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

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 gene...

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Bibliographic Details
Published in:Gene 2006-03, Vol.370, p.75-82
Main Authors: Kurosawa, Gene, Takamatsu, Naofumi, Takahashi, Masayoshi, Sumitomo, Mariko, Sanaka, Emi, Yamada, Kouji, Nishii, Kazuhiro, Matsuda, Masaru, Asakawa, Shuichi, Ishiguro, Hiroshi, Miura, Keiji, Kurosawa, Yoshikazu, Shimizu, Nobuyoshi, Kohara, Yuji, Hori, Hiroshi
Format: Article
Language:English
Subjects:
Animals
BAC clones
Blotting, Southern - methods
Chromosome duplication
Chromosome Mapping - methods
Chromosomes, Artificial, Bacterial - genetics
Danio rerio
Databases, Genetic
Fugu
Gene loss
Genome - genetics
Homeodomain Proteins - genetics
Humans
Multigene Family - genetics
Oryzias - genetics
Oryzias latipes
Quantitative Trait Loci - genetics
Sequence Homology, Nucleic Acid
Shotgun sequencing
Takifugu - genetics
Zebrafish - genetics
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Summary: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.
ISSN:0378-1119
1879-0038
DOI:10.1016/j.gene.2005.11.015