Marine Biotechnology

, Volume 5, Issue 2, pp 130–140 | Cite as

Phylogenetic Identification of Symbiotic Dinoflagellates via Length Heteroplasmy in Domain V of Chloroplast Large Subunit (cp23S)—Ribosomal DNA Sequences

  • Scott R. Santos
  • Carla Gutierrez-Rodriguez
  • Mary Alice Coffroth


A protocol that takes advantage of length heteroplasmy in domain V of chloroplast large subunit (cp23S)–ribosomal DNA to identify members of the symbiotic dinoflagellate genus Symbiodinium is presented. This protocol is highly specific for Symbiodinium, can provide intercladal and intracladal identification of a particular Symbiodinium isolate, and can detect multiple Symbiodinium chloroplast genotypes simultaneously in the same isolate, making his technique attractive for a variety of research questions. We used this technique to characterize variation among Symbiodinium populations associated with a range of phylogenetically diverse and geographically discrete hosts. We also examined symbiont variation within a single host, the Caribbean gorgonian Pseudopterogorgia elisabethae, from 9 sites in the Bahamas, and we report a previously undocumented level of symbiont specificity for particular members of Symbiodinium clade B in this gorgonian.


chloroplast large subunit ribosomal genes dinoflagellate length heteroplasmy Symbiodinium zooxanthellae 



We thank R.A. Kinzie III (University of Hawaii at Manoa and Hawaii Institute of Marine Biology) and M. Hidaka (University of the Ryukyus) for providing access to their Symbiodinium culture collections; L. Bright, D. Brancato, and J. Weaver for culturing assistance; the Kuna Nation and the Republic of Panama, along with the Florida Keys National Marine Sanctuary, for permission to collect and export samples from Panama and Florida, respectively; and we appreciate the technical and logistical support of the staff and scientists of the following institutions: Smithsonian Tropical Research Institute (STRI), Panama; the Keys Marine Laboratory (KML), Florida; Sesoko Station, University of the Ryukyus, Okinawa, Japan; Gerace Research Center, San Salvador, Bahamas. We also thank the crew of the R/V Sea Ray for logistical support during P. elisabethae collections and Sherwood SCUBA for donating SCUBA equipment used in this study. This research was supported by a National Science Foundation Minority Graduate Fellowship and NSF/Monbusho Summer Program Fellowship (S.R.S.); IIE/Conacyt/Fulbright–Garcia Robles Fellowship (C.G.R.); and NSF OCE-95-30057, OCE-99-07319, and grants from the New York State Sea Grant Program (R/XG-9) and the National Undersea Research Center at the Caribbean Marine Research Center (CMRC-99-3301 & 99-NRHL-01-01C) (M.A.C.).


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Copyright information

© Springer-Verlag New York Inc. 2003

Authors and Affiliations

  • Scott R. Santos
    • 1
  • Carla Gutierrez-Rodriguez
    • 1
  • Mary Alice Coffroth
    • 1
  1. 1.Department of Biological ScienceState University of New York at Buffalo, Buffalo, NY 14260-1300USA

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