A Medaka Gene Map: The Trace of Ancestral Vertebrate Proto-Chromosomes Revealed by Comparative Gene Mapping

  1. Kiyoshi Naruse1,6,
  2. Minoru Tanaka2,
  3. Kazuei Mita3,
  4. Akihiro Shima4,
  5. John Postlethwait5, and
  6. Hiroshi Mitani4
  1. 1 Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
  2. 2 Division of Biological Sciences, Graduate School of Science, Hokkaido University, Kita, Sapporo 060-0810, Japan
  3. 3 Department of Genome Research, Laboratory of Insect Genome, National Institute of Agrobiological Sciences, Thukuba Ibaraki 305-8602, Japan
  4. 4 Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
  5. 5 Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403, USA

Abstract

The mapping of Hox clusters and many duplicated genes in zebrafish indicated an extra whole-genome duplication in ray-fined fish. However, to reconstruct the preduplication chromosomes (proto-chromosomes), the comparative genomic studies of more distantly related teleosts are essential. Medaka and zebrafish are ideal for this purpose, because their lineages separated from their last common ancestor ∼140 million years ago. To reconstruct ancient vertebrate chromosomes, including the chromosomes of the vertebrate ancestor of humans from 450 million years ago, we mapped 818 genes and expressed sequence tags (ESTs) on a single meiotic backcross panel obtained from inbred strains of the medaka, Oryzias latipes. Comparisons of linkage relationships of orthologous genes among three species of vertebrates (medaka, zebrafish, and human) indicate the number and content of the chromosomes of the last common ancestor of ray-fined fish and lobe-fined fish (including humans), and the extra whole genome duplication event in the ray-fin lineage occurred in the common ancestor of perhaps all teleosts.

Footnotes

  • [Supplemental material is available online at www.genome.org.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2004004. Article published online before print in April 2004.

  • ↵6 Corresponding author. E-MAIL naruse{at}biol.s.u-tokyo.ac.jp; FAX 81-3-5841-4410.

    • Accepted December 28, 2003.
    • Received September 24, 2003.
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  1. Published in Advance April 12, 2004, doi: 10.1101/gr.2004004 Genome Res. 14: 820-828 Cold Spring Harbor Laboratory Press

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