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 |