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Development of 11 Ecklonia radicosa (Phaeophyceae, Laminariales) SSRs markers using next-generation sequencing and intra-genus amplification analysis

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Abstract

Polymorphic simple sequence repeat (SSR) markers of Ecklonia radicosa were developed using Illumina MiSeq next-generation sequencing (NGS) analysis. In total, 3112 SSRs (di- to hexanucleotide motifs repeated more than six times) were identified from 61.5-Mb assembled genomic DNA using MISA perl script. Among the SSRs, di- (853 loci, 27.4%) and trinucleotides (1813 loci, 58.3%) were dominant, while tetra- (172 loci, 5.5%), penta- (175 loci, 5.6%), and hexanucleotides (99 loci, 3.2%) were not common. After specific amplification and polymorphic tests of 75 selected loci (tri- to hexanucleotide motifs repeated more than eight times), 11 SSR markers (Eradic01–11) were successfully developed. The range of the number of alleles, observed heterozygosity, and expected heterozygosity in the 11 markers was 3–13, 0.200–0.683, and 0.258–0.864, respectively. Polymorphic information content (PIC) analysis indicated that eight markers (Eradic01, 02, 04, 05, 06, 08, 09, and 11) were highly informative (PIC > 0.5) and the other three were reasonably informative (0.5 < PIC < 0.25). In addition, intra-genus amplification was obtained in all markers except for Eradic02, 08, and 11. These markers could help to reveal the genetic diversity and population structure of E. radicosa.

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Acknowledgments

We are grateful to Drs. Ichiro Komazawa, Kouki Tanaka, Ryuta Terada, and Yuki Watanabe, as well as Messrs. Junichi Iijima, Tatsuya Ishikawa, Yusaku Nagao, Kaiji Nanrii, Hirokazu Yamada, and Taku Yoshimura for their help in collecting samples.

Funding

This work was supported by the JSPS Grants-in-Aid for JSPS Fellows (15J11734) to SA.

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Authors and Affiliations

  1. Laboratory of Applied Phycology, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, Japan

    Shingo Akita & Daisuke Fujita

  2. JSPS Research Fellow DC1, Tokyo, Japan

    Shingo Akita

  3. Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, Japan

    Keiichiro Koiwai, Reiko Nozaki, Hidehiro Kondo & Ikuo Hirono

  4. Kobe University Research Center for Inland Seas, Rokkodai 1-1, Kobe, Japan

    Takeaki Hanyuda

  5. Wetlands International Japan, Nihonbashiodenma-cho 17-1, Chuo-ku, Tokyo, Japan

    Syou Kato

  6. Japan Fisheries Research and Education Agency, National Research Institute of Fisheries Science, Fukuura 2-12-4, Kanazawa-ku, Yokohama, Japan

    Tsubasa Uchino

  7. Laboratory of Aquaculture, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, Japan

    Takashi Sakamoto

Authors
  1. Shingo Akita
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  2. Keiichiro Koiwai
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  3. Takeaki Hanyuda
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  4. Syou Kato
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  5. Reiko Nozaki
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  6. Tsubasa Uchino
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  7. Takashi Sakamoto
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  8. Hidehiro Kondo
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  9. Ikuo Hirono
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  10. Daisuke Fujita
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Correspondence to Shingo Akita.

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Akita, S., Koiwai, K., Hanyuda, T. et al. Development of 11 Ecklonia radicosa (Phaeophyceae, Laminariales) SSRs markers using next-generation sequencing and intra-genus amplification analysis. J Appl Phycol 30, 2111–2115 (2018). https://doi.org/10.1007/s10811-018-1406-5

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  • DOI: https://doi.org/10.1007/s10811-018-1406-5

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