Kudo Toru, Kobayashi Masaaki, Terashima Shin, Katayama Minami, Ozaki Soichi, Kanno Maasa, Saito Misa, Yokoyama Koji, Ohyanagi Hajime, Aoki Koh, Kubo Yasutaka, Yano Kentaro
Bioinformatics Laboratory, School of Agriculture, Meiji University,Higashi-mita, Tama-ku, Kawasaki, Kanagawa, Japan.
King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Kingdom of Saudi Arabia.
Plant Cell Physiol. 2017 Jan 1;58(1):e8. doi: 10.1093/pcp/pcw207.
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.
番茄（Solanum lycopersicum）是一种重要的农作物，也是主要的模式产果植物。为推动基础研究和应用研究，随着番茄的发展，现已具备关于番茄的全面实验资源和组学信息。来自矮化品种Micro-Tom的突变体系和cDNA克隆就是其中两种遗传资源。目前仍在持续收集来自Micro-Tom的EST和全长cDNA的大规模测序数据。结合另一个品种Heinz 1706的参考基因组序列信息，Micro-Tom实验资源推动了全面的功能分析。为提高获取番茄生物学组学信息的效率，我们整合了Micro-Tom实验资源和Heinz 1706基因组序列的信息。我们还通过比较Heinz 1706基因组与转录组之间的序列来推断基因结构，转录组由存储在KaFTom和序列读取存档数据库中的Micro-Tom全长cDNA和Heinz 1706 RNA-seq数据组成。为了提供具有简化连接性的大规模组学信息，我们开发并维护了一个网络数据库TOMATOMICS（http://bioinf.mind.meiji.ac.jp/tomatomics/）。在TOMATOMICS中，可通过搜索功能和具有直观图形界面的基因组浏览器访问关于cDNA克隆资源、全长mRNA序列、基因结构、基因表达谱和功能注释的信息。
