Analysis of recent segmental duplications in the bovine genome

BMC Genomics

Table 1 Repeat properties of bovine genome, duplications, and flanking regions

Repeat	Duplications					20-kb flanks					Genome					Enrichment ratio in duplication content
	Length	Count	Ave. Len.	Length%	Count/ 1 Mb	Length	Count	Ave. Len.	Length%	Count/ 1 Mb	Length	Count	Ave. Len.	Length%	Count/ 1 Mb	Length%	Count/ 1 Mb	Ave. Len.
DNA	505,659	2,777	182	1.09%	6.01	281,144	1,599	176	1.62%	9.20	56,383,709	304,851	185	1.93%	10.45	0.57**	0.58	0.98
LINE	10,138,094	23,014	441	21.95%	49.82	3,993,714	10,320	387	22.99%	59.40	624,600,656	1,655,642	377	21.41%	56.74	1.03*	0.88	1.17
SINE	5,870,448	26,627	220	12.71%	57.64	2,699,548	12,975	208	15.54%	74.68	464,030,104	2,203,064	211	15.90%	75.50	0.80**	0.76	1.05
LTR	1,565,238	6,322	248	3.39%	13.68	661,698	2,893	229	3.81%	16.65	99,886,031	444,168	225	3.42%	15.22	0.99	0.90	1.10
Satellite	143,866	49	2,936	0.31%	0.11	22,946	53	433	0.13%	0.31	4,749,093	3,626	1,310	0.16%	0.12	1.91*	0.85	2.24
Simple	214,338	4,972	43	0.46%	10.76	88,930	1,999	44	0.51%	11.51	14,261,600	343,825	41	0.49%	11.78	0.95	0.91	1.04
Low complexity	169,741	4,390	39	0.37%	9.50	80,640	2,050	39	0.46%	11.80	14,280,594	370,243	39	0.49%	12.69	0.75**	0.75	1.00
Other	100,574	1,263	80	0.22%	2.73	63,019	793	79	0.36%	4.56	8,582,076	105,321	81	0.29%	3.61	0.74	0.76	0.98
Total repeat	18,707,958	69,414	270	40.50%	150.26	7,891,639	32,682	241	45.42%	188.11	1,286,773,863	5,430,740	237	44.10%	186.11	0.92	0.81	1.14
Total analyzed	46,196,844	138,828				17,373,955	65,364				2,917,958,192	10,861,480

We compare the repeat content of duplicated regions as detected by both WSSD and WGAC (with ChrUnAll excluded); 20-kb flanking regions immediately flanking the clustered duplications and the genome average. Enrichment ratios were defined as the total repeat length, count/1 Mb and average length of duplicated sequence divided by the repeat length, count/1 Mb and average length of genome. The significance of the enrichment was determined by simulating the repeats in a random sample (n = 1,000) of cattle duplicated genomic sequence (**: P-value < 0.001, *: P-value < 0.01).

ISSN: 1471-2164