The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective

Table 1 An overview of the numbers of transposable elements in the euchromatic genome of D. melanogaster

Class	Arm	Total transposable element sequence (in bp)	% of arm	Total number of transposable elements	Number full length	% Full length	Number of transposable elements perMb in genome	Number of transposable elements perMb in proximal 2 Mb
All families	X	828,370	3.80	276	83	30.43	12.67	50
	2L	878,471	3.95	305	100	32.79	13.73	58.5
	2R	870,914	4.29	313	84	26.84	15.42	89
	3L	938,947	4.02	288	100	34.72	12.33	66.5
	3R	866,971	3.11	288	102	35.76	10.33	24.5
	4	127,874	10.33	102	9	8.82	82.40	-
	Total	4,511,547		1,572	478
	Average		3.86			30.53	13.46	57.70
LTR	X	628,924	2.89	134	54	41.04	6.15	19.00
	2L	603,536	2.72	127	67	52.76	5.72	20.00
	2R	573,034	2.82	140	54	38.57	6.90	30.50
	3L	618,441	2.65	117	58	49.57	5.01	24.00
	3R	621,272	2.23	154	67	44.16	5.52	7.50
	4	44,121	3.56	10	4	40.00	8.08	-
	Total	3,089,328		682	304
	Average		2.65			44.87	5.84	20.20
LINE-like	X	136,348	0.63	71	18	25.35	3.26	14.50
	2L	185,499	0.83	98	20	20.41	4.41	18.50
	2R	225,984	1.11	109	18	16.51	5.37	37.50
	3L	251,077	1.08	106	27	25.47	4.54	24.00
	3R	176,355	0.63	70	19	27.14	2.51	4.50
	4	37,399	3.02	32	1	3.12	25.85	-
	Total	1,012,662		486	103
	Average		0.87			21.19	4.16	19.80
TIR	X	45,324	0.21	59	7	11.86	2.71	14.50
	2L	82,761	0.37	76	11	14.47	3.42	18.00
	2R	69,291	0.34	62	11	17.74	3.05	20.50
	3L	52,743	0.23	57	12	21.05	2.44	16.50
	3R	63,359	0.23	60	14	23.33	2.15	12.50
	4	44,195	3.57	58	3	5.17	46.85	-
	Total	357,673		372	58
	Average		0.31			15.59	3.19	16.40
FB	X	17,774	0.08	12	4	33.33	0.55	2.00
	2L	6,675	0.03	4	2	50.00	0.18	2.00
	2R	2,605	0.01	2	1	50.00	0.1	0.50
	3L	16,686	0.07	8	3	37.50	0.34	2.00
	3R	5,985	0.02	4	2	50.00	0.14	0.00
	4	2,159	0.17	2	1	50.00	1.62	-
	Total	51,884		32	13
	Average		0.04			40.62	0.27	1.30

For each class, the total numbers of each family of element, together with the numbers (and percentage of elements) that are full length is given for each chromosome arm. Column 3 gives the total base pairs contained within transposable elements, column 4 the percentage of each chromosome arm composed of transposable element sequences, column 8 the number of elements perMb, and column 9 the numbers of elements within the most proximal 2 Mb of each of the five major chromosome arms. Differences in density and amount of transposable element sequence were tested by binning major chromosomal arms into 50-kb windows and testing significance by Mann-Whitney U tests. The only significant difference (p < 0.05) observed, either including or excluding the proximal 2 Mb, was an increase in density and amount of sequence on the X chromosome relative to 3R.

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