Advertisement

Journal of Applied Phycology

, Volume 20, Issue 2, pp 161–168 | Cite as

Mitochondrial cox1 and plastid rbcL genes of Gracilaria vermiculophylla (Gracilariaceae, Rhodophyta)

  • Eun Chan Yang
  • Myung Sook Kim
  • Paul John L. Geraldino
  • Dinabandhu Sahoo
  • Jong-Ahm Shin
  • Sung Min Boo
Article

Abstract

The mitochondrial cytochrome c oxidase subunit I gene sequence was recently developed for DNA barcoding of red algal species. We determined the 1245 base pairs of the gene from 27 taxa of an agar-producing species, Gracilaria vermiculophylla, and putative relatives and compared the results with rbcL data from the same species. A total of 392 positions (31.5%) were variable, 282 positions (22.6%) were parsimoniously informative, and average sequence divergence was 13% in an ingroup. Within G. vermiculophylla, pairwise divergence of the gene was variable up to 11 bp (0.9%). Seven recognized haplotypes of cox1 tended to be geographically related. In the aligned 1386 bp of rbcL, three haplotypes were recognized. These results suggest that cox1 is a valuable molecular marker within species and will be very useful in haplotype analyses.

Keywords

DNA barcoding Gracilariales Haplotype Molecular marker Phylogeny 

Notes

Acknowledgements

This research was supported by the Marine and Extreme Genome Research Center Program (program leader: Dr. S. J. Kim), Ministry of Maritime Affairs & Fisheries, Korea, to S. M. Boo.

