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Hypervariable regions (V1–V9) of the dinoflagellate 18S rRNA using a large dataset for marker considerations

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Abstract

DNA sequencing methods have been used for the molecular taxonomic discrimination of dinoflagellate protists, particularly using partial 18S rRNA sequences. This study evaluated the taxonomic discrimination power of rRNA gene hypervariable regions (V1 to V9) in dinoflagellates from a large dataset. These included 77 dinoflagellate species (9 orders, 17 families, 40 genera). The complete 18S rRNA sequences of the dinoflagellates ranged from 1,787 to 1,813 bp in length, and consisted of eight V regions with a total combined length of 678 to 699 bp. Regions longer than 100 bp were recoded for V2, V4, and V8 regions; high nucleotide divergences were detected in V1, V2, and V4 regions. Statistic tests showed that the divergences of individual V regions were significantly different (t-test, P < 0.05) compared with the complete 18S rRNA. The V2 region showed the highest score (83.5%) for PI sites. Moreover, intra-genus DNA similarities of the V2 were considerably low (<93%). Neighbor-joining analyses showed that phylogenetic resolution in the V2–V4 region was 1.32-fold higher than that of the complete 18S rRNA. These results demonstrate that V2 has the highest taxonomic resolving power within the 18S rRNA gene of dinoflagellates, suggesting the V2 and adjacent regions (e.g., V1 to V4) may be the best for marker considerations.

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Acknowledgments

The author would like to thank Professor J. Wuyts, University of Antwerp, Belgium, for the assistances with the secondary structure analyses. This work was supported by both the Marine and Extreme Genome Research Center Program of the Ministry of Land, Transportation and Maritime Affairs, Republic of Korea, and by a National Research Foundation of Korea (NRF) grant, funded by the Korean government (MEST no. 2010–0009669 and NRF-C1ABA001-2010-0020704).

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  1. Department of Green Life Science, Sangmyung University, Seoul, 110-743, South Korea

    Jang-Seu Ki

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Correspondence to Jang-Seu Ki.

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Table S1

Taxa and GenBank accession numbers used in this study (DOC 95 kb)

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Ki, JS. Hypervariable regions (V1–V9) of the dinoflagellate 18S rRNA using a large dataset for marker considerations. J Appl Phycol 24, 1035–1043 (2012). https://doi.org/10.1007/s10811-011-9730-z

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  • DOI: https://doi.org/10.1007/s10811-011-9730-z

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