TOMATOMICS

tomatomics  The Tomato Integrated Database

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New version release
Aug. 7th 2015 The new version of TOMATOMICS, here.
We are glad to announce the release of the new version (beta version) of the TOMATOMICS today.
Please access the omics information through the new database and the interfaces.
The new version of the database also contains the highly-relaiable functional annotations derived from natural language processing and manual curation for the large-scale publication data.
The Tomato Integrated Database
The integrated omics database in tomato "TOMATOMICS" stores various biological information such as DNA markers, microarray data, gene expression networks and metabolic pathways, which are provided from MiBASE and KaFTom. We constructed a new unigene set (KTU4: Kazusa Tomato Unigenes version 4) by clustering the sequences of nrFLcDNAs and ESTs.
Construction of KTU4
To construct the unigene set (KTU4), we employed 125,883 ESTs from nine Micro-Tom cDNA libraries and other publicly available 196,912 ESTs from the Sol Genomics Network (SGN). For these ESTs, repeat regions and low-quality sequences (phred QV < 30) were removed. KTU4 constructed from the processed ESTs consists of
[1] KTU4HTCs
 : 
EST clustering by nrFLcDNAs.
[2] KTU4BACs
 : 
assembling ESTs with homology to the tomato BESs (Bac End Sequences).
[3] KTU4ESTs
 : 
assembling ESTs with no homology to BESs.
The total number of unigenes in KTU4 is 58,083.
Detection of SNPs
We detected SNPs among tomato cultivars. These SNPs were independently identified by the following methods.
(1)  
The ESTs were alighned on KTU4 sequences. Then the mismatched sites among nine cultivars were detected.
(2)  
The BESs were mapped on the Heinz genome, then inconsistent nucleotides were detected.
(3)  
The Micro-Tom NGS reads (genome resequencing data) were mapped on the Heinz genome, then high-quality mismatches between Micro-Tom and Heinz were extracted. These candidate SNPs were stored and visualized in GBrowse.
SNPs detected by EST alignment [ method (1) ] can be searched Misc. Search -> Search SNP/InDel.
References
1   Masaaki Kobayashi, Hideki Nagasaki, Virginie Garcia, Daniel Just, Ce'cile Bres, Jean-Philippe Mauxion, Marie-Christine Le Paslier, Dominique Brunel, Kunihiro Suda, Yohei Minakuchi, Atsushi Toyoda, Asao Fujiyama, Hiromi Toyoshima, Takayuki Suzuki, Kaori Igarashi, Christophe Rothan, Eli Kaminuma, Yasukazu Nakamura, Kentaro Yano, Koh Aoki (2013) Genome-wide analysis of intraspecific DNA polymorphism in ‘Micro-Tom’, a model cultivar of tomato. (Solanum lycopersicum) Plant and Cell Physiology : doi: 10.1093/pcp/pct181. (First published online : December 5, 2013)
2   Rui Yan, Naoki Yokotani, Tatsuya Yamaoka, Kohichiro Ushijima, Ryohei Nakano, Kentaro Yano, Koh Aoki, Yasutaka Kubo (2013) Characterization of ripening-associated genes using a tomato DNA macroarray, 1-methylcyclopropene, and ripening-impaired mutants. Postharvest Biol Technol 86 : 159-70.
3   Erika Asamizu, Kenta Shirasawa, Hideki Hirakawa, Shusei Sato, Satoshi Tabata, Kentaro Yano, Tohru Ariizumi, Daisuke Shibata, Hiroshi Ezura (2012) Mapping of Micro-Tom BAC-end Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms. International Journal of Plant Genomics : 8 pages. (2012 Nov. 27)
