Table 1 |
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|
An overview of the numbers of transposable elements in the euchromatic genome of D. melanogaster |
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|
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 |
|
|
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|
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 |
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|
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 |
||||
|
|
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|
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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|
Kaminker et al. Genome Biology 2002 3:research0084.1-0084.20 doi:10.1186/gb-2002-3-12-research0084 |
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