The DNA sequence of medaka chromosome LG22

Takashi Sasaki, Atsushi Shimizu, Sabine K. Ishikawa, Shuichiro Imai, Shuichi Asakawa, Yuji Murayama, Maryam Zadeh Khorasani, Hiroshi Mitani, Makoto Furutani-Seiki, Hisato Kondoh, Indrajit Nanda, Michael Schmid, Manfred Schartl, Masaru Nonaka, Hiroyuki Takeda, Hiroshi Hori, Heinz Himmelbauer, Akihiro Shima, Nobuyoshi Shimizu

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)124-133
Number of pages10
JournalGenomics
Volume89
Issue number1
DOIs
Publication statusPublished - 2007 Jan

Fingerprint

Oryzias
Vertebrates
Chromosomes
Genome
Synteny
Human Genome
Multigene Family
Genomics
Genes
Fishes
Proteins

Keywords

  • Evolution
  • Genome sequence
  • Medaka

ASJC Scopus subject areas

  • Genetics

Cite this

Sasaki, T., Shimizu, A., Ishikawa, S. K., Imai, S., Asakawa, S., Murayama, Y., ... Shimizu, N. (2007). The DNA sequence of medaka chromosome LG22. Genomics, 89(1), 124-133. https://doi.org/10.1016/j.ygeno.2006.09.003

The DNA sequence of medaka chromosome LG22. / 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.

In: Genomics, Vol. 89, No. 1, 01.2007, p. 124-133.

Research output: Contribution to journalArticle

Sasaki, T, Shimizu, A, Ishikawa, SK, Imai, S, Asakawa, S, Murayama, Y, Khorasani, MZ, Mitani, H, Furutani-Seiki, M, Kondoh, H, Nanda, I, Schmid, M, Schartl, M, Nonaka, M, Takeda, H, Hori, H, Himmelbauer, H, Shima, A & Shimizu, N 2007, 'The DNA sequence of medaka chromosome LG22', Genomics, vol. 89, no. 1, pp. 124-133. https://doi.org/10.1016/j.ygeno.2006.09.003
Sasaki T, Shimizu A, Ishikawa SK, Imai S, Asakawa S, Murayama Y et al. The DNA sequence of medaka chromosome LG22. Genomics. 2007 Jan;89(1):124-133. https://doi.org/10.1016/j.ygeno.2006.09.003
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. / The DNA sequence of medaka chromosome LG22. In: Genomics. 2007 ; Vol. 89, No. 1. pp. 124-133.
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