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Using the ribosomal internal transcribed spacer (ITS) as a complement marker for species identification of red macroalgae

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Abstract

Barcodes based on mitochondrial cytochrome oxidase (mtDNA CO1) sequences are being used for broad taxonomic groups of animals with demonstrated success in species identification and cryptic species discovery, but it has become clear that complementation by a nuclear marker system is necessary, in particular for the barcoding of plants. Here, we propose the nuclear internal transcribed spacer (ITS) as a potentially usable and complementary marker for species identification of red macroalgae, as well as present a primary workflow for species barcoding. Data show that for most red macroalgal genera (except members of the family Delesseriaceae), the size of ITS region ranges from 600 to 1200 bp, and contains enough variation to generate unique identifiers at either the species or genus levels. Consistent with previous studies, we found that the ITS sequence can resolve closely related species with the same fidelity as mtDNA CO1. Significantly, we confirmed that length polymorphism in the ITS region (including 5.8S rRNA gene) can be utilized as a character to discriminate red macroalgal species. As a complementary marker, the verifiable nuclear ITS region can speed routine identification and the detection of species, advance ecological and taxonomic inquiry, and permit rapid and accurate analysis of red macroalgae.

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References

  • Alvarez, I. & J. F. Wendel, 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417–434.

    Article  PubMed  CAS  Google Scholar 

  • Bailey, C. D., T. G. Carr, S. A. Harris & C. E. Hughes, 2003. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Molecular Phylogenetics and Evolution 29: 435–455.

    Article  PubMed  CAS  Google Scholar 

  • Balajee, S. A., L. Sigler & M. E. Brandt, 2007. DNA and the classical way: identification of medically important molds in the 21st century. Medical Mycology 45: 475–490.

    Article  PubMed  CAS  Google Scholar 

  • Barrett, R. D. H. & P. D. N. Hebert, 2005. Identifying spiders through DNA barcodes. Canadian Journal of Zoology 83: 481–491.

    Article  CAS  Google Scholar 

  • Bellorin, A. M., M. C. Oliverira & E. C. Oliverira, 2002. Phylogeny and systematics of the marine algal family Gracilariaceae (Gracilariales, Rhodophyta) based on small subunit rDNA and ITS sequences of Atlantic and Pacific species. Journal of Phycology 38: 551–563.

    Article  CAS  Google Scholar 

  • Brodie, J., P. K. Hayes, G. L. Barker & L. M. Irvine, 1996. Molecular and morphological characters distinguishing two Porphyra species (Rhodophyta: Bangiophycidae). European Journal of Phycology 31: 303–308.

    Article  Google Scholar 

  • Burns J. M., D. H. Janzen, M. Hajibabaei, W. Hallwahcs & P. D. N. Hebert, 2008. DNA barcodes and cryptic species of skipper butterfies in the genus Perichares in Area de Conservation Guanacaste, Costa Rica. Proceedings of National Academic Sciences USA 105: 6350–6355.

    Article  Google Scholar 

  • Chase, M. W., N. Salamin, M. Wilkinson, J. M. Dunwell, R. P. Kesanakurthi, N. Haidar & V. Savolainen, 2005. Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of Royal Society Biological Sciences 360: 1889–1895.

    Article  CAS  Google Scholar 

  • Dasmahapatra, K. K. & J. Mallet, 2006. DNA barcodes: recent successes and future prospects. Heredity 97: 254–255.

    Article  PubMed  CAS  Google Scholar 

  • Gabrielson, P. W., 2008. Molecular sequencing of Northeast Pacific type material reveals two earlier names for Prionitis lyallii, Prionitis jubata and Prionitis sternbergii, with brief comments on Grateloupia versicolor (Halymeniaceae, Rhodophyta). Phycologia 47: 89–97.

    Article  CAS  Google Scholar 

  • Gielly, L. & P. Taberlet, 1994. The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Molecular Biology and Evolution 11: 769–777.

    PubMed  CAS  Google Scholar 

  • Goff, L. J. & D. A. Moon, 1993. PCR amplification of nuclear and plastid genes from algal herbarium specimens and algal spores. Journal of Phycology 29: 381–384.

    Article  CAS  Google Scholar 

  • Goff, L. J., D. A. Moon & A. W. Coleman, 1994. Molecular delineation of species and species relationships in the red algal agarophytes Gracilariopsis and Gracilaria (Gracilariales). Journal of Phycology 30: 521–537.

    Article  CAS  Google Scholar 

  • Hajibabaei M., D. H. Janzen, J. M. Burns, W. Hallwachs & P. D. N. Hebert, 2006. From the cover: DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of National Academic Sciences USA 103: 968–971.

