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The major histocompatibility complex (Mhc) class IIB region has greater genomic structural flexibility and diversity in the quail than the chicken

Posted by on in 2006
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Kazuyoshi Hosomichi (1) Takashi Shiina (1) Shingo Suzuki (2) Masayuki Tanaka (2) Sayoko Shimizu (1) Shigehisa Iwamoto (2) Hiromi Hara (2) Yutaka Yoshida (2) Jerzy K Kulski (1)(3) Hidetoshi Inoko (#1) and Kei Hanzawa (#2)

BMC Genomics. 2006; 7: 322.
Published online 2006 December 21. doi: 10.1186/1471-2164-7-322.
Copyright © 2006 Hosomichi et al; licensee BioMed Central Ltd.

Received October 2, 2006; Accepted December 21, 2006.Abstract

Abstract

Background

The quail and chicken major histocompatibility complex (Mhc) genomic regions have a similar overall organization but differ markedly in that the quail has an expanded number of duplicated class I, class IIB, natural killer (NK)-receptor-like, lectin-like and BG genes. Therefore, the elucidation of genetic factors that contribute to the greater Mhc diversity in the quail would help to establish it as a model experimental animal in the investigation of avian Mhc associated diseases.

Aims and approaches

The main aim here was to characterize the genetic and genomic features of the transcribed major quail MhcIIB (CojaIIB) region that is located between the Tapasin and BRD2 genes, and to compare our findings to the available information for the chicken MhcIIB (BLB). We used four approaches in the study of the quail MhcIIB region, (1) haplotype analyses with polymorphic loci, (2) cloning and sequencing of the RT-PCR CojaIIB products from individuals with different haplotypes, (3) genomic sequencing of the CojaIIB region from the individuals with the different haplotypes, and (4) phylogenetic and duplication analysis to explain the variability of the region between the quail and the chicken.

Results

Our results show that the Tapasin-BRD2 segment of the quail Mhc is highly variable in length and in gene transcription intensity and content. Haplotypic sequences were found to vary in length between 4 to 11 kb. Tapasin-BRD2 segments contain one or two major transcribed CojaIIBs that were probably generated by segmental duplications involving c-type lectin-like genes and NK receptor-like genes, gene fusions between two CojaIIBs and transpositions between the major and minor CojaIIB segments. The relative evolutionary speed for generating the MhcIIBs genomic structures from the ancestral BLB2 was estimated to be two times faster in the quail than in the chicken after their separation from a common ancestor. Four types of genomic rearrangement elements (GRE), composed of simple tandem repeats (STR), were identified in the MhcIIB genomic segment located between the Tapasin-BRD2 genes. The GREs have many more STR numbers in the quail than in the chicken that displays strong linkage disequilibrium.

Conclusion

This study suggests that the Mhc classIIB region has a flexible genomic structure generated by rearrangement elements and rapid SNP accumulation probably as a consequence of the quail adapting to environmental conditions and pathogens during its migratory history after its divergence from the chicken.

1 Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1143, Japan

2 Laboratory of Animal Physiology, Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa 243-0034, Japan

3 Centre for Comparative Genomics, School of Information Technology, Murdoch University, Murdoch, WA 6150, Australia Corresponding author.

#Contributed equally. Kazuyoshi Hosomichi: hoso@is.icc.u-tokai.ac.jp; Takashi Shiina: tshiina@is.icc.u-tokai.ac.jp; Shingo Suzuki: 53050010@nodai.ac.jp; Masayuki Tanaka: matanaka@jbirc.aist.go.jp; Sayoko Shimizu: sshimizu@is.icc.u-tokai.ac.jp; Shigehisa Iwamoto: 54050001@nodai.ac.jp; Hiromi Hara: hiromi-h@nodai.ac.jp; Yutaka Yoshida: yoshida@nodai.ac.jp; Jerzy K Kulski: jkulski@ccg.murdoch.edu.au; Hidetoshi Inoko: hinoko@is.icc.u-tokai.ac.jp; Kei Hanzawa: khanzawa@nodai.ac.jp

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