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Sequence analysis of the ITS region and 5.8S rDNA of Porphyra haitanensis

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Abstract

The sequences of the ITS (internal transcribed spacer) and 5.8S rDNA of three cultivated strains of Porphyra haitanensis thalli (NB, PT and ST) were amplified, sequenced and analyzed. In addition, the phylogenic relationships of the sequences identified in this study with those of other Porphyra retrieved from GenBank were evaluated. The results are as follows: the sequences of the ITS and 5.8S rDNA were essentially identical among the three strains. The sequences of ITS1 were 331 bp to 334 bp, while those of the 5.8S rDNA were 158 bp and the sequences of ITS2 ranged from 673 bp to 681 bp. The sequences of the ITS had a high level of homology (up to 99.5%) with that of P. haitanensis (DQ662228) retrieved from GenBank, but were only approximately 50% homologous with those of other species of Porphyra. The results obtained when a phylogenetic tree was constructed coincided with the results of the homology analysis. These results suggest that the three cultivated strains of P. haitanensis evolved conservatively and that the ITS showed evolutionary consistency. However, the sequences of the ITS and 5.8S rDNA of different Porphyra species showed great variations. Therefore, the relationship of Porphyra interspecies phyletic evolution could be judged, which provides the proof for Porphyra identification study. However, proper classifications of the subspecies and the populations of Porphyra should be determined through the use of other molecular techniques to determine the genetic variability and rational phylogenetic relationships.

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References

  • Alice L A, Campbell C S. 1999. Phylogeny of Rubus (Rosaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. Am. J. Bot., 86: 81–97.

    Article  Google Scholar 

  • Bao S L, Ding X Y, Chang J, Shen J, Tang F. 2004. Identification of Traga Plants along middle-low reaches of Changjiang River by analyzing their DNA sequences. Chin. Tradit. Herbal. Drugs, 35(8): 926–930.

    Google Scholar 

  • Baldwin B G. 1992. Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the composite. Mol. Phylogenet. Evol., 1: 3–16.

    Article  Google Scholar 

  • Baldwin B G, Sanderson M J, Porter J M, Wojciechowski M F, C S Campbell, Donoghue M J. 1995. The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Ann. MO. Bot. Gard., 82: 247–277.

    Article  Google Scholar 

  • Blomster J, Hoey E M, Maggs C A, Stanhope M J. 2000. Species-specific oligonucleotide probes for macroalgae: molecular discrimination of two marine fouling species of Enteromorpha (Ulvophyceae). Mol. Ecol., 9: 177–186.

    Article  Google Scholar 

  • Cai J N, Zhou K Y, Xu L S, Wang Z T, Shen Y, Wang Y Q, Li X B. 2000. Ribosomal DNA ITS sequence analysis of Cnidium monnieri from different geographical origin in China. Acta Pharm. Sin., 35: 56–59.

    Google Scholar 

  • Cerbah M, Souza-Chies T, Jubier M F, Lejeune B, Siljak-Yakovlev S. 1998. Molecular phylogeny of the Genus Hypochaeris using internal transcribed spacers of nuclear rDNA: inferences for chromosomal evolution. Mol. Biol. Evol., 15(3): 345–354.

    Google Scholar 

  • Chen L L, Kong X Y, Zhou L S, Chen L M, Yu Z N. 2005. Sequence analysis of ribosomal DNA internal transcribed spacers of bloody clam, Scapharca broughtonii. J. Fish. Sci. Chin., 12: 104–107.

    Google Scholar 

  • Ding X Y, Wang Z T, Xu H, Xu L S, Zhou K Y. 2000. Database establishment of the whole rDNA ITS region of Dendrobium species of “Feng-dou” and authentication by analysis of their sequences. Acta Pharm. Sin., 37(7): 567–573.

    Google Scholar 

  • Dover G A. 1982. Molecular drive: a cohesive mode of species evolution. Nature, 299: 111–117.

    Article  Google Scholar 

  • Elder J R, Turner B J. 1995. Concerted evolution of repetitive DNA sequence in eukaryotes. Q. Rev. Biol., 70: 297–319.

    Article  Google Scholar 

  • Fan X L, Fang Y J, Hu S N, Wang G C. 2007. Generation and analysis of 5318 expressed sequence tags from the filamentous sporophyte of porphyra haitanensis (Rhodophyta). J. Phycol., 43(6): 1 287–1 294.

