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Unprecedented intraspecific diversity of the MHC class I region of a teleost medaka, Oryzias latipes

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Abstract

The major histocompatibility complex (MHC) is present at a single chromosomal locus of all jawed vertebrate analyzed so far, from sharks to mammals, except for teleosts whose orthologs of the mammalian MHC-encoded genes are dispersed at several chromosomal loci. Even in teleosts, several class IA genes and those genes directly involved in class I antigen presentation preserve their linkage, defining the teleost MHC class I region. We determined the complete nucleotide sequence of the MHC class I region of the inbred HNI strain of medaka, Oryzias latipes (northern Japan population-derived), from four overlapping bacterial artificial chromosome (BAC) clones spanning 540,982 bp, and compared it with the published sequence of the corresponding region of the inbred Hd-rR strain of medaka (425,935 bp, southern Japan population-derived) as the first extensive study of intraspecies polymorphisms of the ectotherm MHC regions. A segment of about 100 kb in the middle of the compared sequences encompassing two class Ia genes and two immunoproteasome subunit genes, PSMB8 and PSMB10, was so divergent between these two inbred strains that a reliable sequence alignment could not be made. The rest of the compared region (about 320 kb) showed a fair correspondence, and an approximately 96% nucleotide identity was observed upon gap-free segmental alignment. These results indicate that the medaka MHC class I region contains an ∼100-kb polymorphic core, which is most probably evolving adaptively by accumulation of point mutations and extensive genetic rearrangements such as insertions, deletions and duplications.

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Acknowledgements

We thank Ms. K. Takada for technical assistance in sequencing. This work was supported by a Grant-in-Aid from Ministry of Education, Culture, Sports, Science and Technology, Japan (11236205 and 15207019) to M.N.

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Authors and Affiliations

  1. Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan

    Kentaro Tsukamoto, Shinpei Hayashi, Megumi Y. Matsuo, Mayumi I. Nonaka, Mariko Kondo & Masaru Nonaka

  2. Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan

    Akihiro Shima

  3. Department of Molecular Biology, Keio University School of Medicine, Tokyo, 160-8582, Japan

    Shuichi Asakawa & Nobuyoshi Shimizu

Authors
  1. Kentaro Tsukamoto
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  2. Shinpei Hayashi
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  3. Megumi Y. Matsuo
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  4. Mayumi I. Nonaka
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  5. Mariko Kondo
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  6. Akihiro Shima
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  7. Shuichi Asakawa
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  8. Nobuyoshi Shimizu
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  9. Masaru Nonaka
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Corresponding author

Correspondence to Masaru Nonaka.

Additional information

The nucleotide sequence data of HNI MHC class I region reported in this paper have been submitted to the DDBJ/EMBL/GenBank and were assigned the accession number AB183488.

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Tsukamoto, K., Hayashi, S., Matsuo, M.Y. et al. Unprecedented intraspecific diversity of the MHC class I region of a teleost medaka, Oryzias latipes . Immunogenetics 57, 420–431 (2005). https://doi.org/10.1007/s00251-005-0009-x

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  • DOI: https://doi.org/10.1007/s00251-005-0009-x

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