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Detecting DNA of multispecies dinoflagellate cysts in the sediment from three estuaries of Makassar strait and fishing port using CO1 primer: Is it CO1 primer suitable for detecting DNA dinoflagellate?


  • Nita Rukminasari Fisheries Department, Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar, South Sulawesi, Indonesia.
  • Andi Aliah Hidayani Fisheries Department, Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar, South Sulawesi, Indonesia.
  • Andi Parenrengi Research Center for Fisheries, National Research and Innovation Agency, Indonesia.
  • Sapto Andriyono Department of Marine, Faculty of Fisheries and Marine, Universitas Airlangga, East Java, Indonesia.



CO1 primer, DNA dinoflagellate cyst, Makassar Strait, Maros-Pangkep and Jeneberang Estuary, PCR method


Most dinoflagellate had a resting cyst in their life cycle.  This cyst was developed in unfavorable environmental condition. The conventional method for identifying dinoflagellate cyst in natural sediment requires morphological observation, isolating, germinating and cultivating the cysts.  PCR is a highly sensitive method for detecting dinoflagellate cyst in the sediment.  The aim of this study is to examine whether CO1 primer could detect DNA of multispecies dinoflagellate cysts in the sediment from our sampling sites. Dinoflagellate cyst DNA was extracted from 16 sediment samples. PCR method using COI primer was running. The sequencing of dinoflagellate cyst DNA was using BLAST. Results showed that there were two clades of dinoflagellate cysts from four locations of study.  Clade 1 was dominated by samples from the Jeneberang Estuary (JB), Maros Estuary (M) and Pangkep Estuary(P), while clade 2 was dominated by samples from the Paotere Port (PP). The genetic distance varied between DNA dinoflagellate cyst samples ranging from 0.5 -0.6. The closest genetic distance was between sample of JB1 and sample of JB2, while the farthest genetic distance was sample PP1 and PP2. The primer CO1 was not suitable for dinoflagellate cyst DNA due to only picking one DNA, which was a diatom (Licmophora sp).


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