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Nucleic Acids Research Advance Access originally published online on October 11, 2007
Nucleic Acids Research 2008 36(Database issue):D747-D752; doi:10.1093/nar/gkm765
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Nucleic Acids Research, 2008, Vol. 36, Database issue D747-D752
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

UTGB/medaka: genomic resource database for medaka biology

Budrul Ahsan1,2, Daisuke Kobayashi2,3, Tomoyuki Yamada1,2, Masahiro Kasahara1, Shin Sasaki1, Taro L. Saito1, Yukinobu Nagayasu1, Koichiro Doi1, Yoichiro Nakatani1, Wei Qu1, Tomoko Jindo3, Atsuko Shimada3, Kiyoshi Naruse3,4, Atsushi Toyoda5, Yoko Kuroki5, Asao Fujiyama5,6, Takashi Sasaki7, Atsushi Shimizu7, Shuichi Asakawa7, Nobuyoshi Shimizu7, Shin-ichi Hashimoto8, Jun Yang8, Yongjun Lee8, Kouji Matsushima8, Sumio Sugano9, Mitsuru Sakaizumi10, Takanori Narita3,11, Kazuko Ohishi11, Shinobu Haga11, Fumiko Ohta11, Hisayo Nomoto11, Keiko Nogata11, Tomomi Morishita11, Tomoko Endo11, Tadasu Shin-I11, Hiroyuki Takeda3, Yuji Kohara11 and Shinichi Morishita1,2,*

1Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, 2Bioinformatics Research and Development (BIRD), Japan Science and Technology Agency (JST), Tokyo 102-8666, 3Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, 4National Institute for Basic Biology, Okazaki 444-8585, 5RIKEN Genomic Sciences Center, Yokohama 230-0045, 6National Institute of Informatics, Tokyo 101-8430, 7Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, 8Department of Molecular Preventive Medicine, School of Medicine, The University of Tokyo, Tokyo 113-0033, 9Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, 10Department of Environmental Science, Faculty of Science, Niigata University, Niigata 950-2181 and 11Center for Genetic Resource Information, National Institute of Genetics, Mishima 411-8540, Japan

* To whom correspondence should be addressed. Tel: +81 47 136 3984; Fax: +81 47 136 3977; Email: moris{at}cb.k.u-tokyo.ac.jp

Received August 15, 2007. Revised September 10, 2007. Accepted September 11, 2007.

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/

The authors wish it to be known that, in their opinion, the second and third authors should be regarded as equally contributed Authors.


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