Comparative genomics of medaka and fugu

Shimizu, Nobuyoshi; Sasaki, Takashi; Asakawa, Shuichi; Shimizu, Atsushi; Ishikawa, Sabine K.; Imai, Satoshi; Murayama, Yuji; Himmelbauer, Heinz; Mikami, Hiroshi; Furutani-Seiki, Makoto; Kondoh, Hisato; Schartl, Manfred; Nonaka, Masaru; Takeda, Hiroyuki; Hori, Hiroshi; Shima, Akihiro

doi:10.1016/j.cbd.2005.10.008

Cited by 7 publications

(7 citation statements)

References 13 publications

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“…Due to the backgrounds of the different strains, the libraries can be used in a complementary way. These BAC clones can be screened by colony hybridization screening or the 4D-PCR screening system and are a powerful tool for the positional cloning of mutated genes [21]. More than 20,000 clones of BAC-end sequences have been determined and are available in M base: http://mbase.bioweb.ne.jp/ϳdclust/medaka_top.html.…”

Section: Bac Libraries and Physical Mapmentioning

confidence: 99%

“…As part of the activities of the MGI, the genomic DNA sequence and the accurate order and orientation of genes of a single chromosome (linkage group 22: LG22) have been determined through a clone-by-clone (CBC) strategy [9,21]. The majority of orthologous genes on LG22 are located on tetraodon chromosome 14, zebrafish LG17, and human chromosome 14 [4,13].…”

Section: Genome Sequencing Project In Medakamentioning

confidence: 99%

“…Moreover, targeted modifications at exact positions within a genomic BAC clone can be introduced by homologous recombination. The high-quality medaka BAC libraries were constructed from two inbred strains, Hd-rR and HNI, covering 20-24 times the medaka genome with an average insert size of 160-200 kb [21]. The third medaka BAC library was constructed from the Cab strain [Amemiya et al, unpublished data].…”

Section: Bac Libraries and Physical Mapmentioning

confidence: 99%

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The Medaka Genome: Why We Need Multiple Fish Models in Vertebrate Functional Genomics

Mikami¹,

Kamei²,

Fukamachi³

et al. 2006

Genome Dynamics

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Medaka (Oryzias latipes) is widely used in research in the fields of biology, medicine, environmental science and fisheries. Zebrafish and medaka are well established as genetic model systems in which large-scale mutagenesis has been successfully performed, and for which EST data, BAC libraries, and fine linkage maps have been accumulated. Among rayfinned fish, there is a large evolutionary distance between medaka and zebrafish. In contrast, the evolutionary distance between medaka and two species of pufferfish, fugu (Takifugu rubripes), and tetraodon (Tetraodon nigroviridis), is almost comparable to that between humans and rodents, and the current genome project is showing that their genome organization is well conserved. Comparison of genome structure among teleosts and mammals helps our understanding of the orthologous gene structure and the evolution of gene families in vertebrates. In addition, gene functions have to be analyzed by both forward and reverse genetics. The Targeting Induced Local Lesions IN Genome (TILLING) system, which includes random mutagenesis, followed by screening for induced mutations in the target genes, is a powerful tool for studying the functional genomics of both medaka and zebrafish.

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Section: Bac Libraries and Physical Mapmentioning

confidence: 99%

Section: Genome Sequencing Project In Medakamentioning

confidence: 99%

Section: Bac Libraries and Physical Mapmentioning

confidence: 99%

See 1 more Smart Citation

The Medaka Genome: Why We Need Multiple Fish Models in Vertebrate Functional Genomics

Mikami¹,

Kamei²,

Fukamachi³

et al. 2006

Genome Dynamics

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“…In recent years due to the efforts made in genome studies of many fish species, especially of model fish species like zebrafish and Tetraodon , genomic information of vertebrates has shown a substantial increase and comparative genomics studies have become a very important method for studying genome evolution in teleosts and vertebrates in general [1] as well as for the identification of regions of conserved synteny (e.g. for review [2]).…”

Section: Introductionmentioning

confidence: 99%

A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis

Sarropoulou

Franch

Louro³

et al. 2007

BMC Genomics

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Background: Comparative teleost studies are of great interest since they are important in aquaculture and in evolutionary issues. Comparing genomes of fully sequenced model fish species with those of farmed fish species through comparative mapping offers shortcuts for quantitative trait loci (QTL) detections and for studying genome evolution through the identification of regions of conserved synteny in teleosts. Here a comparative mapping study is presented by radiation hybrid (RH) mapping genes of the gilthead sea bream Sparus aurata, a non-model teleost fish of commercial and evolutionary interest, as it represents the worldwide distributed species-rich family of Sparidae.

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“…In this study, we utilized approximately 1 Mb genomic DNA sequence of medaka chromosome LG22 (Sasaki et al, 2004;Shimizu et al, 2006;Sasaki et al, 2007) and the corresponding sequence of Takifugu genome (Aparicio et al, 2002) to evaluate the basis for genome size difference and the genomic architecture.…”

Section: Introductionmentioning

confidence: 99%

The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes)

et al. 2007

Self Cite

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Evolution of the genome size in eukaryotes is often affected by changes in the noncoding sequences, for which insertions and deletions (indels) of small nucleotide sequences and amplification of repetitive elements are considered responsible. In this study, we compared the genomic DNA sequences of two kinds of fish, medaka (Oryzias latipes) and fugu (Takifugu rubripes), which show two-fold difference in the genome size (800 Mb vs. 400 Mb). We selected a contiguous DNA sequence of 790 kb from the medaka chromosome LG22 (linkage group 22), and made a precise comparison with the sequence (387 kb) of the corresponding region of Takifugu. The sequence of 178 kb in total was aligned common between two fishes, and the remaining sequences (612 kb for medaka and 209 kb for fugu) were found abundant in various repetitive elements including many types of unclassified low copy repeats, all of which accounted for more than a half (54%) of the genome size difference. Furthermore, we identified a significant difference in the length ratio of the unaligned sequences that locate between the aligned sequences (USBAS), particularly after eliminating known repetitive elements. These USBAS with no repetitive elements (USBAS-nr) located within the intron and intergenic region. These results strongly indicated that amplification of repetitive elements and compilation of indels are major driving forces to facilitate changes in the genome size.

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Comparative genomics of medaka and fugu

Cited by 7 publications

References 13 publications

The Medaka Genome: Why We Need Multiple Fish Models in Vertebrate Functional Genomics

The Medaka Genome: Why We Need Multiple Fish Models in Vertebrate Functional Genomics

A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis

The genome size evolution of medaka (Oryzias latipes) and fugu (Takifugu rubripes)

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