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

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

Gene^a	Primer	Primer sequence	Amplicon Size (bp)	Source^b	Threshold^c	PAE^d
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	mPok2 759 R	5'-aa ccc ttt atc gac gcg aag a		T. Elliott, unpublished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]

^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
^bUnless otherwise indicated, primers were designed for this study
^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]
^dPAE = primer amplification efficiency

ISSN: 1759-8753