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Isolation and characterization of novel polymorphic microsatellite loci for the deep-sea hydrothermal vent limpet, Lepetodrilus nux, and the vent-associated squat lobster, Shinkaia crosnieri

Marine Biodiversity volume 48, pages 677–684 (2018)Cite this article

Abstract

Recent genetic research has begun to reveal population structures of deep-sea, hydrothermal vent species, but detailed assessments of genetic diversity and connectivity in hydrothermal vent populations, based on multiple genetic loci, are still scarce, especially in the Northwest Pacific. Accordingly, we isolated 38 novel polymorphic microsatellite loci from the limpet, Lepetodrilus nux, and 14 from the squat lobster, Shinkaia crosnieri, two dominant hydrothermal vent species, using next-generation sequencing. These loci revealed polymorphism levels of 5–20 alleles per locus in L. nux and 5–25 in S. crosnieri. Observed and expected heterozygosities ranged from 0.240 to 0.960 and 0.283 to 0.938 in L. nux and from 0.450 to 0.950 and 0.620 to 0.941 in S. crosnieri, respectively. Twelve loci in L. nux and four loci in S. crosnieri showed significant deviation from Hardy–Weinberg equilibrium (p < 0.05). Microsatellite loci evaluated in this study will enable detailed measurements of genetic diversity and connectivity among populations, and better understanding of evolutionary divergence processes of L. nux and S. crosnieri in deep-sea communities in the Northwest Pacific.

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Acknowledgments

We are grateful to Dr. Hiroyuki Yamamoto, chief scientist of the KR12-02 and NT13-22 cruises, and to officers and crews of the ‘Natsushima,’ and the operation team of ROV ‘Hyper-Dolphin’ for collecting the specimens. This work was financially supported by The Canon Foundation and Okinawa Institute of Science and Technology Graduate University. We thank Dr. Steven D. Aird (Okinawa Institute of Science and Technology Graduate University) for editing the manuscript.

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Authors and Affiliations

  1. Marine Biophysics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan

    Yuichi Nakajima & Satoshi Mitarai

  2. Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-8564, Japan

    Chuya Shinzato

  3. Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan

    Mariia Khalturina & Noriyuki Satoh

  4. School of Marine Science and Technology, Tokai University, Shimizu, Shizuoka, 424-8610, Japan

    Masako Nakamura

  5. Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, 237-0061, Japan

    Hiromi Kayama Watanabe

  6. Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto, 606-8502, Japan

    Satoshi Nakagawa

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  1. Yuichi Nakajima
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  2. Chuya Shinzato
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  3. Mariia Khalturina
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  5. Hiromi Kayama Watanabe
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  6. Satoshi Nakagawa
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  7. Noriyuki Satoh
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Correspondence to Yuichi Nakajima.

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Communicated by S. Gollner

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Nakajima, Y., Shinzato, C., Khalturina, M. et al. Isolation and characterization of novel polymorphic microsatellite loci for the deep-sea hydrothermal vent limpet, Lepetodrilus nux, and the vent-associated squat lobster, Shinkaia crosnieri . Mar Biodiv 48, 677–684 (2018). https://doi.org/10.1007/s12526-017-0704-5

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  • DOI: https://doi.org/10.1007/s12526-017-0704-5

Keywords

  • Chemosynthetic ecosystem
  • Northwest Pacific
  • Nuclear genetic marker
  • Okinawa Trough
  • Population genetics
  • Simple sequence repeat