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Global gene expression analysis of gill tissues from normal and thermally selected strains of rainbow trout

  • Original Article
  • Aquaculture
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Abstract

The objective of the study reported here was to investigate genes related to upper temperature tolerance in rainbow trout Oncorhynchus mykiss, a cold-water species with considerable economic importance, by global gene expression analysis using a next generation sequencing system. Fifty million paired sequences were collected from the gill tissues of each of five individuals of a thermally selected strain developed by selective breeding and from the gill tissues of a standard Donaldson strain and assembled into transcripts. The data of both strains were integrated, and a BLASTX search identified 13,092 independent, known genes. A back-mapping of raw reads from both strains onto the genes, conducted to investigate their frequency of expression, revealed that 324 genes showed at least a twofold higher expression in the thermally selected strain than in the Donaldson strain. In addition, 44.4 % of commonly expressed genes were categorized into 38 functional groups by annotation. Genes encoding heat shock proteins and c-fos-related proteins were highly expressed in the thermally selected strain. Our strategy to employ next generation sequencing proved to be very useful to find genes responsible for upper temperature tolerance of rainbow trout.

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Acknowledgments

This study was supported in part by a grant from the Ministry of Agriculture, Forestry, and Fisheries of Japan.

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Authors and Affiliations

  1. Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan

    Engkong Tan, Chaninya Wongwarangkana, Shigeharu Kinoshita & Shuichi Asakawa

  2. Laboratory of Functional Genomics, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba, 277-8561, Japan

    Yutaka Suzuki

  3. Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba, 277-8561, Japan

    Kenshiro Oshima & Masahira Hattori

  4. Kobayashi Branch, Miyazaki Prefectural Fisheries Research Institute, Kobayashi, Miyazaki, 886-0005, Japan

    Toshinao Ineno, Koichi Tamaki & Akio Kera

  5. Nikko Station, National Research Institute of Aquaculture, Fisheries Research Agency, Nikko, Tochigi, 321-1661, Japan

    Koji Muto & Takashi Yada

  6. General Planning and Coordination Department, Headquarters, Fisheries Research Agency, Yokohama, Kanagawa, 236-8648, Japan

    Shoji Kitamura

  7. Laboratory of Marine Biochemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan

    Shugo Watabe

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  1. Engkong Tan
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  2. Chaninya Wongwarangkana
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  8. Koichi Tamaki
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  9. Akio Kera
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  10. Koji Muto
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  11. Takashi Yada
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  12. Shoji Kitamura
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  13. Shuichi Asakawa
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  14. Shugo Watabe
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Corresponding author

Correspondence to Shugo Watabe.

Additional information

S. Asakawa and S. Watabe contributed equally to this work.

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Supplementary material 1 (XLS 2,251 kb)

12562_2012_522_MOESM2_ESM.ppt

Bioinformatics workflow of this study. This figure summarizes the analytical steps for quality selection, de novo assembly, annotation, and read mapping with software packages in the respective steps of in this study (PPT 190 kb)

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Tan, E., Wongwarangkana, C., Kinoshita, S. et al. Global gene expression analysis of gill tissues from normal and thermally selected strains of rainbow trout. Fish Sci 78, 1041–1049 (2012). https://doi.org/10.1007/s12562-012-0522-4

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  • DOI: https://doi.org/10.1007/s12562-012-0522-4

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