Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes

BMC Genomics

Table 1 Repetitive elements identified in Triticum aestivum (var. Chinese Spring) homeologous group 4 chromosome arms

	4AS _I			4BS _I			4DS _I			4DS ₄₅₄
	#	Length	%	#	Length	%	#	Length	%	#	Length	%
Retroelements	315566	167160901	59.21	268357	164853117	53.49	112608	69191801	48.69	20607	19344019	50.12
DNA transposons	38628	11506157	4.08	49240	15027055	4.88	25899	8060073	5.67	9835	5969965	15.47
Unclassified:	1117	194275	0.07	1303	311827	0.1	707	161819	0.11	1849	539049	1.40
Small RNA:	265	47072	0.02	319	51039	0.02	184	37472	0.03	69	22419	0.06
Satellites:	819	144631	0.05	3929	2914989	0.95	569	116493	0.08	21	2468	0.01
Simple repeats:	10379	583006	0.21	12326	709023	0.23	5394	329739	0.23	1106	47817	0.12
Low complexity:	9628	497086	0.18	9794	510460	0.17	5487	286086	0.2	1293	83621	0.22
Total	376402	180133128	63.82	345268	184377510	59.84	150848	78183483	55.01	34780	26009358	67.4
	4AL _I			4BL _I			4DL _I			4DL ₄₅₄
	#	Length	%	#	Length	%	#	Length	%	#	Length	%
Retroelements	343182	180465664	49.86	269612	124807259	50.19	328691	116699122	33.57	15107	14212381	52.61
DNA transposons	71092	21753200	6.01	51423	14335731	5.77	53046	12099355	3.48	6296	3030966	11.22
Unclassified:	2334	561199	0.16	1405	345580	0.14	1622	328062	0.09	1258	342679	1.27
Small RNA:	535	101456	0.03	273	42903	0.02	349	46900	0.01	55	14356	0.05
Satellites:	1695	299708	0.08	3051	1041847	0.42	2128	296676	0.09	16	2622	0.01
Simple repeats:	13225	727067	0.2	10237	571582	0.23	47444	3205296	0.92	750	31119	0.12
Low complexity:	14467	772219	0.21	8455	453240	0.18	35801	1723366	0.5	1104	74281	0.27
Total	446530	204680513	56.55	344456	141598142	56.95	469081	134398777	38.66	24586	17708404	65.55

The chromosome arms are expressed by a number that indicates the homeologous group followed by a letter that indicates the genome (A, B or D) and the chromosome arm (S: short; L: long). The subscripts refer to the technology used for sequencing (I: Illumina; 454: Roche 454). For each element class the number of elements (#), the length of the sequence occupied by these elements (length) and the percentage of the sequence that is covered by repetitive elements (%) are given.

ISSN: 1471-2164