Sensitive, Accurate PCR Assays for Detecting Harmful Dinoflagellate Cochlodinium polykrikoides Using a Specific Oligonucleotide Primer Set
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Abstract
Harmful Cochlodinium polykrikoides is a notorious harmful algal bloom (HAB) species that is causing mass mortality of farmed fish along the Korean coast with increasing frequency. We analyzed the sequence of the large subunit (LSU) rDNA D1-D3 region of C. polykrikoides and conducted phylogenetic analyses using Bayesian inference of phylogeny and the maximum likelihood method. The molecular phylogeny showed that C. polykrikoides had the genetic relationship to Amphidinium and Gymnodinium species supported only by the relatively high posterior probabilities of Bayesian inference. Based on the LSU rDNA sequence data of diverse dinoflagellate taxa, we designed the C. polykrikoides-specific PCR primer set, CPOLY01 and CPOLY02 and developed PCR detection assays for its sensitive, accurate HAB monitoring. CPOLY01 and CPOLY02 specifically amplified C. polykrikoides and did not cross-react with any dinoflagellates tested in this study or environmental water samples. The effective annealing temperature (Tp) of CPOLY01 and CPOLY02 was 67℃. At this temperature, the conventional and nested PCR assays were sensitive over a wide range of C. polykrikoides cell numbers with detection limits of 0.05 and 0.0001cells/reaction, respectively.
참고문헌 (54)
- "The oligonucleotide The oligonucleotide database project. database project.", 62,, pp.3557~3559 (1996)
- "Physiology and bloom dynamics of toxic Alexandrium species, with emphasis on life cycle transitions. In: Physiological Ecology of Harm- ful Algal Blooms, Anderson, D.M., A.D. Cembella and G.M. Hallegraeff, eds.", 41, pp.29~48 (1998), Springer-Verlag,
- "De- velopment of real-time PCR assay for rapid detection of Pfiesteria piscicida and related dinoflagellates", 66, pp.4641~4648 (2000)
- "Discrimination of three species of dino- flagellates Cochlodinium polykrikoides, Gyrodinium impudicum and Gymnodinium catenatum using FITC- lectins.", 15,, pp.175~178 (2000)
- "A comparative study of the harmful dinoflagellates Cochlodinium poly- krikoides and Gyrodinium impudicum using trans- mission electron microscope, fatty acid composition, carotenoid content, DNA quantification and gene sequences.", 44, pp.57~66 (2001)
- "Phylogeny of some of the major genera of dinoflagellates based on ultrastructure and partial LSU rDNA sequence data, including the erection of three new genera of unarmored dinoflagellates.", 39, pp.302~317 (2000)
- "Genetic variability and molecular phylogeny of Dinophysis species (Dinophyceae) from Norwegian waters inferred from single cell analysis of rDNA.", 39, pp.395~408 (2003)
- "Confidence limits on phylogenies", tion, pp.16~24 (1985)
- "PCR detection of dinoflagellate cysts in field sediment samples from tropic and temperate environments.", 1, pp.361~373 (2002)
- "Molecular detection and quantitation of the red tide dinoflagellate Karenia brevis in the marine environ- ment.", 69,, pp.5726~5730 (2003)
- "Ultrastructure of Gyrodinium spirale, the type species of Gyrodinium (Dinophyceae), including a phylogeny of G. domi- nans, G. rubrum and G. spirale deduced from partial LSU rDNA sequences." (2004)
- "DNA extraction conditions from Porphyra perforata using LiCl.", 7, pp.101~107 (1995)
- "MRMAYES: Bayesian inference of phylogenetic trees.", 17,, pp.754~755 (2001)
- "Bayesian inference of phylogeny and its impact on evolutionary biology.", 294,, pp.2310~2314 (2001)
- "Discrimination of the toxigenic dinoflagellates Alexandrium tamarense and A. ostenfeldii in co-occurring natural populations from Scottish coastal waters.", 38, pp.25~40 (2003)
- "The application of a molecular clock based on molecular sequences and the fossil record to explain biogeo- graphic distributions within the Alexandrium tamarense "species complex" (Dinophyceae).", 20,, pp.1015~1027 (2003)
- "Recent harmful algal blooms and mi- tigation strategies in Korea", 19,, pp.185~192 (1997)
- "Reactive oxygen species as causative agents in the ichthyotoxicity of the red tide dinoflagellate Cochlodinium polykrikoides.", 21, pp.2105~2115 (1999)
- "Biochemical response of fish exposed to a harmful dinoflagellate Cochlodinium polykrikoides.", 254, pp.131~141 (2000)
- "Physico-chemical factors on the growth of Cochlodinium polykrikoides and nutrient utilization.", 34, pp.445~456 (2001)
- "The spatio-temporal progress of Cochlodinium poly- krikoides blooms in the coastal waters of Korea.", 34, pp.691~696 (2001)
