Table 1.
Total number of TE copies detected in the chromosome arms 2L, 2R, 3L, 3R, and X
|
Number of copies on chromosome arm
|
CS
|
DS
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Class | Name | Access number of canonical sequences | 2L | 2R | 3L | 3R | X | Identical copies/complete copiesa/Total copies | % | Average age (Myr) | % | Average age (Myr) |
| LTR retrotransposons | mdg1 | X59545b | 3 | 8 | 4 | 3 | 3 | 18/14/21 | 99.13 (0.07) | 0.25±0.043 | 85.39 (17) | 4.56±1.29 |
| 412 | X04132b | 0 | 6 | 11 | 5 | 8 | 29/25/30 | 99.77 (0.02) | 0.07±0.05 | 80.75 | 7.19 | |
| stalker | AF420242b | 0 | 1 | 4 | 3 | 3 | 11/1/11 | 97.99 (7.23) | 1.49±0.89 | - | - | |
| new-stalker | - | 0 | 1 | 2 | 1 | 3 | 7/3/7 | 99.80 (0.002) | 0.062±0.044 | - | - | |
| blood | X04671b | 11 | 2 | 2 | 5 | 1 | 21/20/21 | 99.92 (0.001) | 0.023±0.009 | - | - | |
| tirant | X93507b | 3 | 3 | 4 | 5 | 4 | 19/15/19 | 99.93 (0.008) | 0.021±0.03 | - | - | |
| zam | AJ000387b | 0 | 0 | 0 | 0 | 0 | - | - | - | - | - | |
| copia | M11240b | 13 | 5 | 5 | 4 | 4 | 30/26/31 | 99.88 (0.007) | 0.036±0.027 | 78.00 | 6.87 | |
| 297 | X03431b | 13 | 8 | 6 | 8 | 19 | 44/11/54 | 99.34 (0.014) | 0.21±0.04 | 86.23 (12.58) | 4.30±1.11 | |
| 17.6 | X01472b | 0 | 3 | 5 | 2 | 4 | 14/2/14 | 99.46 (0.14) | 0.17±0.12 | - | - | |
| rover | AF492764b | 0 | 1 | 0 | 2 | 2 | 4/1/5 | 99.21 (1.43) | 0.25±0.38 | 82.00 | 5.60 | |
| roo/B104 | AL031366b | 20 | 25 | 25 | 25 | 30 | 125/30/125 | 99.61 (0.82) | 0.12±0.30 | - | - | |
| bel | U23420b | 0 | 1 | 2 | 0 | 4 | 5/4/7 | 99.94 (0.002) | 0.019±0.015 | 87.10 | 4.58 | |
| tinker | EBIc | 1 | 3 | 2 | 3 | 1 | 9/8/10 | 99.85 (0.007) | 0.047±0.026 | 85.00 | 5.31 | |
| Non-LTR retrotransposons | jockey | M22874b | 9 | 18 | 14 | 14 | 17 | 66/0/72 | 99.63 (0.11) | 0.20±0.22 | 84.28 (3.85) | 4.91±0.61 |
| F | M17214b | 9 | 13 | 11 | 10 | 3 | 39/5/46 | 99.41 (2.80) | 0.10±0.16 | 83.55 (6.36) | 5.14±0.79 | |
| doc | X17551b | 15 | 5 | 17 | 10 | 5 | 50/19/52 | 99.81 (0.08) | 0.06±0.09 | 88.53 | 3.58 | |
| doc2 | BDGPd | 0 | 2 | 0 | 0 | 0 | 1/0/2 | 98.44 | 0.49 | 85.00 | 4.69 | |
| doc3 | BDGPd | 1 | 5 | 1 | 0 | 0 | 7/0/7 | 95.61 (0.81) | 2.05±0.83 | - | - | |
| Transposons | hobo | M69216b | 16 | 6 | 1 | 12 | 7 | 19/0/42 | 99.97 (0.002) | 0.01±0.015 | 87.84 (8.79) | 3.80±0.93 |
| pogo | X59837b | 12 | 5 | 7 | 11 | 8 | 43/5/43 | 99.88 (0.07) | 0.04±0.08 | - | - | |
| bari-1 | X67681b | 2 | 1 | 0 | 2 | 0 | 1/3/5 | 99.85 (0.007) | 0.04±0.026 | 81.02 | 5.93 | |
CS: % of similarity of conserved sequences
DS: % of similarity of diverged sequences
The variances of CS and DS are in parentheses
a
Copies with all functional features, and without internal deletions or truncations
b
Genbank accession number
c
EBI reference (European Bioinformatics Institute)
d
BDGP reference (Berkley Drosophila Genome Project)