UTGB/medaka: Genomic resource database for medaka biology

Budrul Ahsan, Daisuke Kobayashi, Tomoyuki Yamada, Masahiro Kasahara, Shin Sasaki, Taro I. Saito, Yukinobu Nagayasu, Koichiro Doi, Yoichiro Nakatani, Wei Qu, Tomoko Jindo, Atsuko Shimada, Kiyoshi Naruse, Atsushi Toyoda, Yoko Kuroki, Asao Fujiyama, Takashi Sasaki, Atsushi Shimizu, Shuichi Asakawa, Nobuyoshi ShimizuShin Ichi Hashimoto, Jun Yang, Yongjun Lee, Kouji Matsushima, Sumio Sugano, Mitsuru Sakaizumi, Takanori Narita, Kazuko Ohishi, Shinobu Haga, Fumiko Ohta, Hisayo Nomoto, Keiko Nogata, Tomomi Morishita, Tomoko Endo, Tadasu Shin-i, Hiroyuki Takeda, Yuji Kohara, Shinichi Morishita

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka genome sequence (700 Mb) was reported in June 2007, and its substantial genomic resources have been opened to the public through the University of Tokyo Genome Browser Medaka (UTGB/medaka) database. This database provides basic genomic information, such as predicted genes, expressed sequence tags (ESTs), guanine/cytosine (GC) content, repeats and comparative genomics, as well as unique data resources including (i) 2473 genetic markers and experimentally confirmed PCR primers that amplify these markers, (ii) 142 414 bacterial artificial chromosome (BAC) and 217 344 fosmid end sequences that amount to 15.0- and 11.1-fold clone coverage of the entire genome, respectively, and were used for draft genome assembly, (iii) 16 519 460 single nucleotide polymorphisms (SNPs), and 2 859 905 insertions/deletions detected between two medaka inbred strain genomes and (iv) 841 235 5′-end serial analyses of gene-expression (SAGE) tags that identified 344 266 transcription start sites on the genome. UTGB/medaka is available at: http://medaka.utgenome.org/.

Original languageEnglish
JournalNucleic Acids Research
Volume36
Issue numberSUPPL. 1
DOIs
Publication statusPublished - 2008 Jan

Fingerprint

Oryzias
Tokyo
Genome
Databases
Bacterial Artificial Chromosomes
Far East
Transcription Initiation Site
Expressed Sequence Tags
Base Composition
Genomics
Fresh Water
Genetic Markers
Single Nucleotide Polymorphism
Ovum
Clone Cells
Gene Expression
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Genetics

Cite this

Ahsan, B., Kobayashi, D., Yamada, T., Kasahara, M., Sasaki, S., Saito, T. I., ... Morishita, S. (2008). UTGB/medaka: Genomic resource database for medaka biology. Nucleic Acids Research, 36(SUPPL. 1). https://doi.org/10.1093/nar/gkm765

UTGB/medaka : Genomic resource database for medaka biology. / Ahsan, Budrul; Kobayashi, Daisuke; Yamada, Tomoyuki; Kasahara, Masahiro; Sasaki, Shin; Saito, Taro I.; Nagayasu, Yukinobu; Doi, Koichiro; Nakatani, Yoichiro; Qu, Wei; Jindo, Tomoko; Shimada, Atsuko; Naruse, Kiyoshi; Toyoda, Atsushi; Kuroki, Yoko; Fujiyama, Asao; Sasaki, Takashi; Shimizu, Atsushi; Asakawa, Shuichi; Shimizu, Nobuyoshi; Hashimoto, Shin Ichi; Yang, Jun; Lee, Yongjun; Matsushima, Kouji; Sugano, Sumio; Sakaizumi, Mitsuru; Narita, Takanori; Ohishi, Kazuko; Haga, Shinobu; Ohta, Fumiko; Nomoto, Hisayo; Nogata, Keiko; Morishita, Tomomi; Endo, Tomoko; Shin-i, Tadasu; Takeda, Hiroyuki; Kohara, Yuji; Morishita, Shinichi.

In: Nucleic Acids Research, Vol. 36, No. SUPPL. 1, 01.2008.

