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MBE Advance Access published online on January 6, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msn305
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Dichotomous haplotypic lineages of the immunoproteasome subunit genes, PSMB8 and PSMB10, in the MHC class I region of a teleost medaka, Oryzias latipes

Kentaro Tsukamoto1, Mitsuru Sakaizumi2, Masayoshi Hata3, Yuji Sawara4, Jaeyoung Eah5, Chang-Bae Kim6 and Masaru Nonaka1

1 Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
2 Department of Environmental Science, Faculty of Science, Niigata University, Niigata, Japan
3 Iwate Prefectural Mizusawa High School, Iwate, Japan
4 Faculty of Agriculture and Life Science, Hirosaki University, Aomori, Japan
5 Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
6 Department of Biological Sciences, College of Natural Sciences, Sangmyung University, Seoul, South Korea

Address correspondence and reprint requests to Masaru Nonaka, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 113-0033, Japan. E-mail: mnonaka{at}biol.s.u-tokyo.ac.jp, Tel: +81-3-58417589, Fax: +81-3-58414990

Received for publication September 4, 2008. Revision received November 20, 2008. Accepted for publication December 24, 2008.

Sequence comparison of the medaka, Oryzias latipes, MHC class I region between two inbred strains, the HNI (derived from the Northern Population) and the Hd-rR (from the Southern Population), revealed a ~100 kb highly divergent segment encompassing two MHC class IA genes, Orla-UAA and Orla-UBA, and two immunoproteasome beta subunit genes, PSMB8 and PSMB10. To elucidate the genetic diversity of this region, we analyzed polymorphisms of the PSMB8 and PSMB10 genes using wild populations of medaka from three genetically different groups: the Northern Population, the Southern Population, and the China–West Korean Population. A total of 1245 specimens from ten localities were analyzed, and all the PSMB8 and PSMB10 alleles were classified into the N (fixed in the HNI strain) or the d (fixed in the Hd-rR strain) lineage. PCR analysis of the region from PSMB8 to PSMB10 indicated that the two allelic lineages of these genes are segregating together constituting dichotomous haplotypic lineages. Both haplotypic lineages were identified in all three groups, although the frequency of d haplotypic lineage (73–100%) was much higher than that of N haplotypic lineage (0–27%) in all analyzed populations. The two allelic lineages of the PSMB8 gene showed curious substitutions at the 31st and 53rd residues of the mature peptide, which are likely involved in formation of the S1 pocket, suggesting that these alleles have a functional difference in cleavage specificity. These results indicate that the two medaka MHC haplotypic lineages encompassing the PSMB8 and PSMB10 genes are maintained in wild populations by a balancing selection.

Key Words: Medaka fish • MHC class I region • Immunoproteasome subunit gene • Dimorphism • Balancing selection


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