Fast Breaking Comment by Shoshi Kikuchi

Shoshi Kikuchi answers a few questions about this month's fast breaking paper in the field of Multidisciplinary.

From •>>August 2004

Field: Multidisciplinary
Article Title: Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice
Authors: Kikuchi, S;Satoh, K;Nagata, T;Kawagashira, N;Doi, K;Kishimoto, N;Yazaki, J;Ishikawa, M;Yamada, H;Ooka, H;Hotta, I;Kojima, K;Namiki, T;Ohneda, E;Yahagi, W;Suzuki, K;Li, CJ;Ohtsuki, K;Shishiki, T;Otomo, Y;Murakami, K;Iida, Y;Sugano, S;Fujimura, T;Suzuki, Y;Tsunoda, Y;Kurosaki, T;Kodama, T;Masuda, H;Kobayashi, M;Xie, QH;Lu, M;Narikawa, R;Sugiyama, A;Mizuno, K;Yokomizo, S;Niikura, J;Ikeda, R;Ishibiki, J;Kawamata, M;Yoshimura, A;Miura, J;Kusumegi, T;Oka, M;Ryu, R;Ueda, M;Matsubara, K;Kawai, J;Carninci, P;Adachi, J;Aizawa, K;Arakawa, T;Fukuda, S;Hara, A;Hashidume, W;Hayatsu, N;Imotani, K;Ishii, Y;Itoh, M;Kagawa, I;Kondo, S;Konno, H;Miyazaki, A;Osato, N;Ota, Y;Saito, R;Sasaki, D;Sato, K;Shibata, K;Shinagawa, A;Shiraki, T;Yoshino, M;Hayashizaki, Y
Journal: SCIENCE
Volume: 301
Page: 376-379
Year: JUL 18 2003
* Natl Inst Agrobiol Sci, Dept Mol Biol, 2-1-2 Kannon Dai, Tsukuba, Ibaraki 3058602, Japan.
* Natl Inst Agrobiol Sci, Dept Mol Biol, Tsukuba, Ibaraki 3058602, Japan.
* Hitachi Software Engn Co, Naka Ku, Yokohama, Kanagawa 2310015, Japan.
* FAIS, Lab Genome Sequencing, Tsukuba, Ibaraki 3050062, Japan.
* Univ Tokyo, Inst Med Sci, Dept Virol, Minato Ku, Tokyo 1088639, Japan.
* Univ Tsukuba, Inst Agr & Forest Engn, Tsukuba, Ibaraki 3058577, Japan.
* NAIST, Nara 6300101, Japan.
* RIKEN, RIKEN Yokohama Inst, Inst Phys & Chem Res, Lab Genome Explorat Res Grp, Tsurumi Ku, Yokohama, Kanagawa 2300045, Japan.
* Genome Sci Lab, Wako, Saitama 3510198, Japan.
* FAIS, Anal Grp, Tsukuba, Ibaraki 3050062, Japan.

Why do you think your paper is highly cited?

“The understanding of rice in a molecular-biological view leads to finding the best ways to improve rice, such as high yield, an examination of the resistance to some severe environmental conditions for cultivation, and finding good grain quality through biotechnology.”

Rice is one of Japan’s most important crops as well as one of our daily food staples. The size of the rice genome is 430 Mb, smallest among the many Poaceae species, such as wheat, barley, corn, and oats—each of which are highly conserved with a well-defined syntenic relationship in their genome. Now rice is considered as a model cereal crop, as Arabidopsis is considered as a model of a vegetable crop. The International Rice Genome Sequencing Project (IRGSP) was launched in 1998 and the completion of the precise sequencing of rice is due to be achieved at the end of this year (2004). The rice full-length cDNA project had been initiated at the beginning of 2000 and was concluded in September of 2003. BRAIN (Bio-oriented Technology Research Advancement Institution), NIAS (National Institute of Agrobiological Sciences), FAIS (Foundation of Advancement of International Science), and RIKEN (Institute of Physical and Chemical Research) have collaborated to collect more than 30,000 cDNA clones from japonica rice in full-length cDNA form. This paper is the key paper of the project.

The full-length cDNA clones give many kinds of information, such as correct structural information of the genes on the genomic sequence data, large-scale gene expression data (transcriptome data) and the information of the proteins encoded in the cDNA sequence.

In this paper, various kinds of information, such as mapping information and the protein informatic analyses results of over 28,000 full-length cDNA clones were described. Collection of the many numbers of cDNA clones in full-length form and their complete nucleotide sequencing have had a lot of impact for researchers, especially in the plant-research fields. Along with the database in which individual clone information is shown via the internet: KOME: Knowledge-based Oryza Molecular Biological Encyclopedia at

http://cdna01.dna.affrc.go.jp/cDNA/, this paper provides a large amount of data on rice genes and useful information of the functional analyses and biotechnology of plant genes.

In November 2003, we also contributed to the distribution of the rice 22K oligo-microarray system based on the full-length cDNA clones’ sequencing data from Agilent Technologies. Microarray system technology is considered to be one of the best high-throughput gene expression data analysis systems. The researchers who used the microarray system also referred to the information of the full-length cDNA data shown on the KOME site.

Does it describe a new discovery or new methodology that’s useful to others?

Information on more than 28,000—currently more than 32,000 independent full-length cDNA clones—is, according to our mapping analysis, the information of about over 20,000 expressed genes (Transcription units) contained in the rice genome. It is very useful for not only researchers in rice-plant physiology but also for the researchers in other research fields such as through comparative genome analysis.

Could you summarize the significance of your paper in layman's terms?

What is the best way to understand rice? In our research field of Molecular Biology, the answer is to know the structure, biological function, and the interactive networks of the genes and the proteins encoded by genes. Genome sequence analysis has made a great contribution to understanding the whole genome structure of rice. However, it is not enough to understand the structure of genes, because current computer programs could not predict the precise gene structure. Structure of full-length cDNA information helps clarify understanding of the genes and also provides a large amount of information on the proteins. The understanding of rice in a molecular-biological view leads to finding the best ways to improve rice, such as high yield, an examination of the resistance to some severe environmental conditions for cultivation, and finding good grain quality through biotechnology. For the basal biological understanding and comparative genomics of rice and for the applied improvement of rice through biotechnology, functional information on rice genes contributes so much of value.

How did you become involved in this research?

We have been contributing to the establishment of the rice gene expression system using microarray technology since 1999. At that time, we had established the rice cDNA microarray system using about 11,000 semi-unique Expressed Sequence Tags, or EST sequences as probes which were collected by Sasaki et al, during the first phase of the rice genome project (1991-1997). One of the reasons for the launch of the rice full-length cDNA project in Japan is to collect much more expressed gene information from the rice genome. Our research team has been dedicated to this project.

For additional details, you can visit us online at the Rice Microarray Opening Site (RMOS): http://cdna01.dna.affrc.go.jp/RMOS/index.html

Shoshi Kikuchi, Ph.D.
Head of the Laboratory of Gene Expression
Department of Molecular Genetics
National Institute of Agrobiological Sciences
Tsukuba, Ibaraki, Japan

ESI Special Topics, August 2004
Citing URL - http://www.esi-topics.com/fbp/2004/august04-ShoshiKikuchi.html