    Google Scholar 

  • Hazkani-Covo, E. & D. Graur, 2007. A comparative analysis of Numt evolution in Human and Chimpanzee. Molecular Biology and Evolution 24: 13–18.

    Article  PubMed  CAS  Google Scholar 

  • Hebert P. D. N., A. Cywinska, S. L. Ball & J. R. deWaard, 2003. Biological identifications through DNA barcodes. Proceedings of Royal Society Biology 270: 313–321.

    Article  CAS  Google Scholar 

  • Hebert, P. D. N., M. Y. Stoeckle, T. S. Zemlak & C. M. Francis, 2004. Identification of birds through DNA barcodes. PloS Biology 2: e312.

    Article  PubMed  CAS  Google Scholar 

  • Hu, Z. M., X. Q. Zeng, A. H. Wang, C. J. Shi & D. L. Duan, 2004. An efficient method for DNA isolation from red algae. Journal of Applied Phycology 16: 161–166.

    Article  CAS  Google Scholar 

  • Hu, Z. M., A. T. Critchley, T. X. Gao, X. Q. Zeng, S. L. Morrell & D. L. Duan, 2007. Delineation of Chondrus (Gigartinales, Florideophyceae) in China and the origin of C. crispus inferred from molecular data. Marine Biology Research 3: 145–154.

    Article  Google Scholar 

  • Hudson, R. R. & M. Turrelli, 2003. Stochasticity overrules the ‘three-times rule’: genetic drift, genetic draft, and coalescent times for nuclear loci versus mitochondrial DNA. Evolution 57: 182–190.

    PubMed  Google Scholar 

  • Hughey, J. R., P. C. Silva & M. H. Hommersand, 2001. Solving taxonomic and nomenclatural problems in Pacific Gigartinaceae (Rhodophyta) using DNA from type material. Journal of Phycology 37: 1091–1109.

    Article  CAS  Google Scholar 

  • Hughey, J. R., P. C. Silva & M. H. Hommersand, 2002. ITS1 sequences of type specimens of Gigartina and Sarcothalia and their significance for the classification of South African Gigartinaceae (Gigartinales, Rhodophyta). European Journal of Phycology 37: 209–216.

    Article  Google Scholar 

  • Keller, I., I. C. Chintauan-Marquier, P. Veltsos & R. A. Nichols, 2006. Ribosomal DNA in the grasshopper Podisma pedestris: escape from concerted evolution. Genetics 174: 863–874.

    Article  PubMed  CAS  Google Scholar 

  • Kmiec, B., M. Woloszynska & H. Janska, 2006. Heteroplasmy as a common state of mitochoondrial genetic information in plants and animals. Current Genetics 50: 149–159.

    Article  PubMed  CAS  Google Scholar 

  • Koch, M. A., C. Dobe & T. Mitchell-Olds, 2003. Multiple hybrid formation in natural populations: concerted evolution of the internal transcribed spacer of nuclear ribosomal DNA (ITS) in North American Arabis divaricarpa (Brassicaceae). Molecular Biology and Evolution 20: 338–350.

    Article  PubMed  CAS  Google Scholar 

  • Kovarik, A., J. C. Pires, A. R. Leitch, K. Y. Lim, A. M. Sherwood, R. Matyasek, J. Rocca, D. E. Soltis & P. S. Soltis, 2005. Rapid concerted evolution of nuclear ribosomal DNA in two Tragopogon allopolyploids of recent and recurrent origin. Genetics 169: 931–944.

    Article  PubMed  CAS  Google Scholar 

  • Kress W. J., K. J. Wurdack, E. A. Zimmer, L. A. Weigt & D. H. Janzen, 2005. Use of DNA barcodes to identify flowering plants. Proceedings of National Academic Sciences USA 102: 8369–8374.

    Article  CAS  Google Scholar 

  • Krieger, J., A. K. Hett, P. A. Fuerst, V. J. Bristein & A. Ludwig, 2004. Unusual intraindividual variation of the nuclear 18S rRNA gene is widespread within the acipenseridae. Journal of Heredity 97: 218–225.

    Article  Google Scholar 

  • Lahaye R., M. Bank, D. Bogarin, J. Warner, F. Pupulin, G. Gigot, O. Maurin, S. Duthoit, T. G. Barraclough & V. Savolainen, 2008. DNA barcoding the floras of biodiversity hotspots. Proceedings of National Academic Sciences USA 105: 2923–2928.

    Article  Google Scholar 

  • Lane, C. E., S. C. Lindstrom & G. W. Saunders, 2007. A molecular assessment of northeast Pacific Alaria species (Laminariales, Phaeophyceae) with reference to the utility of DNA barcoding. Molecular Phylogenetics and Evolution 44: 634–648.

