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Table 4 Primer pairs used for qPCR of the Pokey family and rRNA genes in the Daphnia pulex complex

From: Distribution of the DNA transposon family, Pokey in the Daphnia pulex species complex

Genea Primer Primer sequence Amplicon Size (bp) Sourceb Thresholdc PAEd
18S 18S 1864 F 5'-ccg cgt gac agt gag caa ta 50 [17] 0.200 0.947
  18S 1913 R 5'-ccc agg aca tct aag ggc atc   [17]   
28S 28S 2508 F 5'-gcc tgc tcg tac cga tat cc 50   0.200 0.937
  28S 2558 R 5'-cta gag gct gtt cac ctt gga ga     
tPokeyA Pok 3720 F 5'-cag ttc aaa gag tgg ctc ctc c 50   0.200 0.868
  Pok 3770 R 5'-cgg gtc tga ctt ctg gtt cg     
tPokeyB PokB 1375 F 5'-aaa gag gag aag aat gac ccg g 50   0.200 0.897
  PokB 1425 R 5'-tca gaa gag cac cct acc ttg g     
tmPok1 mPok1 524 F 5'-gga cac cta tgg cgg gat t 50   0.200 0.874
  mPok1 574 R 5'-cgc tga ggt ctg tcg gga     
tmPok2 mPok2 714 F 5'-ggt cag ttg gct ccg aca a 45   0.185 0.911
  mPok2 759 R 5'-aa ccc ttt atc gac gcg aag a   T. Elliott, unpublished   
rPokeyA + rmPok1 Pok 6561 F 5'-caa tcg aat ccg acc atc g 66   0.237 0.914
  28S 3073 R 5'-tga cga ggc att tgg cta cc     
rPokeyB PokB 4283 F 5'-aat ttc agt caa gca cgg cc 70   0.244 0.903
  28S 3073 R 5'-tga cga ggc att tgg cta cc     
rmPok2 mPok 714 F 5'-ggt cag ttg gct ccg aca a 68   0.240 0.900
  28S 3073 R 5'-tga cga ggc att tgg cta cc     
Tif TIF392F 5'-gac atc atc ctg gtt ggc ct 50 [17] 0.200 0.936
  TIF442R 5'-aac gtc agc ctt ggc atc tt   [17]   
Gtp GTP385R 5'-tat tca gca tgg aga gac ggc 50 [17] 0.200 0.928
  GTP435R 5'-gat gtc gac tga cgc tgg aa   [17]   
  1. a18S = 18S rRNA genes, 28S = total 28S rRNA genes, tPokey = total Pokey, tmPok = total mPok, rPokey = Pokey inserted in 28S, rmPok = mPok1 inserted in 28S
  2. bUnless otherwise indicated, primers were designed for this study
  3. cA threshold of 0.2 was used for 50 bp amplicons. The threshold for larger amplicons was determined using the formula, 0.2 x 2^[1-(50/length in bp)] as in Eagle and Crease [10]
  4. dPAE = primer amplification efficiency