Table 2. Primer pairs, annealing temperatures and resulting fragment sizes for PCR reactions.

Primer pairs—forward/reverse	5′–3′ Forward primer sequence	5′–3′ Reverse primer sequence	Ta (°C)	Approximate amplicon size (bps)	Reference
CO1
dgLCO1490/dgHCO2198	GGTCAACAAATCATAAAGAYATYGG	TAAACTTCAGGGTGACCAAARAAYCA	50 and 45	650	Meyer (2003)
jgLCO1490/jgHCO2198	TITCIACIAAYCAYAARGAYATTGG	TAIACYTCIGGRTGICCRAARAAYCA	50 and 45	650	Geller et al. (2013)
16S rRNA + tRNA-Leu + NADH1
NDH5/16L2	GCYAAYCTWACTTCATAWGAAAT	TGCCTGTTTATCAAAAACAT	48 and 44	1,200	Schubart, Cuesta & Felder (2002)
16S rRNA
16H11/16L2	AGATAGAAACCRACCTGG	See above	48 and 44	580	Schubart (2009)
crust16sF1/crust16sR2	CCGGTYTGAACTCAAATCATGTAAA	TTGCCTGTTTATCAAAAACATGTYTRTT	50 and 45	515	Lai et al. (2009)
28S (D1–D2 region)
LSUfw1brach/LSUrev1brach	AGCGGAGGAAAAGAAACYA	TACTAGATGGTTCGATTAGTC	50 and 45	1,300	This study*
LSUfw2brach/LSUrev2brach	ACAAGTACCGTGAGGGAAAGTTG	ACAATCGATTTGCACGTCAG	55 and 50	890	This study*
F635/LSUrev2brach	CCGTCTTGAAACACGGACC	See above	55 and 50	600	Medina et al. (2001)
H3
H3af/H3ar	TGGCTCGTACCAAGCAGACVGC	TATCCTTRGGCATRATRGTGAC	50 and 47	327	Colgan et al. (1998)

Notes:

^*Modified from Sonnenberg, Nolte & Tautz (2007).

T_a, annealing temperatures used here in a “step-down” PCR approach (see text).