    Google Scholar 

  • Gonzalez I L, Sylvester J E, Smith T F, Stambolian D, Schmickel R D. 1990. Ribosomal RNA gene sequences and hominoid phylogeny. Mol. Biol. Evol., 7: 203–219.

    Google Scholar 

  • Guo B T, Bi Y P, Shan L, Li G C, Dai J X. 2000. Extraction of plasmid-like DNA and high-quality total DNA from Porphyra yezoensis. Acta Oceanol. Sin., 22(2): 87–91.

    Google Scholar 

  • Hall T A. 1999. BioEdit: a user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser., 41: 95–98.

    Google Scholar 

  • Hillis M D M, Davis S K, 1988. Ribosomal DNA: Intraspecific polymorphism, concerned evolution and phylogeny reconstruction. Syst. Zool., 37: 63–66.

    Article  Google Scholar 

  • Jia J H, Wang P, Jin D M, Qu X P, Wang Q, Li C Y, Weng M L, Wang B, 2000. The application of RAPD markers in diversity detection and variety identification of Porphyra. Acta Bot. Sin., 42: 403–407.

    Google Scholar 

  • Kumar S, Tamura K, Jakobsen I B, Nei M. 2001. MEGA 2: molecular evolutionary genetics analysis software. Bioinformatics, 17: 1 244–1 245.

    Article  Google Scholar 

  • Kunimoto M, Kito H, Kaminishi Y, Mizukami Y, Murase N. 1999. Molecular divergence of the ssu rRNA gene and internal transcribed spacer 1 in Porphyra yezoensis (Rhodophyta). J. Appl. Phycol., 11: 211–216.

    Article  Google Scholar 

  • Kyosuke N, Yusho A. 2003. Rapid DNA extraction from conchocelis and ITS-1 rDNA sequences of seven strains of cultivated Porphyra yezoensis (Bangiales, Rhodophyta). J. Appl. Phycol., 15: 29–35.

    Article  Google Scholar 

  • Leskinen E, Pamilo P. 1997. Evolution of the ITS sequences of ribosomal DNA in Enteromorpha (Chlorophyceae). Hereditas, 126: 17–23.

    Article  Google Scholar 

  • Li X Y, Peng J Y, Bai R X. 2005. Use of ITS sequences Based on Nuclear rDNA for Phylogenetic Research of Seed Plants. Acta Bot. Boreal. Occident. Sin., 25(4): 829–834.

    Google Scholar 

  • Ma J H, Xu P, Zhu J Y. 2005. Marin Rhodophyta Genetics-Porphyra. In: Zhang X C, Ma J H, Qin S and Xu P, ed. The Genetic of Marine Algae. Chinese Agriculture Press, Beijing, China. p. 185–186.

    Google Scholar 

  • Ma X J, Wang X Q, Xiao P G, Hong D Y. 2000. Comparison of ITS sequences between wild ginseng DNA and garden ginseng DNA. Chin. J. Chin. Mat Med., 25: 206–209.

    Google Scholar 

  • Mizukami Y, Okauchi M, Kito H, Kobayashi M. 1996. Discrimination of laver cultivars with RAPD markers. Fish. Sci., 62(4): 547–551.

    Google Scholar 

  • Mizukami Y, Kito H, Kaminishi Y, Murase N, Kunimoto M. 1999. Nucleotide sequence variation in the ribosomal internal transcribed spacer regions of cultivated (cultivars) and field collected thalli of Porphyra yezoensis. Fish. Sci., 65: 788–789.

    Google Scholar 

  • Morales V M, Pelcher L E, Taylor J L. 1993. Composition of the 5. 8S rDNA and internal transcribed spacer sequences of isolates of Leptos phaeria maculans from different pathogenicity groups. Curr. Genet., 23: 490–495.

    Article  Google Scholar 

  • Pang G X, Wang G C, Hu S N, Zeng C K. 2005. Acquirement and analysis of expressed sequences tags of filamentous sporophyte of Porphyra haitanensis. Oceanol. Limnol. Sin., 36(5): 452–457.

    Google Scholar 

  • Shi Q L, Zhu G Q, Huang M R. 2001. The principal of molecular systematics and the application in forest tree. Chin. Bulletin Life Sci., 1: 90–91.

    Google Scholar 

  • Steane D A, Scotland R W, Mabberley D J, Olmstead R G. 1999. Molecular systematic of Clerodendrum (Lamiaceae): ITS sequences and total evidence. Am. J. Bot., 86(1): 98–107.