References

  1. Bellorin AM, Oliveira MC, Oliveira EC (2002) Phylogeny and systematics of the marine algal family Gracilariaceae (Gracilariales, Rhodophyta) based on SSU rDNA and ITS sequences of Atlantic and Pacific species. J Phycol 38:551–563CrossRefGoogle Scholar
  2. Bellorin AM, Oliveira MC, Oliveira EC (2004) Gracilaria vermiculophylla: a western Pacific species of Gracilariaceae (Rhodophyta) first recorded from the eastern Pacific. Phycol Res 52:69–79CrossRefGoogle Scholar
  3. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1669PubMedCrossRefGoogle Scholar
  4. Destombe C, Douglas SE (1991) Rubisco spacer sequence divergence in the rhodophyte alga Gracilaria verrucosa and closely related species. Curr Genet 19:395–398PubMedCrossRefGoogle Scholar
  5. Freshwater DW, Rueness J (1994) Phylogenetic relationships of some European Gelidium (Gelidiales, Rhodophyta) species based on rbcL nucleotide sequence analysis. Phycologia 33:187–194Google Scholar
  6. Freshwater DW, Fredericq S, Butler BS, Hommersand MH, Chase MW (1994) A gene phylogeny of the red algae (Rhodophyta) based on plastid rbcL. Proc Natl Acad Sci USA 91:7281–7285PubMedCrossRefGoogle Scholar
  7. Gavio B, Fredericq S (2002) Grateloupia turuturu (Halymeniaceae, Rhodophyta) is the correct name of the non-native species in the Atlantic known as Grateloupia doryphora. Eur J Phycol 37:349–360CrossRefGoogle Scholar
  8. Geraldino PJL, Yang EC, Boo SM (2006) Morphology and molecular phylogeny of Hypnea flexicaulis (Gigartinales, Rhodophyta) from Korea. Algae 21:417–423CrossRefGoogle Scholar
  9. Goff LJ, Moon DA, Coleman AW (1994) Molecular delineation of species and species relationships in red algal agarophytes Gracilariopsis and Gracilaria (Gracilariales). J Phycol 30:521–537CrossRefGoogle Scholar
  10. Gurgel CFD, Fredericq S (2004) Systematics of the Gracilariaceae (Gracilariales, Rhodophyta): a critical assessment based on rbcL sequence analyses. J Phycol 40:138–159CrossRefGoogle Scholar
  11. Irvine L, Steentoft M (1995) Proposal to reject the name Fucus verrucosus Huds. (Rhodophyta). Taxon 44:223–224CrossRefGoogle Scholar
  12. Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA 102:8369–8374PubMedCrossRefGoogle Scholar
  13. Lee IK, Kim MS, Boo SM (1995) A taxonomic appraisal of Korean Gracilaria verrucosa (Rhodophyta, Gracilariales). In: Abbott IA (ed) Taxonomy of economic seaweeds with reference to some Pacific species. California Sea Grant, California, pp 213–222Google Scholar
  14. Lim P-E, Wong C-L, Phang S-M (2006) Molecular taxonomy of seaweeds with emphasis on Rhodophyta and Phaeophyta. In: Phang S-M, Critchley AT, Ang PO Jr (eds) Advances in seaweed cultivation and utilization in Asia. University of Malaya, Kuala Lumpur, pp 105–142Google Scholar
  15. Lin SM, Fredericq S, Hommersand MH (2001) Systematics of the Delesseriaceae (Ceramiales, Rhodophyta) based on large subunit rDNA and rbcL sequences, including the Phycoryoideae, subfam. nov. J Phycol 37:881–899CrossRefGoogle Scholar
  16. Ohmi H (1956) Contributions to the knowledge of Gracilariaceae from Japan. II. On a new species of the genus Gracilariopsis, with some considerations on its ecology. Bull Fac Fish Hokkaido Univ 6:271–279Google Scholar
  17. Ragan MA, Bird CJ, Rice EL, Gutell RR, Murphy CA (1994) A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proc Natl Acad Sci USA 91:7276–7280PubMedCrossRefGoogle Scholar
  18. Robba L, Russell SJ, Barker GL, Brodie J (2006) Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta). Am J Bot 93:1101–1108CrossRefGoogle Scholar
  19. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574PubMedCrossRefGoogle Scholar
  20. Rozas J, Rozas R (2000) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174–175CrossRefGoogle Scholar
  21. Rueness J (2005) Life history and molecular sequences of Gracilaria vermiculophylla (Gracilariales, Rhodophyta), a new introduction to European waters. Phycologia 44:120–128CrossRefGoogle Scholar
  22. Saunders GW (2005) Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philos Trans R Soc B-Biol Sci 360:1879–1888CrossRefGoogle Scholar
  23. Sullivan J, Abdo Z, Joyce P, Swofford DL (2005) Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Mol Biol Evol 22:1386–1392PubMedCrossRefGoogle Scholar
  24. Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0b10. Sinauer Associates, Sunderland, MassachusettsGoogle Scholar
  25. Terada R, Ohno M (2000) Notes on Gracilaria (Gracilariales, Rhodophyta) from Tosa Bay and adjacent waters I: Gracilaria chorda, Gracilaria gigas and Gracilaria incurvata. Bull Mar Sci Fish Kochi Univ 20:81–88Google Scholar
  26. Terada R, Yamamoto H (2002) Review of Gracilaria vermiculophylla and other species in Japan and Asia. In: Abbott IA, McDermid K (eds) Taxonomy of economic seaweeds, with reference to some Pacific species, Vol 8. California Sea Grant College System, USA, pp 215–224Google Scholar
  27. Yamamoto H (1973) Gracilariopsis chorda (Holm.) Ohmi from Hakodate Bay. Bull Jap Soc Phycol 21:8–91Google Scholar
  28. Yang EC, Boo SM (2004) Evidence for two independent lineages of Griffithsia (Ceramiaceae, Rhodophyta) based on plastid protein-coding psaA, psbA, and rbcL gene sequences. Mol Phylogenet Evol 31:680–688PubMedCrossRefGoogle Scholar
  29. Yang EC, Boo SM (2006) A red alga-specific phycoerythrin gene for biodiversity surveys of callithamnioid red algae. Mol Ecol Notes 6:533–535CrossRefGoogle Scholar
  30. Zuccarello GC, Burger G, West JA, King RJ (1999) A mitochondrial marker for red algal intraspecific relationships. Mol Ecol 8:1443–1447PubMedCrossRefGoogle Scholar
  31. Zuccarello GC, Buchanan J, West JA (2006) Increased sampling for inferring phylogeographic patterns in Bostrychia radicans/B. moritziana (Rhodomelaceae, Rhodophyta) in the eastern USA. J Phycol 42:1349–1352CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Eun Chan Yang
    • 1
  • Myung Sook Kim
    • 2
  • Paul John L. Geraldino
    • 1
  • Dinabandhu Sahoo
    • 3
  • Jong-Ahm Shin
    • 4
  • Sung Min Boo
    • 1
  1. 1.Department of BiologyChungnam National UniversityDaejeonSouth Korea
  2. 2.Research Institute of Basic SciencesPusan National UniversityPusanSouth Korea
  3. 3.Marine Biotechnology Laboratory, Department of BotanyUniversity of DelhiDelhiIndia
  4. 4.Fisheries and Ocean ScienceChonnam National UniversityYeosuSouth Korea

Personalised recommendations