Table 1

Estimated copy numbers and total length for families of Class 2 DNA transposons identified in D. pulex listed by subclass and superfamily.

Superfamily

Element type

Number of copies (BLASTN)

Number of copies (RM)

Total DNA length


Subclass 1

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

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


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.

Schaack et al. Genome Biology 2010 11:R46   doi:10.1186/gb-2010-11-4-r46

Open Data