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Table 1 TE display and qPCR primers and linkers used in this study

From: Impact of ploidy level on the distribution of Pokey element insertions in the Daphnia pulex complex

Purpose Annealing temperature Primer name Sequence (Dye) Percent amplification efficiency Amplicon size
Linkers for TED / BfaI Linker F 5′-TACTCAGGACTCAT / /
BfaI Linker R 5′-GACGATGAGTCCTGAG
Primary PCR for TED 50°C/55°C Pok6456F 5′-GACAACGGTGGCCGAAACGCGG / /
BfaIR 5′-GACGATGAGTCCTGAGTAG
Secondary PCR for TED 50°C/55°C Pok6464F 5′-TGGCCAAAACACGGTTTGGCCG (HEX) / /
BfaIR 5′-GACGATGAGTCCTGAGTAG
18S genes for qPCR 60°C 18S1864F 5′-CCGCGTGACAGTGAGCAATA 0.9556 50
18S1913R 5′-CCCAGGACATCTAAGGGCATC
28S genes for qPCR 60°C 28S3054F 5′-GGTAGCCAAATGCCTCGTCA 0.9246 150
28S3204R 5′-GAGTCAAGCTCAACAGGGTCTTCTTTCCC
Total Pokey for qPCR 60°C Pok6456F 5′-GACAACGGTGGCCGAAACGCGG 0.9136 122
Pok6578R 5′-GATGGTCGGATTCGATTGAATGCTCG
Pokey in rDNA for qPCR 60°C Pok6456F 5′-GACAACGGTGGCCGAAACGCGG 0.8957 192
28S3104R 5′-GTTAATCCATTCGTGCGCG
Tif for qPCR 60°C TIF392F 5′-GACATCATCCTGGTTGGCCT 0.9493 50
TIF442R 5′-AACGTCAGCCTTGGCATCTT
Gtp for qPCR 60°C GTP385R 5′-TATTCAGCATGGAGAGACGGC 0.9369 50
GTP435R 5′-GATGTCGACTGACGCTGGAA