, Volume 61, Issue 5, pp 385–399 | Cite as

Comparative genomic analysis of the major histocompatibility complex class I region in the teleost genus Oryzias

  • Ratnesh Bhai Mehta
  • Mayumi I. Nonaka
  • Masaru NonakaEmail author
Original Paper


The major histocompatibility complex (MHC) class I region of teleosts harbors a tight cluster of the class IA genes and several other genes directly involved in class I antigen presentation. Moreover, the dichotomous haplotypic lineages (termed d- and N- lineages) of the proteasome subunit beta genes, PSMB8 and PSMB10, are present in this region of the medaka, Oryzias latipes. To understand the evolution of the Oryzias MHC class I region at the nucleotide sequence level, we analyzed bacterial artificial chromosome clones covering the MHC class I region containing the d- lineage of Oryzias luzonensis and the d- and N- lineages of Oryzias dancena. Comparison among these three elucidated sequences and the published sequences of the d- and N- lineages of O. latipes indicated that the order and orientation of the encoded genes were completely conserved among these five genomic regions, except for the class IA genes, which showed species-specific variation in copy number. The PSMB8 and PSMB10 genes showed trans-species dimorphism. The remaining regions flanking the PSMB10, PSMB8, and class IA genes showed high degrees of sequence conservation at interspecies as well as intraspecies levels. Thus, the three independent evolutionary patterns under apparently distinctive selective pressures are recognized in the Oryzias MHC class I region.


Major histocompatibility complex Oryzias BAC sequence Comparative genomics Evolution 



We thank Dr. Asao Fujiyama and Dr. Kiyoshi Naurse for constructing and providing us the O. luzonensis (LMB) and O. dancena (IMBX, IMBY) BAC genomic library. This work was supported by KAKENHI (Grant-in-Aid for Scientific Research) on Priority Areas Comparative Genomics from the Ministry of Education, Culture, Sports, Science and Technology, Japan (20017009) to M.N.

Supplementary material

251_2009_371_MOESM1_ESM.pdf (78 kb)
Supplementary Fig. 1 Multiple alignment of the predicted amino acid sequences of the UDA (a), ABCB3 (b), PSMB9 (c), PSMB9L (d), PSMB10 (e), and PSMB8 (f) genes. The deduced amino acid sequences of Orda(d), Orda(N), and Orlu(d) were aligned with those of Orla(d) (BA000027) and Orla(N) (AB183488) by ClustalX using the zebrafish orthologs as a reference ( Dare-ABCB3: BC163453, Dare-PSMB9: NP571466.1, Dare-PSMB9L: NP571751.1, Dare-PSMB10: NP571752.1, Dare-PSMB8: BC165541). No UDA ortholog is present in the zebrafish, and fugu classical class I gene (Furu-I103: AJ271723) was used as a reference for the UDA alignment. a The residues involved in anchoring of the N-terminal and C-terminal of the peptide of Furu-I103 are shown with light gray background. The conserved FYP motif is shown with the dotted box. Cysteine residues involved in disulfide bond are marked by the number sign. f The amino acid residues involved in the S1 pocket formation are numbered starting from the mature peptide denoted by +1. Dots and dashes indicate the identity to the uppermost gene sequence and deletion, respectively (PDF 78 kb)


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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Ratnesh Bhai Mehta
    • 1
  • Mayumi I. Nonaka
    • 1
  • Masaru Nonaka
    • 1
    Email author
  1. 1.Department of Biological Sciences, Graduate School of ScienceThe University of TokyoBunkyo-kuJapan

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