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Evaluation of the 5′ end of the 16S rRNA gene as a DNA barcode marker for the Cephalopoda

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Abstract

The present study seeks to incorporate a highly variable DNA barcode marker, additional to the standard regions of the cytochrome oxidase I gene and the 3′ end of the 16S large ribosomal subunit (16S rRNA), for a more effective species-level identification among cephalopods. Thus, we evaluated whether the 5′ end region of the 16S rRNA gene can be suitable as a DNA barcode marker among these taxa. Using a novel primer set, 28 different species were evaluated based on the pairwise intra- and interspecific distance and neighbor-joining (NJ) analysis. Except for Enteroctopus dofleini, we were able to obtain the sequences for the remaining species which formed highly supported clusters in the NJ tree. Divergence at the interspecific level may indicate high genetic variation of the region being proposed as compared to the standard of 16S rRNA. In addition, two well-supported clades and high levels of divergence within Sthenoteuthis oualaniensis, Loliolus japonica and Sepia pharaonis suggest the occurrence of cryptic species. This study confirms the efficiency of the 5′ end region of the 16S rRNA gene as a DNA barcode marker which can be used along with the standard DNA markers in future studies.

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Acknowledgments

This research was partly supported by “Grants-in-Aid for Scientific Research” (no. 26292106 for T.U.) and a “Graduate Student Scholarship for Foreign Student”, both from the Japanese Government through the Ministry of Education, Culture, Sport, Science and Technology in Japan (Monbukagakusho: MEXT). We are also grateful to the following professors who kindly provided samples for this study: Dr. Taeko Miyazaki of Mie University with Sepioteuthis sp. 3, Dr. Ian G. Gleadall of Tohoku University with Opisthoteuthis sp. and Dr. John Bower of Hokkaido University with E. dofleini. We wish to thank Miyajima Aquarium (Hiroshima Prefecture) for providing samples of A. dux and Toba Aquarium (Mie Prefecture) for the samples of Nautilus macromphalus and Nautilus pompilius. We also wish to thank to Li Qiang and Dr. Zhizhi Liu from Shanghai Ocean University for providing samples of Uroteuthis chinensis, Atsushi Tsuyuki from Hiroshima University for his support during the sample collection in Japan, Dr. Lawrence Liao from Hiroshima University and his student Dan Anthony Uy Bataan from the Philippines for the great help with the collection of samples in their country. Finally, the authors gratefully acknowledge the criticism of two anonymous reviewers who greatly improved the manuscript.

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Authors and Affiliations

  1. Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8528, Japan

    Gustavo Sanchez, Satoshi Tomano & Tetsuya Umino

  2. Department of Fisheries Science and Technology, National Fisheries University, Shimonoseki, Yamaguchi, 759-6595, Japan

    Toshie Wakabayashi

  3. Tohoku National Fisheries Research Institute, Hachinohe, Aomori, 031-0841, Japan

    Mitsuo Sakai

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  1. Gustavo Sanchez
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  2. Satoshi Tomano
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  3. Tetsuya Umino
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  4. Toshie Wakabayashi
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  5. Mitsuo Sakai
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Correspondence to Tetsuya Umino.

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Sanchez, G., Tomano, S., Umino, T. et al. Evaluation of the 5′ end of the 16S rRNA gene as a DNA barcode marker for the Cephalopoda. Fish Sci 82, 279–288 (2016). https://doi.org/10.1007/s12562-015-0962-8

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