Primers
COI
Folmer et al. 1994
LCO1490: 5' GGTCAACAAATCATAAAGATATTGG 3'
HCO2198: 5' TAAACTTCAGGGTGACCAAAAAATCA 3'
Recommended for Hexacorallia:
Sinniger et al. 2010
LCOant: 5' TTTTCYACTAATCATAAAGATAT 3'
COIantr: 5' GCCCACACAATAAAGCCCAATAYYCCAAT 3'
(793 bp: this primer pair was designed based on zoanthids, scleractinians, antipatharians, Metridium and Sarcophyton, tested on zoanthids, scleractinians and sea anemones)
Recommended for Octocorallia:
McFadden et al. 2011
COII8068x-F: 5'- CCA TAA CAG GRC TWG CAG CAT C - 3'
COIOCT-R: 5' - ATC ATA GCA TAG ACC ATA CC - 3'
(900-950 bp: This primer pair also amplifies igr1, the intergenic region between COI and COII)
alternative COI primers (may be paired with COII8068x-F or COIOCT-R):
COI8414-F: 5' - CCAGGTAGTATGTTAGGRGA - 3' (McFadden unpubl.; starts at nt 135 of COI)
HCO2198-R: 5' - TAAACTTCAGGGTGACCAAAAAATCA - 3' (Folmer et al. 1994)
16S
Anthozoans
Sinniger et al. 2005
16Sant1a: 5' GCCATGAGTATAGACGCACA 3'
16SbmoH: 5' CGAACAGCCAACCCTTGG 3'
16Sant1a-16SbmoH: 650-780 bp
Sinniger et al. 2008
16Sarml: 5' GGCCTCGACTGTTTACCAAA 3'
16Sarml-16SbmoH: 430-540 bp
V5a: 5' ATTCGTAGTGAAGATGCTAC 3'
V5r: 5' TCGCCCCAACCAAACTGTCC 3'
Tested on zoanthids, sea anemones, scleractinians, antipatharians and cerianthids, 150-250bp.
Msh1
Octocorallians
ND42599F 5' GCCATTATGGTTAACTATTAC 3' (France & Hoover 2002))
mut3458R 5' TSGAGCAAAAGCCACTCC 3' (Sanchez et al. 2003)
an alternative forward primer is necessary for Keratoisidinae:
CO3BAM5657F 5' GCTGCTAGTTGGTATTGGCAT 3' (Brugler & France 2008)
ITS2
ITSc2-5: 5'-AGCCAGCTGCGATAAGTAGTG-3'
R28S1: 5'-GCTGCAATCCCAAACAACCC-3'
These primers works on all cnidarian tested and beyond (sponges, bryozoa,...), but they do not amplify the ITS2 of dinoflagellates such as Symbiodinium