Fisheries and Aquatic Sciences

The Korean Society of Fisheries and Aquatic Science (한국수산과학회)
권호 표지
DOI QR코드

DOI QR Code

Detection of Laminariaceae Species Based on PCR by Family-specific ITS Primers

  • Choi, Chang-Geun (Department of Ecological Engineering, Pukyong National University) ;
  • Kim, Jong-Myoung (Department of Marine Bio-Materials and Aquaculture, Pukyong National University)
  • Received : 2012.02.28
  • Accepted : 2012.05.24
  • Published : 2012.06.30
Download PDF
⟨ Previous Next ⟩

Abstract

To analyze nucleotide sequence encoding internal transcribed spacer (ITS) regions specific to the Laminariaceae family, genomic DNA was isolated from six brown algae species distributed along the east coast of Korea. These included three species from the Laminariaceae family (Agarum clathratum Dumortier, Costaria costata [C. Agardh] Saunders, and Saccharina japonica Areschoug) and two species from the Alariaceae family (Undaria pinnatifida [Harvey] Suringer and Ecklonia cava Kjellman), both in the order Laminariales, and one species from the family Sargassaceae in the order Fucales (Sargassum serratifolium). Based on a sequence analysis of ITS-1 and ITS-2 for A. clathratum, C. costata, and E. cava, oligonucleotides were designed from the regions that showed sequence conservation in Laminariaceae. Following polymerase chain reaction using three sets of primers, amplification of ITS-1 and ITS-2 was detected in reactions using genomic DNA isolated from the species belonging to Laminariaceae, but not from the species belonging to the other families. The results indicate that this method can be used for the detection and identification of Laminariaceae species.

Keywords

References

  1. Bird CJ, Murphy CA, Rice EL and Ragan MA. 1992. The 18S rRNA gene sequences of four commercially important seaweeds. J Appl Phycol 4, 379-384. https://doi.org/10.1007/BF02185796
  2. Coleman AW and Mai JC. 1997. Ribosomal DNA ITS-1 and ITS-2 sequence comparison as a tool for predicting genetic relatedness. J Mol Evol 45, 168-177. https://doi.org/10.1007/PL00006217
  3. Guiry MD and Guiry GM. 2011. Algaebase, World-wide electronic publication [Internet]. National University of Ireland, Galway, IE, Accessed 28 Jun 2011, http://www.algaebase.org.
  4. Hoarau G, Coyer JA, Stam WT and Olsen JL. 2007. A fast and inexpensive DNA extraction/purification protocol for brown macroalgae. Mol Ecol Notes 7, 191-193. https://doi.org/10.1111/j.1471-8286.2006.01587.x
  5. Kawai H and Sasaki H. 2000. Molecular phylogey of the brown algal genera Akkesiphycus and Halosiphon (Laminariales), resulting in the circumscription of the new families Akkesiphycaceae and Halosiphonaceae. Phycologia 39, 416-428. https://doi.org/10.2216/i0031-8884-39-5-416.1
  6. Kim JM and Choi CG. 2010. Phylogenetic analysis of Phyllospadix iwatensis based on nucleotide sequences encoding 18S rRNA and ITS-1. Fish Aquat Sci 13, 272-277.
  7. Koonjul PK, Brandt WF, Farrant JM and Lindsey GG. 1999. Inclusion of polyvinylpyrrolidone in the polymerase chain reaction reverses the inhibitory effects of polyphenolic contamination of RNA. Nucleic Acids Res 27, 915-916. https://doi.org/10.1093/nar/27.3.915
  8. Lee YP and Kang SY. 2002. A Catalogue of the Seaweeds in Korea. Cheju National University Press, Jeju, KR.
  9. Ragan MA, Bird CJ, Rice EL, Gutell RR, Murphy CA and Singh RK. 1994. A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proc Natl Acad Sci U S A 91, 7276-7280. https://doi.org/10.1073/pnas.91.15.7276
  10. Sambrook J and Russell DW. 2001. Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press, Plainview, NY, US.
  11. Saunders GW. 2005. Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philos Trans R Soc Lond B Biol Sci 360, 1879-1888. https://doi.org/10.1098/rstb.2005.1719
  12. Snirc A, Silberfeld T, Bonnet J, Tillier A, Tuffet S and Sun JS. 2010. Optimization of DNA extraction from brown algae (Phaeophyceae) based on a commercial kit. J Phycol 46, 616-621. https://doi.org/10.1111/j.1529-8817.2010.00817.x
  13. Thompson JD, Higgins DG and Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  14. Torres-Machorro AL, Hernandez R, Cevallos AM and Lopex-Villasenor I. 2010. Ribosomal RNA genes in eukaryotic microorganisms: witnesses of phylogeny? FEMS Microbiol Rev 34, 59-86. https://doi.org/10.1111/j.1574-6976.2009.00196.x
  15. Varela-Alvarez E, Andreakis N, Lago-Leston A, Pearson GA, Serrao EA, Procaccini G, Duarte CM and Marba N. 2006. Genomic DNA isolation from green and brown algae (Caulerpales and Fucales) for microsatellite library construction. J Phycol 42, 741-745. https://doi.org/10.1111/j.1529-8817.2006.00218.x
  16. Varma A, Padh H and Shrivastava N. 2007. Plant genomic DNA isolation: an art or a science. Biotechnol J 2, 386-392. https://doi.org/10.1002/biot.200600195
  17. Yoon HS, Lee JY, Boo SM and Bhattacharya D. 2001. Phylogeny of Alariaceae, Laminariaceae, and Lessoniaceae (Phaeophyceae) based on plastid-encoded Rubisco spacer and nuclear-encoded ITS sequence comparisons. Mol Phylogenet Evol 21, 231-243. https://doi.org/10.1006/mpev.2001.1009
  18. Yotsukura N, Denboh T, Motomura T, Horiguchi T, Coleman AW and Ichimura T. 1999. Little divergence in ribosomal DNA internal transcribed spacer-1 and -2 sequences among non-digitate species of Laminaria (Phaeophyceae) from Hokkaido, Japan. Phycol Res 47, 71-80. https://doi.org/10.1111/j.1440-1835.1999.tb00286.x