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 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.
Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 460-8602, Japan. gene@fujita-hu.ac.jp
Gene
G
Kurosawa
Naofumi
N
Takamatsu
Masayoshi
M
Takahashi
Mariko
M
Sumitomo
Emi
E
Sanaka
Kouji
K
Yamada
Kazuhiro
K
Nishii
Masaru
M
Matsuda
Shuichi
S
Asakawa
Hiroshi
H
Ishiguro
Keiji
K
Miura
Yoshikazu
Y
Kurosawa
Nobuyoshi
N
Shimizu
Yuji
Y
Kohara
Hiroshi
H
Hori
D000818:Animals; D015139:Blotting, Southern / Q000379:methods; D002874:Chromosome Mapping / Q000379:methods; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D030541:Databases, Genetic; D016678:Genome / Q000235:genetics*; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D005810:Multigene Family / Q000235:genetics*; D009990:Oryzias / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D023741:Takifugu / Q000235:genetics; D015027:Zebrafish / Q000235:genetics
D018398:Homeodomain Proteins