- "Regeneration from hyaline cysts of Cochlodinium polykrikoides (Gymnodiniales, Dino- phyceae), a red tide organism along the Korean coast.", 41, pp.667~669 (2002)
- "Phylogenetic analysis of harmful algal blooming (HAB)-causing dinoflagellates along the Korean coasts based on the SSU rRNA gene." (2004)
- "Performance of an RT-nested PCR ELISA for detection of Newcastle disease virus.", 86, pp.71~83 (2000)
- "Abundance of harmful algae, Cochlodinium polykrikoides, Gyrodinium impudicum and Gymnodinium catenatum in the coastal area of south sea of Korea and their effects of temperature, salinity, irradiance and nutrient on the growth in culture.", 34, pp.536~544 (2001)
- "Direct iden- tification of Vibrio vulnificus in clinical specimens by nested PCR.", 36,, pp.2887~2892 (1998)
- "The outbreak, main- tenance and decline of the red tide dominated by Cochlodinium polykrikoides in the coastal waters off southern Korea from August to October, 2000.", 7,, pp.68~77 (2002)
- "Identification of Pfiesteria piscicida (Dinophyceae) and Pfiesteria-like organisms using internal transcribed spacer-specific PCR assays.", 39, pp.754~761 (2003)
- "A seawater medium for dino- flagellates and the nutrition of Cachonina niei", pp.80~86 (1975)
- "Identification and enumeration of cultured and wild Pseudo-nitzschia (Bacillariophyceae) using species-specific LSU rRNA- targeted fluorescent probes and filter-based whole cell hybridization.", 34, pp.371~382 (1998)
- "Simplicity-correlated size growth of the nuclear 28S ribosomal RNA D3 expansion segment in the crustacean order Isopoda.", 42, pp.211~223 (1996)
- "Comparison of the mor- phological characteristics and the 24S rRNA se- quences of Cochlodinium polykrikoides and Gyro- dinium impudicum.", 4, pp.363~371 (1999)
- "MODELTEST: testing the model of DNA substitution.", 14,, pp.817~818 (1998)
- "Partial sequence of the 28S rRNA and polymerase chain reaction based assay for the toxic dinoflagellate Dinophysis acuminata.", 55,, pp.597~604 (1998)
- "Molecular studies of Dinophysis (Dinophyceae) species from Sweden and North America.", 41,(T), pp.348~357 (2002)
- "The design and optimization of the PCR Principles and Application for DNA Amplification", pp.7~16 (1994), Oxford Uni- versity Press
- "Characterization of the rRNA locus of Pfiesteria piscicida and development of standard and quantitative PCR-based detection assays targeted to the nontranscribed spacer.", 68, pp.5394~5407 (2002)
- "Detection and quantification of Pseudo-nitzschia australis in cultured and natural populations using LSU rRNA-targeted probes.", 42, pp.1265~1272 (1997)
- "Detection of HAB species using lectin, antibody and DNA probes. In: Manual on Harmful Marine Microalgae, Hallegraeff, G.M., D.M. Anderson and A.D. Cembella eds.", pp.131~163 (2003), Intergovernmental Oceanographic Commission, UNESCO
- "Identification of group- and strain-specific genetic markers for globally distributed Alexandrium Sequence analysis of a fragment of the LSU rRNA gene", di(phyceae), pp.999~1011 (1994)
- "The design of primers for PCR", pp.5~11 (1994), CRC Press
- "Relationship between sea surface temperature derived from NOAA satellites and Cochlodinium polykrikoides red tide occurrence in Korean coastal waters.", 9,, pp.215~221 (2000)
- ""PAUP": Phylogenetic Analysis Using Parsimony (and Other Methods), Version 4.0b10," (2002), Sinauer Associates,
- "Surface ultrastructure and molecular phylogenetics of four unarmored he- terotrophic dinoflagellates, including the type species of the genus Gyrodinium (Dinophyceae).", 52, pp.107~116 (2004)
- "Apical grooves of unarmored dino- flagellates", 32, pp.129~140 (1985)
- "Genetic polymorphism in Gym- nodinium galatheanum chloroplast DNA sequences and development of a molecular detection assay.", 10,, pp.515~523 (2001)
- "improving the sensitivity of progres- sive multiple sequence alignment through sequence weighting", pp.4673~4680 (1994)
- "Moni- toring for Heterosigma akashiwo using a sandwich hybridization assay", 1, pp.205~214 (2002)
- "First record of blooms of Cochlodinium sp. (Gymnodiniales, Dinophyceae) causing mortality to aquacultured salmon on the west coast of Canada.", 40, pp.298~304 (2001)
- "The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction", pp.233~238 (1991)
- "The European large subunit ribosomal RNA database.", 29,, pp.175~177 (2001)
- "Two fish-killing species of Cochlodinium from Harima-Nada", pp.451~454 (1989)
- "Revised dino- flagellate phylogeny inferred from molecular analysis of large-subunit ribosomal RNA gene sequences.", 41, pp.637~645 (1995)
- "Detection and quantification of Pfiesteria piscicida by using the mitochondrial cytochrome b gene.", 68, pp.989~994 (2002)
