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Automated screening and primer design of fish microsatellite DNA loci on pyrosequencing data

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Abstract

In recent years, massive sequencing approaches have allowed us to determine genomic structures of various organisms rapidly, raising novel applicability of the high-throughput sequence data obtained to various fields of biological studies. We present here a pipeline to search for microsatellite DNA and design PCR primers encompassing the microsatellites on genomic sequence data produced by 454 pyrosequencing. We tested this pipeline, called ‘Auto-primer’, on several fish genomic sequences and obtained many and various candidates for microsatellite DNA loci useful for detecting intraspecies genetic variability. This in silico search for microsatellite DNA is superior to conventional cloning methods, since any sequence patterns of repeat unit can be screened.

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Acknowledgments

This study was partly supported by a fund from research and development projects for application in promoting new policy of Agriculture Forestry and Fisheries (#21062). We appreciate all the constructive comments from three anonymous reviewers and the corresponding editor for improvement of our manuscript.

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Authors and Affiliations

  1. National Research Institute of Fisheries Science, Fukuura, Kanazawa, Yokohama, 236-8648, Japan

    Yoji Nakamura, Yuya Shigenobu & Kenji Saitoh

  2. Momoshima Branch, National Research Institute of Fisheries and Environment of Inland Sea, Momoshima 1760, Onomichi, Hiroshima, 722-0061, Japan

    Takuma Sugaya

  3. Tohoku National Fisheries Research Institute, Shinhama, Shiogama, 985-0001, Japan

    Tadahide Kurokawa

Authors
  1. Yoji Nakamura
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  2. Yuya Shigenobu
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  3. Takuma Sugaya
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  4. Tadahide Kurokawa
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  5. Kenji Saitoh
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Corresponding author

Correspondence to Kenji Saitoh.

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Nakamura, Y., Shigenobu, Y., Sugaya, T. et al. Automated screening and primer design of fish microsatellite DNA loci on pyrosequencing data. Ichthyol Res 60, 184–187 (2013). https://doi.org/10.1007/s10228-012-0317-8

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  • DOI: https://doi.org/10.1007/s10228-012-0317-8

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