4   Fabien Mounet, Annick Moing, Mariusz Kowalczyk, Johannes Rohrmann, Johann Petit, Virginie Garcia, Mickael Maucourt, Kentaro Yano, Catherine Deborde, Koh Aoki, Hélène Bèrges, Antonio Granell, Alisdair R. Fernie, Catherine Bellini, Christophe Rothan, Martine Lemaire-Chamley (2012) Down-regulation of a Single Auxin Efflux Transport Protein in Tomato Induces Precocious Fruit Development. Journal of Experimental Botany 63 (13) : 4901-4917. (2012 Jul. 27)
5   The Tomato Genome Consortium (2012) The Tomato Genome Sequence Provides Insights into Fleshy Fruit Evolution. Nature 485 : 635- 641. (2012 May 30)
6   K.Aoki, K.Yano, N.Sakurai, T. Tsugane, M. Watanabe, Y.-G. Yin, C. Matsukura and D. Shibata (2007) Expressed-based approach toward functional characterization of tomato genes that have no or weak similarity to Arabidopsis genes. Acta Hortic. 745, 457-464.
7   K. Aoki, K. Yano, A. Suzuki, S. Kawamura, N. Sakurai, K. Suda, A. Kurabayashi, T. Suzuki, T. Tsugane, M. Watanabe, K. Ooga, M. Torii, T. Narita, T. Shin-i, Y. Kohara, N. Yamamoto, H. Takahashi, Y. Watanabe, M. Egusa, M. Kodama, Y. Ichinose, M. Kikuchi, S. Fukushima, A. Okabe, T. Arie, Y. Sato, K. Yazawa, S. Satoh, T. Omura, H. Ezura and D. Shibata (2010) Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics. BMC Genomics, 11,210.
8   K.Aoki, K.Yano, N.Sakurai, T. Tsugane, M. Watanabe, Y.-G. Yin, C. Matsukura and D. Shibata (2007) Expressed-based approach toward functional characterization of tomato genes that have no or weak similarity to Arabidopsis genes. Acta Hortic. 745, 457-464.
9   K. Yano, M. Watanabe, N. Yamamoto, T. Tsugane, K. Aoki, N. Sakurai and D. Shibata (2006) MiBASE: A database of a miniature tomato cultivar Micro-Tom. Plant Biotechnology, 23, 195-198.
10   T. Tsugane, M. Watanabe, K. Yano, N. Sakurai, H. Suzuki and D. Shibata (2005) Expressed sequence tags of full-length cDNA clones from the miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom. Plant Biotechnology, 22, 161-165.
11   N. Yamamoto, T. Tsugane, M. Watanabe, K. Yano, F. Maeda, C. Kuwata, T. Moez, Y. Ban, S. Nishimura and D. Shibata (2005) Expressed sequence tags from the laboratory-grown miniature tomato (Lycopersicon esculentum) cultivar Micro-Tom and mining for single nucleotide polymorphisms and insertions/deletions in tomato cultivars. GENE, 356, 127-134.

What's New
August 7, 2015
Aug. 7th 2015 The new version of TOMATOMICS, here.
We are glad to announce the release of the new version (beta version) of the TOMATOMICS today.
Please access the omics information through the new database and the interfaces.
The new version of the database also contains the highly-relaiable functional annotations derived from natural language processing and manual curation for the large-scale publication data.

April 7, 2015
Amono acid sequences of HTCs is downloadable. -> Download

(1)A table for Heinz 1706 transcript IDs in ITAG2.5, Micro-Tom names (EST,HTC), and INSDC Accession numbers
(2)A table for Heinz 1706 transcript IDs in ITAG2.5, SGN EST names, and INSDC Accession numbers



MiBASE
MiBASE provides information about Micro-Tom ESTs and Kazusa Tomato Unigenes ver.3 (KTU3) constructed from Micro-Tom ESTs and publicly available tomato ESTs.



KaFTom
KaFTom provides information about Tomato full-length cDNA clones derived from Micro-Tom.



Micro-Tom resources for functional genomics
A miniature cultivar, Solanum lycopersicum cv. Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance.


This work is supported in part by Research Funding for Computational Software Supporting Program from Meiji University.