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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

Flot & Tillier 2006

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