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Interchromosomal duplication of major histocompatibility complex class I regions in rainbow trout (Oncorhynchus mykiss), a species with a presumably recent tetraploid ancestry

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Abstract

Salmonid fishes are among the few animal taxa with a probable recent tetraploid ancestor. The present study is the first to compare large (>100 kb) duplicated genomic sequence fragments in such species. Two contiguous stretches with major histocompatibility complex (MHC) class I genes were detected in a rainbow trout BAC library, mapped and sequenced. The MHC class I duplicated regions, mapped by fluorescence in situ hybridization (FISH), were shown to be located on different metaphase chromosomes, Chr 14 and 18. Gene organization in both duplications is similar to that in other fishes, in that the class I loci are tightly linked with the PSMB8, PSMB9, PSMB10 and ABCB3 genes. Whereas one region, Onmy-IA, has a classical MHC class I locus (UBA), Onmy-IB encodes only non-classical class Ib proteins. The nucleotide diversity between the Onmy-IA and Onmy-IB noncoding regions is about 14%. This suggests that the MHC class I duplication event has occurred about 60 mya close to the time of an hypothesized ancestral tetraploid event. The present article is the first convincing report on the co-existence of two closely related MHC class I core regions on two different chromosomes. The interchromosomal duplication and the homology levels are supportive of the tetraploid model.

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Acknowledgments

We thank David Dunn for his assistance with Dotter. This study was supported by The Promotion of Basic Research Activities for Innovative Biosciences funded by Bio-oriented Technology Research Advancement Institution (BRAIN), Japan, and also by a Grant-in-Aid for Scientific Research on Priority Areas (C) Genome Science from the Ministry of Education, Culture, Sports, Science and Technology of Japan. All of the work reported here was performed in compliance with all applicable institutional and federal regulations. Takashi Shiina and Johannes Martinus Dijkstra contributed equally to this work.

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  1. Department of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, 259–1193, Japan

    Takashi Shiina, Sayoko Shimizu, Atsushi Watanabe, Kazuyo Yanagiya, Hidetoshi Inoko & Jerzy Kazimierz Kulski

  2. Inland Station, National Research Institute of Aquaculture, Tamaki, Mie, 519-0423, Japan

    Johannes Martinus Dijkstra, Ikunari Kiryu, Atushi Fujiwara, Yasutoshi Yoshiura & Mitsuru Ototake

  3. College of Advanced Science and Technology, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan

    Chizuko Nishida-Umehara

  4. Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan

    Yuuichi Kaba, Ikuo Hirono & Takashi Aoki

  5. Centre for Bioinformatics and Biological Computing, School of Information Technology, Division of Arts, Murdoch University, Murdoch, WA, 6150, Australia

    Jerzy Kazimierz Kulski

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  1. Takashi Shiina
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Correspondence to Takashi Shiina.

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Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank database under the accession numbers AB162342, AB162343 and from AY525774 to AY525776.

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Shiina, T., Dijkstra, J.M., Shimizu, S. et al. Interchromosomal duplication of major histocompatibility complex class I regions in rainbow trout (Oncorhynchus mykiss), a species with a presumably recent tetraploid ancestry. Immunogenetics 56, 878–893 (2005). https://doi.org/10.1007/s00251-004-0755-1

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