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. Author manuscript; available in PMC: 2010 Apr 20.
Published in final edited form as: J Phycol. 2006 Dec 1;42(6):1333–1348. doi: 10.1111/j.1529-8817.2006.00285.x

Table 3.

Primers and probes for species-specific real-time PCR assays targeting various raphidophytes. Five different assays were designed and validated against the panel of cultures listed in Table 1.

Target organism Oligo Primer/probe Target loci Sequence 5′–3′ Amplicon length Annealing temperature
Chattonella verruculosa 227 58° C
ChattaqFor Forward 18S rRNA CCGTAGTAATTCTAGAGCTAATACRTGCA
ChattaqRev Reverse 18S rRNA AATTCTCCGTTACCCGTTAAAGCCAT
CVerrProbe Probe 18S rRNA [6~FAM]AATGGCGCGCAAGCG-TGTATTATG[TAMRA~Q]
C. marina 224 60° C
C. antiqua CmarinaFor Forward ITS2 rRNA GGTAGTTGCCGTACATTTTGCTCTT
C. ovata CmarinaRev Reverse ITS2 rRNA AAAAGTGGATTCAGCCGAAGCTTC
CmarinaProbe Probe ITS2 rRNA [6~FAM]TTGAGTTCAACGGGCGTG-GTAGC[BHQ~6~FAM]
C. subsalsa 156 60° C
SubsalsaFor Forward ITS2 rRNA TTGGATTCCGACGGGC
SubsalsaRev Reverse ITS2 rRNA ATATGCTTAAATTCAGCGGGTTTT
SubsalsaProbe Probe ITS2 rRNA [6~FAM]TTCGGCCAAGCACACAT-CCTC[TAMRA~6~FAM]
Fibrocapsa japonica 167 57° C
Fjap490For Forward 28S rRNA TGAAAACGGCCCGTACACA
Fjap657Rev Reverse 28S rRNA CGGGAACAGCTCATGATGT
Fjap578Probe Probe 28S rRNA [6~FAM]CGGCTGGACACGCTTCTG[BHQ1~Q]
Heterosigma akashiwo 228 62° C
Haka127For Forward 28S rRNA AAAGGTGCGTGCTCAGTCGTGGT
Haka355Rev Reverse 28S rRNA CAAAAGTCTTTTCATCTTTCCCT
Haka222Probe Probe 28S rRNA [5TET]TACGAGCCGTTTCCGACGA[BHQ1~Q]

Loci were chosen based on ability to distinguish target species from others. Amplicon length and annealing temperatures are provided.