Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes

Gene Kurosawa, Naofumi Takamatsu, Masayoshi Takahashi, Mariko Sumitomo, Emi Sanaka, Kouji Yamada, Kazuhiro Nishii, Masaru Matsuda, Shuichi Asakawa, Hiroshi Ishiguro, Keiji Miura, Yoshikazu Kurosawa, Nobuyoshi Shimizu, Yuji Kohara, Hiroshi Hori

Research output: Contribution to journalArticlepeer-review

43 Citations (Scopus)


We isolated BAC clones that cover the entire hox gene loci in the medaka fish Oryzias latipes. The BAC clones were characterized by the Southern hybridization with many hox gene probes isolated in our previous study and by PCR using primers designed for selective amplification of respective hox genes. Then, the BAC clones have been subjected to shotgun sequencing. The results revealed the organization of the entire hox gene loci. Forty-six hox genes in total are encoded in seven clusters as follows: 10 hox genes in Aa cluster; 5 in Ab; 9 in Ba; 4 in Bb; 10 in Ca; 6 in Da; and 2 in Db. Together with the information on the hox gene loci registered in the Fugu genome database and in the Danio genome database, the physical maps of three fish genomes were constructed and compared one another. Not only numbers of hox genes but also the distances between the neighboring hox genes are highly similar between medaka and fugu. As for six clusters, Aa, Ab, Ba, Bb, Ca and Da that are commonly present in the three fishes, only few or no differences were found in each cluster. Thus, the hox gene sets should have been well conserved once they had been established in respective species.

Original languageEnglish
Pages (from-to)75-82
Number of pages8
Issue number1-2
Publication statusPublished - 29-03-2006

All Science Journal Classification (ASJC) codes

  • Genetics


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