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 language | English |
|---|---|
| Pages (from-to) | 124-133 |
| Number of pages | 10 |
| Journal | Genomics |
| Volume | 89 |
| Issue number | 1 |
| DOIs | |
| Publication status | Published - 2007 Jan |
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Keywords
- Evolution
- Genome sequence
- Medaka
ASJC Scopus subject areas
- Genetics
Cite this
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 journal › Article
}
TY - JOUR
T1 - The DNA sequence of medaka chromosome LG22
AU - Sasaki, Takashi
AU - Shimizu, Atsushi
AU - Ishikawa, Sabine K.
AU - Imai, Shuichiro
AU - Asakawa, Shuichi
AU - Murayama, Yuji
AU - Khorasani, Maryam Zadeh
AU - Mitani, Hiroshi
AU - Furutani-Seiki, Makoto
AU - Kondoh, Hisato
AU - Nanda, Indrajit
AU - Schmid, Michael
AU - Schartl, Manfred
AU - Nonaka, Masaru
AU - Takeda, Hiroyuki
AU - Hori, Hiroshi
AU - Himmelbauer, Heinz
AU - Shima, Akihiro
AU - Shimizu, Nobuyoshi
PY - 2007/1
Y1 - 2007/1
N2 - 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.
AB - 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.
KW - Evolution
KW - Genome sequence
KW - Medaka
UR - http://www.scopus.com/inward/record.url?scp=33845224414&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33845224414&partnerID=8YFLogxK
U2 - 10.1016/j.ygeno.2006.09.003
DO - 10.1016/j.ygeno.2006.09.003
M3 - Article
C2 - 17067776
AN - SCOPUS:33845224414
VL - 89
SP - 124
EP - 133
JO - Genomics
JF - Genomics
SN - 0888-7543
IS - 1
ER -