TOMATOMICS: A Web Database for Integrated Omics Information in Tomato

Handle URI:
http://hdl.handle.net/10754/622730
Title:
TOMATOMICS: A Web Database for Integrated Omics Information in Tomato
Authors:
Kudo, Toru; Kobayashi, Masaaki; Terashima, Shin; Katayama, Minami; Ozaki, Soichi; Kanno, Maasa; Saito, Misa; Yokoyama, Koji; Ohyanagi, Hajime; Aoki, Koh; Kubo, Yasutaka; Yano, Kentaro
Abstract:
Solanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Kudo T, Kobayashi M, Terashima S, Katayama M, Ozaki S, et al. (2017) TOMATOMICS: A Web Database for Integrated Omics Information in Tomato. Plant and Cell Physiology: pcw207. Available: http://dx.doi.org/10.1093/pcp/pcw207.
Publisher:
Oxford University Press (OUP)
Journal:
Plant and Cell Physiology
Issue Date:
29-Nov-2016
DOI:
10.1093/pcp/pcw207
Type:
Article
ISSN:
0032-0781; 1471-9053
Sponsors:
This work was supported in part by Grants-in-Aid for Scientific Research (No. 24113518 and No. 26113716 to K.Y.) from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (MEXT) and for Scientific Research (B) (No. 16H04873 to Y.K.) from the Japan Society for Promotion of Science (JSPS). Support was also provided by the MEXT-Supported Program for the Strategic Research Foundation at Private Universities (2014–2018), Research Project Grant (A) by Institute of Science and Technology, Meiji University and by Research Funding for the Computational Software Supporting 70 Program from Meiji University to K.Y.
Additional Links:
https://academic.oup.com/pcp/article/doi/10.1093/pcp/pcw207/2849735/TOMATOMICS-A-Web-Database-for-Integrated-Omics
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorKudo, Toruen
dc.contributor.authorKobayashi, Masaakien
dc.contributor.authorTerashima, Shinen
dc.contributor.authorKatayama, Minamien
dc.contributor.authorOzaki, Soichien
dc.contributor.authorKanno, Maasaen
dc.contributor.authorSaito, Misaen
dc.contributor.authorYokoyama, Kojien
dc.contributor.authorOhyanagi, Hajimeen
dc.contributor.authorAoki, Kohen
dc.contributor.authorKubo, Yasutakaen
dc.contributor.authorYano, Kentaroen
dc.date.accessioned2017-01-25T08:57:41Z-
dc.date.available2017-01-25T08:57:41Z-
dc.date.issued2016-11-29en
dc.identifier.citationKudo T, Kobayashi M, Terashima S, Katayama M, Ozaki S, et al. (2017) TOMATOMICS: A Web Database for Integrated Omics Information in Tomato. Plant and Cell Physiology: pcw207. Available: http://dx.doi.org/10.1093/pcp/pcw207.en
dc.identifier.issn0032-0781en
dc.identifier.issn1471-9053en
dc.identifier.doi10.1093/pcp/pcw207en
dc.identifier.urihttp://hdl.handle.net/10754/622730-
dc.description.abstractSolanum lycopersicum (tomato) is an important agronomic crop and a major model fruit-producing plant. To facilitate basic and applied research, comprehensive experimental resources and omics information on tomato are available following their development. Mutant lines and cDNA clones from a dwarf cultivar, Micro-Tom, are two of these genetic resources. Large-scale sequencing data for ESTs and full-length cDNAs from Micro-Tom continue to be gathered. In conjunction with information on the reference genome sequence of another cultivar, Heinz 1706, the Micro-Tom experimental resources have facilitated comprehensive functional analyses. To enhance the efficiency of acquiring omics information for tomato biology, we have integrated the information on the Micro-Tom experimental resources and the Heinz 1706 genome sequence. We have also inferred gene structure by comparison of sequences between the genome of Heinz 1706 and the transcriptome, which are comprised of Micro-Tom full-length cDNAs and Heinz 1706 RNA-seq data stored in the KaFTom and Sequence Read Archive databases. In order to provide large-scale omics information with streamlined connectivity we have developed and maintain a web database TOMATOMICS (http://bioinf.mind.meiji.ac.jp/tomatomics/). In TOMATOMICS, access to the information on the cDNA clone resources, full-length mRNA sequences, gene structures, expression profiles and functional annotations of genes is available through search functions and the genome browser, which has an intuitive graphical interface.en
dc.description.sponsorshipThis work was supported in part by Grants-in-Aid for Scientific Research (No. 24113518 and No. 26113716 to K.Y.) from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (MEXT) and for Scientific Research (B) (No. 16H04873 to Y.K.) from the Japan Society for Promotion of Science (JSPS). Support was also provided by the MEXT-Supported Program for the Strategic Research Foundation at Private Universities (2014–2018), Research Project Grant (A) by Institute of Science and Technology, Meiji University and by Research Funding for the Computational Software Supporting 70 Program from Meiji University to K.Y.en
dc.publisherOxford University Press (OUP)en
dc.relation.urlhttps://academic.oup.com/pcp/article/doi/10.1093/pcp/pcw207/2849735/TOMATOMICS-A-Web-Database-for-Integrated-Omicsen
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectGenomeen
dc.subjectDatabaseen
dc.subjectTranscriptomeen
dc.subjectMicro-tomen
dc.subjectSolanum Lycopersicum (Tomato)en
dc.titleTOMATOMICS: A Web Database for Integrated Omics Information in Tomatoen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalPlant and Cell Physiologyen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionBioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan.en
dc.contributor.institutionGraduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531 Japan.en
dc.contributor.institutionGraduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530 Japan.en
dc.contributor.institutionBioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan. kyano@isc.meiji.ac.jp.en
kaust.authorOhyanagi, Hajimeen
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