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          Institute: MPI für molekulare Genetik     Collection: Department of Vertebrate Genomics     Display Documents

ID: 335667.0, MPI für molekulare Genetik / Department of Vertebrate Genomics
The DNA sequence of medaka chromosome LG22
Authors:Sasaki, Takashi; Shimizu, Atsushi; Ishikawa, Sabine K.; Imai, Shuichiro; Asakawa, Shuichi; Murayama, Yuji; Khorasani, Maryam Zadeh; Mitani, Hiroshi; Furutani-Seiki, Makoto; Kondoh, Hisato; Nanda, Indrajit; Schmid, Michael; Schartl, Manfred; Nonaka, Masaru; Takeda, Hiroyuki; Hori, Hiroshi; Himmelbauer, Heinz; Shima, Akihiro; Shimizu, Nobuyoshi
Date of Publication (YYYY-MM-DD):2007-01
Title of Journal:Genomics
Issue / Number:1
Start Page:124
End Page:133
Copyright:© 2007 Elsevier Inc.
Review Status:not specified
Audience:Experts Only
Abstract / Description:We report the genomic DNA sequence of a single chromosome (linkage group 22; LG22) of the small teleost fish medaka (Oryzias latipes) as a first whole chromosome sequence from a non-mammalian vertebrate. The order and orientation of 633 protein-coding genes were deduced from 18,803,338 bp of DNA sequence, providing the opportunity to analyze chromosome evolution of vertebrate genomes by direct comparison with the human genome. The average number of genes in the “conserved gene cluster” (CGC), a strict definition of “synteny” at the sequence basis, between medaka and human was 1.6. These and other data suggest that approximately 38.8% of pair-wise gene relationships would have been broken from their common ancestor in the human and medaka lineages and further imply that approx 20,000 (15,520–23,280) breaks would have occurred from the entire genome of the common ancestor. These breaks were generated mainly by intra-chromosomal shufflings at a specific era in the vertebrate lineage. These precise comparative genomics allowed us to identify the pieces of ancient chromosomes of the common vertebrate ancestor and estimate chromosomal evolution in the vertebrate lineage.
Free Keywords:Genome sequence; Medaka; Evolution
External Publication Status:published
Document Type:Article
Communicated by:Hans Lehrach
Affiliations:MPI für molekulare Genetik
External Affiliations:Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan;
Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan;
Department of Integrated Bioscience, Graduate School of Frontier Science, The University of Tokyo, Bioscience Building 102, Kashiwa, Chiba 277-8562, Japan;
Developmental Mutants Group, Kondoh Differentiation Signaling Project, Japan Science and Technology Corporation, 14 Kawara-cho Yoshida, Sakyo-ku, Kyoto 606-8305, Japan;
Department of Human Genetics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany;
Department of Physiological Chemistry I, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany;
Department of Biological Science, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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