BackgroundThe Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, 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.ResultsTo accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%.ConclusionThe collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional genomics and molecular breeding. Full-length cDNA sequences and their annotations are provided in the database KaFTom http://www.pgb.kazusa.or.jp/kaftom/ via the website of the National Bioresource Project Tomato http://tomato.nbrp.jp.

The impact of overexpression of the 3-hydroxy-3-methylglutaryl coenzyme A reductase gene on microbial diversity in the rhizosphere of a transgenic tomato was examined using a ribosomal intergenic spacer analysis (RISA) and a terminal restriction fragment length polymorphism (T-RFLP) analysis of two functional bacterial genes (bacterial chitinase and nifH genes). While the overall profiles of both RISA and T-RFLP revealed high similarity between the transgenic and non-trangenic tomato, several polymorphic DNAs were detected as differential bands in both the qualitative and quantitative evaluations. Sequence analysis suggested that differential bands cloned in RISA showed low levels of similarity to known species but were most likely derived from uncultured microbes. The phylogenetic analyses of two differential bands cloned in the T-RFLP analysis of the chitinase and nifH genes indicated that these bands belonged to Streptomyces like chitinase group and cyanobacterial nifH group, respectively.

Mevalonic acid (MVA) pathway, in parallel with methylerythritol phosphate (MEP) pathway, produces precursor metabolites for isoprenoids, and affect fruit development in plants. 3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is supposed to be a key enzyme in the MVA pathway. To understand the role of HMGR in fruit development, we previously generated transgenic tomato (Solanum lycopersicum) expressing a melon HMGR gene (CmHMGR) and observed increased fruit size in these plants. To further examine this effect, we performed molecular and genetic characterization of the transgenic tomato line in the T 4 generation. The line showed stable expression of CmHMGR mRNA and protein, an effect that could lead to the increase in fruit weight observed, which exceeded 20%. Interestingly, the CmHMGR mRNA was highly expressed during tomato fruit development, whereas expression of the endogenous HMGRs (SlHMGR1, SlHMGR2, and SlHMGR3) was lower than in the wild type, suggesting the presence of a regulatory mechanism at the transcriptional level, as in mammalian systems. A preliminary analysis using cDNA macroarray filters was performed, and genes showing more than 2.5-fold differences in expression between transgenic and wild-type plants were identified. Most of the genes involved in isoprenoid biosynthesis did not show significantly different transcription levels, but 121 annotated genes and 152 genes of unknown function were found to be differentially expressed. These results demonstrate that the transgenic tomato line expressing the HMGR gene is genetically stable and could be used as a comprehensive material to elucidate the roles of HMGRs in tomato fruit development.