Digital fruit ripening: Data mining in the TIGR tomato gene index

Many sequences of genes now are contained in databases available to the public. These databases will be the foundation and starting points of research in the future. Extracting information from these databases is useful to all forms of genetic, biochemical, and molecular biological research. We are interested in improving the nutrition of the tomato (Lycopersicon esculentum) through an understanding of the fundamentals of the molecular biological and biochemical processes that occur during tomato fruit development. The TIGR Tomato Gene Index has been of much use to our laboratory in determining new areas of molecular analysis for this research. We have examined this database for genes involved in ripening by using the nucleic acid and protein sequence searching software, BLAST, and by comparing gene expression information contained within the database. In this article, we report a number of previously unobserved genes that possibly are involved in tomato fruit development. Transcripts for MADS Box genes, zinc-finger genes, homeobox genes, and polycomb genes are among the transcripts that reveal upregulation during tomato fruit ripening. We believe that the information contained in this article will be valuable in considering approaches to analyzing the developmental processes involved in tomato fruit ripening.