P0956 Large-Scale Omics Analysis and Database Construction in Tomato

Hiroko Tsuchida , Meiji University, Kawasaki, Japan
Taishi Nagayama , Meiji University, Kawasaki, Japan
Kei Fujita , Meiji University, Kawasaki, Japan
Taiki Kuchiki , Meiji University, Kawasaki, Japan
Kazuki Hamada , Meiji University, Kawasaki, Japan
Koji Yokoyama , Meiji University, Kawasaki, Japan
Kaori Igarashi , Meiji University, Kawasaki, Japan
Koh Aoki , Osaka Prefecture University, Sakai, Japan
Kentaro Yano , Meiji University, Kawasaki, Japan
We have generated and analyzed ESTs and high throughput cDNAs (HTCs) from a laboratory-grown miniature tomato cultivar "Micro-Tom". With Micro-Tom ESTs and publicly available tomato ESTs, Kazusa Tomato Unigenes (KTUs; a non-redundant sequence set of transcripts) have been constructed. On the basis of the sequence information, omics analyses for structural annotations of the genome, DNA polymorphisms, functional protein domains, gene expression networks (GENs) and metabolic pathways have been also performed. The obtained data from cDNA resources and omics analyses have been provided from databases: MiBASE (http://www.pgb.kazusa.or.jp/mibase/) and KaFTom (http://www.pgb.kazusa.or.jp/kaftom/).

The current version of KTUs [KTU4 (KTU ver. 4)] have been constructed with ESTs of tomato and wild relatives. ESTs were classified based on sequence homology with sequences of HTCs from Micro-Tom and BACs from the International Tomato Genome Sequencing (ITAG) Project (bacs.v782.seq). A set of ESTs classified with each HTC/BAC sequence were assembled into a unigene(s) by CAP3. ESTs without sequence homology to any HTC/BAC sequence were also assembled into unigenes. For each unigene, functional annotations from BLAST and InterProScan searches against public sequence databases, metabolic pathway searches in KEGG and LycoCyc, and detections of SNPs and SSRs were executed. With sequence comparisons between KTUs and the genome in ITAG, gene structures and structural variants among paralogues and cultivars have been also predicted. To provide the omics data, we have developed an integrated database 'TOMATOMICS', which also stores information from MiBASE and KaFTom, with layers of information from the bioinformatics analyses and manual curation.