Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome

Table 1 Abundance of D. melanogaster TEs annotated in Release 4 genome sequence by genomic region

	Class	Total bp TE	% TE	No. of TEs	No. of TE per Mbp	No. of TE full length	% TE full length	No. of TE nested	% TE nested
Genome	LTR	3,896,903	3.29	1,321	11.16	325	24.60	327	24.75
	Non-LTR	1,502,997	1.27	1,019	8.61	121	11.87	197	19.33
	TIR	559,234	0.47	752	6.35	57	7.58	157	20.88
	INE-1	490,996	0.41	2,238	18.91	26	1.16	91	4.07
	FB	60,509	0.05	60	0.51	1	1.67	13	21.67
	Total	6,510,639	5.50	5,390	45.54	530	9.83	785	14.56
Non-pericentromeric	LTR	2,510,569	2.42	515	4.96	250	48.54	80	15.53
	Non-LTR	646,020	0.62	336	3.24	80	22.92	9	2.68
	TIR	151,997	0.15	214	2.06	25	11.68	12	5.61
	INE-1	106,597	0.10	660	6.36	5	0.76	8	1.21
	FB	28,125	0.03	23	0.22	1	4.35	3	13.04
	Total	3,443,308	3.32	1,748	16.85	361	20.48	112	6.41
Pericentromeric	LTR	1,324,428	9.94	776	58.24	70	9.02	241	31.06
	Non-LTR	802,040	6.02	623	46.75	42	6.58	169	27.13
	TIR	323,226	2.43	436	32.72	29	6.65	115	26.38
	INE-1	300,615	2.26	1,234	92.61	17	1.38	71	5.75
	FB	27,773	0.21	32	2.40	0	0.00	9	28.13
	Total	2,778,082	20.85	3,101	232.72	158	5.06	605	19.51
Chromosome 4	LTR	61,906	4.83	30	23.41	5	16.67	6	20.00
	Non-LTR	54,937	4.29	60	46.82	3	5.00	19	31.67
	TIR	84,011	6.55	102	79.59	3	2.94	30	29.41
	INE-1	83,784	6.54	344	268.41	4	1.16	12	3.49
	FB	4,611	0.36	5	3.90	0	0.00	1	20.00
	Total	289,249	22.57	541	422.12	15	2.77	68	12.57

Overall abundance was partitioned into pericentromeric and non-pericentromeric regions according to the text. Full-length elements were defined as ± 3% of the canonical element. Both inner and outer components of a TE nest were considered nested.

ISSN: 1474-760X