Research output: Contribution to journalArticle

Ahsan, B, Kobayashi, D, Yamada, T, Kasahara, M, Sasaki, S, Saito, TI, Nagayasu, Y, Doi, K, Nakatani, Y, Qu, W, Jindo, T, Shimada, A, Naruse, K, Toyoda, A, Kuroki, Y, Fujiyama, A, Sasaki, T, Shimizu, A, Asakawa, S, Shimizu, N, Hashimoto, SI, Yang, J, Lee, Y, Matsushima, K, Sugano, S, Sakaizumi, M, Narita, T, Ohishi, K, Haga, S, Ohta, F, Nomoto, H, Nogata, K, Morishita, T, Endo, T, Shin-i, T, Takeda, H, Kohara, Y & Morishita, S 2008, 'UTGB/medaka: Genomic resource database for medaka biology', Nucleic Acids Research, vol. 36, no. SUPPL. 1. https://doi.org/10.1093/nar/gkm765
Ahsan B, Kobayashi D, Yamada T, Kasahara M, Sasaki S, Saito TI et al. UTGB/medaka: Genomic resource database for medaka biology. Nucleic Acids Research. 2008 Jan;36(SUPPL. 1). https://doi.org/10.1093/nar/gkm765
Ahsan, Budrul ; Kobayashi, Daisuke ; Yamada, Tomoyuki ; Kasahara, Masahiro ; Sasaki, Shin ; Saito, Taro I. ; Nagayasu, Yukinobu ; Doi, Koichiro ; Nakatani, Yoichiro ; Qu, Wei ; Jindo, Tomoko ; Shimada, Atsuko ; Naruse, Kiyoshi ; Toyoda, Atsushi ; Kuroki, Yoko ; Fujiyama, Asao ; Sasaki, Takashi ; Shimizu, Atsushi ; Asakawa, Shuichi ; Shimizu, Nobuyoshi ; Hashimoto, Shin Ichi ; Yang, Jun ; Lee, Yongjun ; Matsushima, Kouji ; Sugano, Sumio ; Sakaizumi, Mitsuru ; Narita, Takanori ; Ohishi, Kazuko ; Haga, Shinobu ; Ohta, Fumiko ; Nomoto, Hisayo ; Nogata, Keiko ; Morishita, Tomomi ; Endo, Tomoko ; Shin-i, Tadasu ; Takeda, Hiroyuki ; Kohara, Yuji ; Morishita, Shinichi. / UTGB/medaka : Genomic resource database for medaka biology. In: Nucleic Acids Research. 2008 ; Vol. 36, No. SUPPL. 1.
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abstract = "Medaka (Oryzias latipes) is a small egg-laying freshwater teleost native to East Asia that has become an excellent model system for developmental genetics and evolutionary biology. The draft medaka genome sequence (700 Mb) was reported in June 2007, and its substantial genomic resources have been opened to the public through the University of Tokyo Genome Browser Medaka (UTGB/medaka) database. This database provides basic genomic information, such as predicted genes, expressed sequence tags (ESTs), guanine/cytosine (GC) content, repeats and comparative genomics, as well as unique data resources including (i) 2473 genetic markers and experimentally confirmed PCR primers that amplify these markers, (ii) 142 414 bacterial artificial chromosome (BAC) and 217 344 fosmid end sequences that amount to 15.0- and 11.1-fold clone coverage of the entire genome, respectively, and were used for draft genome assembly, (iii) 16 519 460 single nucleotide polymorphisms (SNPs), and 2 859 905 insertions/deletions detected between two medaka inbred strain genomes and (iv) 841 235 5′-end serial analyses of gene-expression (SAGE) tags that identified 344 266 transcription start sites on the genome. UTGB/medaka is available at: http://medaka.utgenome.org/.",
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AU - Saito, Taro I.

AU - Nagayasu, Yukinobu

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AU - Asakawa, Shuichi

AU - Shimizu, Nobuyoshi

AU - Hashimoto, Shin Ichi

AU - Yang, Jun

AU - Lee, Yongjun

AU - Matsushima, Kouji

AU - Sugano, Sumio

AU - Sakaizumi, Mitsuru

AU - Narita, Takanori

AU - Ohishi, Kazuko

AU - Haga, Shinobu

AU - Ohta, Fumiko

AU - Nomoto, Hisayo

AU - Nogata, Keiko

AU - Morishita, Tomomi

AU - Endo, Tomoko

AU - Shin-i, Tadasu

AU - Takeda, Hiroyuki

AU - Kohara, Yuji

AU - Morishita, Shinichi

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