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.
Kurosawa
Gene
G
Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 460-8602, Japan. gene@fujita-hu.ac.jp
Takamatsu
Naofumi
N
Takahashi
Masayoshi
M
Sumitomo
Mariko
M
Sanaka
Emi
E
Yamada
Kouji
K
Nishii
Kazuhiro
K
Matsuda
Masaru
M
Asakawa
Shuichi
S
Ishiguro
Hiroshi
H
Miura
Keiji
K
Kurosawa
Yoshikazu
Y
Shimizu
Nobuyoshi
N
Kohara
Yuji
Y
Hori
Hiroshi
H
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