    Article  Google Scholar 

  • Sun X, Yang R, Liu B Q, Pei L Q. 2006. Sequence analyses of rbcS and rbcL-rbcS intergenic spacer region in laver Porphyra haitanensis. Fish. Sci., 25(1): 24–26.

    Google Scholar 

  • Tang B P, Zhou K Y, Song D X. 2002. Application of sequences of nrDNA ITS to molecular systematics of invertebrates. Chin. J. Zool., 37: 67–73.

    Google Scholar 

  • Thompson J D, Gibson T J, Plewniak F, Jeanmougin F, Higgins D G. 1997. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res., 24: 4 876–4 882.

    Google Scholar 

  • Wang X Q, Hong D Y. 1997. Progress in molecular systematics of plants in recent five years. Acta Phytotax. Sin., 35(5): 465–480.

    Google Scholar 

  • Wang Y, Liu B Q, Luo Q J, Fei Z Q, Pei L Q, Xue Q Z. 2000. RAPD Analysis of genetic variation among Porphyra haitanensis strains. J. Ocean. Univ. Qingdao, 30(2): 225–229.

    Google Scholar 

  • Wei Q. 1999. Molecular biology laboratory procedure. Springer Press and Higher Education Press, Beijing, China. p. 53–56. (in Chinese)

    Google Scholar 

  • Xiang Q P, Xiang Q Y, Liston A, Fu L G, Fu D Z. 2000. Length variation of the nuclear ribosomal DNA internal transcribed spacer in the genus abies, with reference to ITS systematic utility in Pinaceae. Acta Bot. Sin., 42(9): 946–951.

    Google Scholar 

  • Xie C T, Ji D H, Chen C S, Xu Y, Zhang Y. 2007. Application of ISSR markers in germplasm identification of different color’s Porphyra haitanensis filament strains. J. Fish. Chin., 31(1): 105–112.

    Google Scholar 

  • Xu T J, Liu C W, Liu L, Dong Q F and Yang Y X. 2006. The application of internal transcribed space (ITS) in germplasm identification and the genetic diversity analysis of the aquatic animal. J. Zhanjiang. Ocean. Univ., 26: 84–88.

    Google Scholar 

  • Yang J, Wang Q, Liu M H, An L J. 1999. A simple method for extracting total DNA of seaweeds. Biotechonl., 9(4): 39–42.

    Google Scholar 

  • Yang R, Liu B Q, Luo Q J, Wang Y J, Zhou X C, Dai J X. 2002. Genetic variation of Porphyra haitanensis by applying AFLP. High Technol. Lett., 12: 83–86.

    Google Scholar 

  • Yoshida T, Notoya M, Kikuchi N, Miyata M. 1997. Catalogue of species of Porphyra in the world, with special reference to the type locality and bibliography. Nat. Hist. Res. (Special Issue), 3: 5–18.

    Google Scholar 

  • Zhang B Y, Wang G C, Lv S H, Qi Y Z, Zou J Z, Zeng C K. 2006. The cloning and sequence analysis of the 5.8S rDNA and ITS region from three strains of marine diatoms. Acta Oceanol. Sin., 28: 111–117.

    Google Scholar 

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Authors and Affiliations

  1. Department of Cell Biology, Medical College of Soochow University, Suzhou, 215123, China

    Yanyan Li  (李艳燕), Songdong Shen  (沈颂东) & Lihong He  (贺丽虹)

  2. Department of Biology and Food Engineering, Changshu Institute of Technology, Suzhou, 215500, China

    Pu Xu  (许璞)

  3. Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China

    Guangce Wang  (王广策)

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  1. Yanyan Li  (李艳燕)
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  2. Songdong Shen  (沈颂东)
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  3. Lihong He  (贺丽虹)
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  4. Pu Xu  (许璞)
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  5. Guangce Wang  (王广策)
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Correspondence to Songdong Shen  (沈颂东).

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Supported by the National Natural Science Foundation of China (No. 40576074), and the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences (No. KFN92007NO1)

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Li, Y., Shen, S., He, L. et al. Sequence analysis of the ITS region and 5.8S rDNA of Porphyra haitanensis . Chin. J. Ocean. Limnol. 27, 493–501 (2009). https://doi.org/10.1007/s00343-009-9168-1

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