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Tuesday Morning Contributed Talks

Aoki, Koh [1], Iijima, Yoko [1], Yano, Kentaro [1], Nakamura, Yukiko [2], Ogata, Yoshiyuki [1], Sakurai, Nozomu [1], Narita, Takanori [3], Shin-i, Tadasu [3], Mizoguchi, Tsuyoshi [4], Ezura, Hiroshi [4], Kohara, Yuji [3], Shibata, Daisuke [1].

Resources of full-length cDNA and metabolite information for tomato functional genomics.

TO accelerate tomato research in the coming post-genome era, we have started a systematic development of resources for the functional genomic studies. First, we developed a full-length cDNA (FL-cDNA) clone library. Our analysis of FL-cDNA clones currently focuses on the tomato genes that do not have similarity with the genes of other model plants. Secondly, we place metabolomics among novel approaches of functional genomics, and have done a comprehensive metabolite profiling using liquid chromatography Fourier transform mass spectrometry (LC-FT-MS). FL-cDNA libraries were constructed from leaves, fruits, and roots of Micro-Tom. At present (March, 2006), 37,600 and 28,900 5-ESTs were obtained from leaf- and fruit libraries, respectively. The 5 ESTs were assembled into 16,502 non-redundant sequences. A comparison of these non-redundant sequences with Arabidopsis sequences demonstrated that 17 % (2800) did not have similarity with Arabidopsis genes. Since functional annotations (e.g. GO annotation) for these genes, so called non-Arabidopsis genes, were limited, gene expression data from DNA array experiment were combined with the sequence data to get insights into the function of the non-Arabidopsis genes. This analysis demonstrated that the emergence of non-Arabidopsis genes did not have bias to any functional groups. For the metabolomic analysis of Micro-Tom, the extracts from leaves, stems, flowers, and fruits were analyzed by using LC-FT-MS to obtain a comprehensive dataset. The ultra-high accuracy of m/z measurement allowed a prediction of molecular formula and chemical structures. The metabolite profiling by LC-FT-MS turned out to be an efficient way for the chemical annotation of metabolites, thus possibly accelerate an integration of genetic and metabolic data for functional annotation of tomato genes. These resources will serve as one of the pivotal tools to investigate the link between genetic and phenotypic diversity seen in Solanaceae. A support from Research and Development Program for New Bio-industry Initiatives is gratefully acknowledged.


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1 - Kazusa DNA Research Institute, Dept. Plant Gene Research, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
2 - Nara Institute of Science and Technology, Laboratory of Comparative Genomics, Takayama-cho 8916-5, Ikoma, 630-0192, Japan
3 - National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan
4 - University of Tsukuba, Tennohdai 1-1-1, Tsukuba, 305-8572, Japan

Keywords:
Full-length cDNA
metabolite
annotation
tomato.


Session: SOL04-4
Location: Ballroom AB/Monona Terrace
Date: Tuesday, July 25th, 2006
Time: 9:10 AM
Abstract ID:136


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