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, Koji Yamada, Kazuhiro Nishii, Masaru Matsuda, Shuichi Asakawa, Hiroshi Ishiguro, Keiji Miura, Yoshikazu Kurosawa, Nobuyoshi Shimizu, Yuji Kohara, Hiroshi Hori

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

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
JournalGene
Volume370
Issue number1-2
DOIs
Publication statusPublished - 29-03-2006

Fingerprint

Tetraodontiformes
Oryzias
Homeobox Genes
Zebrafish
Genome
Takifugu
Fishes
Clone Cells
Databases
Firearms

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Kurosawa, Gene ; Takamatsu, Naofumi ; Takahashi, Masayoshi ; Sumitomo, Mariko ; Sanaka, Emi ; Yamada, Koji ; Nishii, Kazuhiro ; Matsuda, Masaru ; Asakawa, Shuichi ; Ishiguro, Hiroshi ; Miura, Keiji ; Kurosawa, Yoshikazu ; Shimizu, Nobuyoshi ; Kohara, Yuji ; Hori, Hiroshi. / Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes. In: Gene. 2006 ; Vol. 370, No. 1-2. pp. 75-82.
@article{06f8584b2bb34d4089fb7c4295de08f6,
title = "Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes",
abstract = "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.",
author = "Gene Kurosawa and Naofumi Takamatsu and Masayoshi Takahashi and Mariko Sumitomo and Emi Sanaka and Koji Yamada and Kazuhiro Nishii and Masaru Matsuda and Shuichi Asakawa and Hiroshi Ishiguro and Keiji Miura and Yoshikazu Kurosawa and Nobuyoshi Shimizu and Yuji Kohara and Hiroshi Hori",
year = "2006",
month = "3",
day = "29",
doi = "10.1016/j.gene.2005.11.015",
language = "English",
volume = "370",
pages = "75--82",
journal = "Gene",
issn = "0378-1119",
publisher = "Elsevier",
number = "1-2",

}

Kurosawa, G, Takamatsu, N, Takahashi, M, Sumitomo, M, Sanaka, E, Yamada, K, Nishii, K, Matsuda, M, Asakawa, S, Ishiguro, H, Miura, K, Kurosawa, Y, Shimizu, N, Kohara, Y & Hori, H 2006, 'Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes', Gene, vol. 370, no. 1-2, pp. 75-82. https://doi.org/10.1016/j.gene.2005.11.015

Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes. / Kurosawa, Gene; Takamatsu, Naofumi; Takahashi, Masayoshi; Sumitomo, Mariko; Sanaka, Emi; Yamada, Koji; Nishii, Kazuhiro; Matsuda, Masaru; Asakawa, Shuichi; Ishiguro, Hiroshi; Miura, Keiji; Kurosawa, Yoshikazu; Shimizu, Nobuyoshi; Kohara, Yuji; Hori, Hiroshi.

In: Gene, Vol. 370, No. 1-2, 29.03.2006, p. 75-82.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes

AU - Kurosawa, Gene

AU - Takamatsu, Naofumi

AU - Takahashi, Masayoshi

AU - Sumitomo, Mariko

AU - Sanaka, Emi

AU - Yamada, Koji

AU - Nishii, Kazuhiro

AU - Matsuda, Masaru

AU - Asakawa, Shuichi

AU - Ishiguro, Hiroshi

AU - Miura, Keiji

AU - Kurosawa, Yoshikazu

AU - Shimizu, Nobuyoshi

AU - Kohara, Yuji

AU - Hori, Hiroshi

PY - 2006/3/29

Y1 - 2006/3/29

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=33644856151&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33644856151&partnerID=8YFLogxK

U2 - 10.1016/j.gene.2005.11.015

DO - 10.1016/j.gene.2005.11.015

M3 - Article

C2 - 16472944

AN - SCOPUS:33644856151

VL - 370

SP - 75

EP - 82

JO - Gene

JF - Gene

SN - 0378-1119

IS - 1-2

ER -