincII	2; 620, 249,	0	0	1; 605, 383	0	2; 746, 158, 15	2; 826, 118, 24	0	1; 815, 144	2; 825, 121, 76
	147
HindIII	0	1; 767, 220	0	1; 817, 171	0	0	0	0	0	1; 858, 164
HinfI	4; 378, 377,	3; 372, 268,	3; 611, 194,	0	0	4; 422, 202,	1; 620, 348	4; 613, 194,	2; 616, 237,	2; 682, 244,
	168, 62, 31	241, 106	166, 9			143, 113, 39		147, 10, 9	106	96
MaeIII	4; 322, 243	3; 564, 154,	5; 353, 269,	3; 374, 315	2; 734, 194	4; 307, 284,	4; 376, 405,	7; 270, 187,	2; 675, 153,	5; 438, 182
	183,131, 127	138, 131	170,131, 40, 17	168, 131	133	161, 131, 36	156, 84, 47	171, 148, 131,	131	156, 131, 68,
								30, 19, 17		47
Enzyme	bicornutum	carpocapsae	feltiae	glaseri	intermedium	monticolum	neocurtillae	oregonense	scapterisci	sp.
	(1016 bp)	(987 bp)	(980 bp)	(988 bp)	(1061 bp)	(916 bp)	(968 bp)	(973 bp)	(959 bp)	(1022 bp)
MseI	19; 151, 101,	9; 324, 134,	8; 252, 189,	3; 550, 295	13; 173, 167,	7; 224, 187,	22; 202, 100,	7; 334, 243,	11; 378, 136,	8; 348, 180,
	100, 100,79,	102,100, 93,	168, 144, 100,	100, 43	166,104, 102,	169, 100, 93,	92, 60, 57, 56,	168, 100, 43,	100, 92, 73, 68,	145, 100, 79,
	76, 66, 64, 60,	85, 60, 43, 32,	43, 41, 29		101, 80, 51, 43,	86, 46, 14	50, 43, 43, 43,	41, 29, 15	43, 28, 13, 12,	51, 43, 42, 34
	45, 44, 30, 21,	14			29, 17, 15, 8, 5		35, 29,29,23,		9, 7
	20, 15, 13, 10,						21, 16, 15, 13,
	9, 7, 5						13, 11, 8, 5, 4
MwoI	4; 335, 231,	5; 429, 200,	3; 461, 425, 53,	6; 225, 224	6; 264, 249,	3; 411, 262,	1; 501, 467	4; 417, 257,	6; 397, 199,	4; 476, 247,
	200, 156, 94	112, 53, 41	41	205,177, 63,	215, 187, 53,	152, 94		205, 53, 41	157, 73, 53, 41,	205, 53, 41
				53, 41	50, 43				39
PvuII	1; 716, 300	0	0	2; 494, 293	0	0	0	0	1; 619, 340	1; 729, 293
				201
RsaI	2; 806, 208, 2	3; 363, 316,	5; 431, 236,	5; 652, 130,	2; 688, 371, 2	5; 656, 137,	3; 767, 180,	4; 423, 240,	3; 642, 183,	3; 693, 190,
		306, 2	148, 117, 46, 2	129, 63, 12, 2		67, 47, 10, 2	19, 2	189, 119, 2	132, 2	137, 2
SalI	0	0	0	1; 603, 385	0	1; 759, 160	0	0	0	0
Sau3A1	4; 532, 164,	3; 521, 235,	4; 518, 239,	3; 522, 263	5; 500, 168,	5; 468, 164	3; 524, 280,	7; 231, 203,	3; 525, 252,	2; 533, 325,
	162, 142, 16	164, 67	87,77, 59	164, 39	166, 157, 54,	107, 90, 67, 23	87, 77	165, 120, 87,	164, 18	164
					16			77, 59, 31
Sau96I	0	0	1; 827, 153	0	1; 671, 390	0	0	0	0	0
SimI	1; 604, 412	1; 602, 385	2; 382, 341,	2; 386, 369,	1; 627, 434	1; 587, 332	1; 580, 388	1; 590, 383	1; 570, 389	2; 397, 392,
			257	233						233
TaqI	8; 383, 119,	5; 419, 309,	9; 275, 155,	9; 254, 148,	6; 404, 308,	9; 366, 119,	5; 359, 346,	10; 241, 138,	5: 347, 223,	13; 244, 205,
	107,103, 92,	83, 72, 66, 38	119,112, 102,	148, 119, 85,	119, 85, 68, 39,	87, 72, 66, 64,	119, 66, 40, 38	125, 119, 102,	159, 126, 66,	138, 119, 84,
	68, 66, 40, 38		66, 49, 40, 38,	84, 66, 38, 37,	38	49, 40, 38, 18		66, 52, 50, 38,	38	66, 38, 38,28,
			24	9				26, 16		22,14, 12, 9, 5
Tth111II	1; 698, 318	3; 497, 254,	2; 576, 355,	3; 433, 359,	6; 292, 229,	3; 304, 302,	2; 558, 361,	3; 356, 354,	2; 706, 197	1; 222, 800
		164, 72	49	147, 49	186, 133, 127,	261, 52	49	214, 49	56
					49, 45

Last Updated on 06/11/2001
By Khuong Nguyen