Skip to main content

Table 1 Estimated copy numbers and total length for families of Class 2 DNA transposons identified in D. pulex listed by subclass and superfamily.

From: DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex

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

  1. 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.
Back to article page

Genome Biology

ISSN: 1474-760X

Contact us