Integrated Genome Informatics Research Unit

The importance of utilization of information technology for life science has increased. The information integration through genome and phenome is important for understanding of life science as systems. Our unit promotes the implementation of the research platform that is freely accessible to various species information. We also develop data mining technology based on sequence technology and comparative genomics, and provide analysis environment of transcriptomics and metabolomics. Furthermore, we are challenging to construct an integrated plant database which is a synthesis of these technologies and information infrastructure.

Research Fields

Biology & Biochemistry / Molecular Biology & Genetics / Agricultural Sciences

Research Subjects

• Provision of analysis environment for transcriptomics and metabolomics
• Improvement of information infrastructure with high flexibility (Database development)
• Promotion of genomics and comparative analysis based on sequence information

Publications

1. Sakurai T, Yamada Y, Sawada Y, Matsuda F, Akiyama K, Shinozaki K, Hirai MY, Saito K.:
   "PRIMe Update: Innovative Content for Plant Metabolomics and Integration of Gene Expression and Metabolite Accumulation."
   Plant Cell Physiol., in press.
2. Sawada Y, Nakabayashi R, Yamada Y, Suzuki M, Sato M, Sakata A, Akiyama K, Sakurai T, Matsuda F, Aoki T, Hirai MY, Saito KSawada Y, Nakabayashi R, Yamada Y, Suzuki M, Sato M, Sakata A, Akiyama K, Sakurai T, Matsuda F, Aoki T, Hirai MY, Saito K.:
   "RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database."
   Phytochemistry, 82, 38-45 (2012).
3. Sakurai T, Kondou Y, Akiyama K, Kurotani A, Higuchi M, Ichikawa T, Kuroda H, Kusano M, Mori M, Saitou T, Sakakibara H, Sugano S, Suzuki M, Takahashi H, Takahashi S, Takatsuji H, Yokotani N, Yoshizumi T, Saito K, Shinozaki K, Oda K, Hirochika H, Matsui M.MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA.:
   "RiceFOX: a database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function."
   Plant Cell Physiol., 52, 265-273 (2011).
4. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA.:
   "Genome sequence of the palaeopolyploid soybean"
   Nature, 463, 178-183 (2010).
5. Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K.:
   "TriFLDB: A database of Clustered full-length coding sequences from triticeae with applications to comparative grass genomics"
   Plant Physiol., 150,1135-1146 (2009)
6. Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K.:
   "PRIMe: a Web site that assembles tools for metabolomics and transcriptomics"
   In Silico Biol., 8, 339-345 (2008).
7. Umezawa T, Sakurai T, Totoki Y, Toyoda A, Seki M, Ishiwata A, Akiyama K, Kurotani A, Yoshida T, Mochida K, Kasuga M, Todaka D, Maruyama K, Nakashima K, Enju A, Mizukado S, Ahmed S, Yoshiwara K, Harada K, Tsubokura Y, Hayashi M, Sato S, Anai T, Ishimoto M, Funatsuki H, Teraishi M, Osaki M, Shinano T, Akashi R, Sakaki Y, Yamaguchi-Shinozaki K, Shinozaki K.:
   "Sequencing and analysis of approximately 40,000 soybean cDNA clones from a full-length-enriched cDNA library"
   DNA Res, 15, 333-346 (2008).
8. Sakurai T, Plata G, Rodriguez-Zapata F, Seki M, Salcedo A, Toyoda A, Ishiwata A, Tohme J, Sakaki Y, Shinozaki K, Ishitani M.:
   "Sequencing analysis of 20.000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response"
   BMC Plant Biology, 7, 66 (2007).
9. Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing Y, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, OOta S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda JI, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, and Sasaki T.:
   "Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana"
   Genome Res., 17, 175-183 (2007).
10. Sakurai, T., Satou, M., Akiyama, K., Iida, K., Seki, M., Kuromori, T., Ito, T., Konagaya, A., Toyoda, T., and Shinozaki, K.:
    "RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome"
    Nucleic Acids Res., 33, D647-D650 (2005).