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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.