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A new resource of single nucleotide polymorphisms in the Japanese eel Anguilla japonica derived from restriction site-associated DNA

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An Erratum to this article was published on 04 August 2016

Abstract

We present a new resource of single nucleotide polymorphisms (SNPs) in the Japanese eel Anguilla japonica, a catadromous eel species distributed along the west Pacific margin. We used the restriction site-associated DNA (RAD) sequencing for the detection of SNPs. On the basis of glass eel samples collected from two Japanese coastal areas, 33,976 SNP sites that occurred among 18,353 RAD loci were identified. Using the RAD loci, we preliminarily tested genetic differentiation between the two geographical samples. No evidence of genetic population heterogeneity was obtained (F ST = 0.0015, P = 0.073), although a small portion of loci (0.8 %) exhibited an elevated level of genetic differentiation (F ST ≥ 0.100). A catalogue of SNPs constructed in the present study, in which we provide the positions of SNP sites within RAD loci and the scaffolds in the reference genome, and, if available, the position of RAD loci on genetic linkage groups, will be of great use for advancing ecological and breeding studies in A. japonica.

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Acknowledgements

This study was supported by a research fund from the Fisheries Agency, Ministry of Agriculture, Forestry and Fisheries of Japan (molecular genetic research project for developing stock management and breeding technologies of the Japanese eel). We thank Drs K. Sota, Shimane Prefectural Fisheries Technology Center, and M. Okabe, Kochi Prefectural Fresh-water Fisheries Center, who helped us to collect glass eel specimens in their respective prefectures. We prepared Figure 1 by modifying a geographical map provided by courtesy of Dr S. Chow, National Research Institute of Fisheries Science, Fisheries Research Agency. The manuscript was significantly improved by constructive comments from two anonymous reviewers.

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Authors and Affiliations

  1. Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, 2-12-4 Fuku-ura, Kanazawa, Yokohama, Kanagawa, 2368648, Japan

    Masashi Sekino, Reiichiro Nakamichi, Yuki Iwasaki, Akifumi S. Tanabe, Atushi Fujiwara, Motoshige Yasuike & Kenji Saitoh

  2. Marino-Forum 21, 1-5-2 Hagoromo bldg., Hatchobori, Chuo-ku, Tokyo, 1040032, Japan

    Manabu Shiraishi

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  1. Masashi Sekino
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  2. Reiichiro Nakamichi
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Correspondence to Masashi Sekino.

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An erratum to this article can be found at http://dx.doi.org/10.1007/s10228-016-0542-7.

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Sekino, M., Nakamichi, R., Iwasaki, Y. et al. A new resource of single nucleotide polymorphisms in the Japanese eel Anguilla japonica derived from restriction site-associated DNA. Ichthyol Res 63, 496–504 (2016). https://doi.org/10.1007/s10228-016-0518-7

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