    Article  PubMed  CAS  Google Scholar 

  • Lindstrom, S. C., 2008. Cryptic diversity and phylogenetic relationships within the Mastocarpus papillatus species complex (Rhodophyta, Phyllophoraceae). Journal of Phycology 44: 1300–1308.

    Article  Google Scholar 

  • Markmann, M. & D. Tautz, 2005. Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Philosophical Transactions of Royal Society Biological Sciences 360: 1917–1924.

    Article  CAS  Google Scholar 

  • Moritz, C. & C. Cicero, 2004. DNA barcoding: promise and pitfalls. PloS Biology 2: e354.

    Article  PubMed  CAS  Google Scholar 

  • Newmaster, S. G., A. J. Fazekas & S. Ragupathy, 2006. DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Canadian Journal of Botany 84: 335–341.

    Article  CAS  Google Scholar 

  • Pons, J. & A. P. Vogler, 2005. Complex patterns of coalescence and fast evolution of a mitochondrial rRNA pseudogene in a recent radiation of tiger beetles. Molecular Biology and Evolution 22: 991–1000.

    Article  PubMed  CAS  Google Scholar 

  • Posada, D. & K. A. Crandall, 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817–818.

    Article  PubMed  CAS  Google Scholar 

  • Robba, L., S. J. Russell, G. L. Barker & J. Brodie, 2006. Assessing the use of the mitochondrial cox1 marker for use in DNA barcoding of red algae (Rhodophyta). American Journal of Botany 93: 1101–1108.

    Article  CAS  Google Scholar 

  • Ross, P. J., S. L. Donaldson & G. W. Saunders, 2003. A molecular investigation of Mazzaella (Gigartinales, Rhodophyta) morphologically intermediate between Mazzaella linearis and M. splendens. Botanica Marina 46: 202–213.

    Article  CAS  Google Scholar 

  • Sass, C., D. P. Little, D. W. Stevenson & C. D. Specht, 2007. DNA barcoding in the Cycadales: testing the potential of proposed barcoding markers for species identification of Cycads. PloS One 2: e1154.

    Article  PubMed  CAS  Google Scholar 

  • Saunders, G. W., 2005. Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications. Philosophical Transactions of Royal Society Biological Sciences 360: 1879–1888.

    Article  CAS  Google Scholar 

  • Seifert K. A., R. A. Samson, J. R. deWaard, J. Houbraken, C. A. Lévesque, J. M. Moncalvo, G. L. Seize & P. D. N. Hebert, 2007. From the cover: prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proceedings of National Academic Sciences USA 104: 3901–3906.

    Article  CAS  Google Scholar 

  • Selig, C., M. Wolf, T. Müller, T. Dandekar & J. Schultz, 2008. The ITS2 database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Research 36: 377–380.

    Article  CAS  Google Scholar 

  • Sonnenberg, R., A. W. Nolte & D. Tautz, 2007. An evaluation of LSU rDNA D1-D2 sequences for their use in species identification. Frontiers in Zoology 4: 6.

    Article  PubMed  CAS  Google Scholar 

  • Stoeckle, M., 2003. Taxonomy, DNA, and the barcode of life. Bioscience 53: 796–797.

    Article  Google Scholar 

  • Tamura, K., J. Dudley, M. Nei & S. Kumar, 2007. MEGA4: molecular evolutionary genetics analysis (MEGA4) software version 4.0. Molecular Biology and Evolution 24: 1596–1599.

    Article  PubMed  CAS  Google Scholar 

  • Verlaque, M., P. M. Brannock, T. Komatsu, M. Villalard-Bohnsack & M. Marston, 2005. The genus Grateloupia C. Agardh (Halymeniaceae, Rhodophyta) in the Thau Lagoon (France, Mediterranean): a case study of marine plurispecific introductions. Phycologia 44: 477–496.

    Article  Google Scholar 

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Acknowledgements

The authors thank the anonymous reviewers for their comments on an earlier version of this manuscript. The study was supported by China Postdoctoral Science Foundation funded project (200904501238) and Knowledge Innovation Program of the Chinese Academy of Sciences (KSCX2-yw-n-47-02).

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Authors and Affiliations

  1. The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, People’s Republic of China

    ZiMin Hu & DeLin Duan

  2. Martin Ryan Institute, National University of Ireland, Galway, Ireland

    ZiMin Hu & Michael D. Guiry

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  1. ZiMin Hu
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  2. Michael D. Guiry
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Correspondence to DeLin Duan.

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Hu, Z., Guiry, M.D. & Duan, D. Using the ribosomal internal transcribed spacer (ITS) as a complement marker for species identification of red macroalgae. Hydrobiologia 635, 279–287 (2009). https://doi.org/10.1007/s10750-009-9920-8

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