Table 1 |
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|
Estimated copy numbers and total length for families of Class 2 DNA transposons identified in D. pulex listed by subclass and superfamily. |
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|
Superfamily |
Element type |
Number of copies (BLASTN) |
Number of copies (RM) |
Total DNA length |
|
|
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|
Subclass 1 |
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|
CACTA |
CactaA1.1*§ |
18 |
26 |
26,334 |
|
CactaA2.1* |
3 |
4 |
2,494 |
|
|
CactaA3.1*§ |
11 |
11 |
10,397 |
|
|
CactaA4.1*§ |
10 |
12 |
16,296 |
|
|
CactaA5.1*§ |
5 |
7 |
8,933 |
|
|
CactaA6.1* |
3 |
6 |
6,614 |
|
|
CactaA7.1*§ |
11 |
10 |
8,537 |
|
|
CactaA8.1* |
3 |
7 |
7,483 |
|
|
CactaA9.1*§ |
11 |
19 |
24,438 |
|
|
CactaA10.1* |
5 |
7 |
10,255 |
|
|
hAT |
hATA1.1*§ |
2 |
3 |
6,007 |
|
hATNA1.1 |
8 |
2 |
711 |
|
|
hATA2.1* |
5 |
3 |
3,680 |
|
|
hATA3.1*§ |
7 |
7 |
9,743 |
|
|
hATA4.1*§ |
5 |
13 |
12,565 |
|
|
hATA5.1*§ |
10 |
5 |
8,087 |
|
|
Merlin |
MerlinA1.1*§ |
11 |
26 |
36,439 |
|
Mutator |
MutatorA1.1*§ |
7 |
22 |
21,983 |
|
MutatorA2.1*§ |
24 |
39 |
32,291 |
|
|
MutatorA3.1*§ |
4 |
28 |
15,279 |
|
|
MutatorA4.1*§ |
9 |
15 |
18,443 |
|
|
MutatorA5.1*§ |
13 |
9 |
8,898 |
|
|
MutatorA6.1*§ |
19 |
20 |
8,207 |
|
|
MutatorA7.1* |
4 |
8 |
8,831 |
|
|
MutatorA8.1* |
9 |
23 |
10,058 |
|
|
MutatorA9.1*§ |
6 |
5 |
3,015 |
|
|
MutatorA10.1*§ |
6 |
26 |
22,288 |
|
|
P-element |
PelementA1.1* |
6 |
8 |
12,256 |
|
PelementA2.1* |
20 |
21 |
34,335 |
|
|
PelementA3.1* |
1 |
5 |
7,053 |
|
|
PelementA4.1* |
5 |
6 |
11,047 |
|
|
PelementA5.1* |
3 |
3 |
6,727 |
|
|
PelementA6.1* |
1 |
6 |
5,300 |
|
|
PelementA7.1 |
4 |
2 |
1,605 |
|
|
PelementA8.1* |
6 |
2 |
717 |
|
|
PelementNA9.1§ |
19 |
17 |
14,218 |
|
|
PIF |
PIFA1.1*§ |
4 |
6 |
5,918 |
|
PIFA2.1§ |
4 |
9 |
8,033 |
|
|
PiggyBac/TTAAa |
Pokey*§ |
35 |
123 |
271,056 |
|
TTAANA1.1*§ |
130 |
445 |
216,417 |
|
|
TTAANA2.1*§ |
40 |
117 |
39,552 |
|
|
Tc1/mariner |
AntA1.1* |
1 |
1 |
1,041 |
|
PogoA1.1*§ |
4 |
14 |
34,069 |
|
|
PogoA2.1*§ |
9 |
35 |
37,953 |
|
|
PogoA3.1* |
3 |
4 |
7,615 |
|
|
Tc1A1.1*§ |
2 |
2 |
3,519 |
|
|
Tc1NA1.1*§ |
247 |
143 |
63,916 |
|
|
Tc1NA2.1*§ |
7 |
18 |
23,803 |
|
|
Sublclass 2 |
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|
Helitron |
HeliDaphA1.1*§ |
58 |
60 |
136,160 |
|
HeliDaphA2.1*§ |
42 |
55 |
107,599 |
|
|
HeliDaphNA1.1§ |
346 |
389 |
159,331 |
|
|
HeliDaphNA2.1§ |
27 |
69 |
52,123 |
|
|
Maverick |
MaverickA1.1* |
2 |
1 |
2,179 |
|
MaverickA2.1* |
1 |
1 |
1,181 |
|
|
MaverickA3.1* |
2 |
1 |
3,380 |
|
|
MaverickA4.1* |
2 |
2 |
1,892 |
|
|
Total |
1,260 |
1,708 |
1,466,236 |
|
|
|
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|
Copy number estimates are based on filtered outputs from BLASTN (e-value < 0.00001 and >20% of the length of the query) and RepeatMasker (RM; >50 bp in length, >70% similarity, and >20% of the length of the query), respectively. Families with asterisks (*) contain ORFs greater than 100 amino acids in length and families with section sign (§) have hits in the D. pulex genome of >90% over >80% of their length at the nucleotide level, indicating they may be capable of current activity. aElements flanked by TTAA nucleotides, but with insufficient evidence to be confirmed PiggyBac elements, were classified as TTAA elements, along with the previously identified Pokey element [14], known to exhibit this characteristic flanking sequence. |
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|
Schaack et al. Genome Biology 2010 11:R46 doi:10.1186/gb-2010-11-4-r46 |
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