Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/2/2004
Publication Date: 10/10/2004
Citation: Fei, Z., Tang, X., Alba, R., Ronning, C., Martin, G., Tanksley, S., Giovannoni, J.J. 2004. Comprehensive EST analysis of tomato and comparative genomics of fruit ripening. Plant Journal. 40:47-59. Interpretive Summary: We present digital expression data for 6758 genes across 25 different tissues. We identified sets of differentially expressed genes associated with pathogen response and plant development with an emphasis on fruit ripening. We also performed similar analysis with available grape ESTs derived from fruit and compared fruit ripening induced genes between tomato and grape to gain insights into common and distinctive features of diverse ripening types at the molecular level. A public database that allows researchers to mine the tomato EST expression data interactively was created as a result of this study.
Technical Abstract: A large tomato expressed sequenced tag (EST) data set was mined to gain insights into differential gene expression among diverse plant tissues representing a range of developmental programs and biological responses. The EST collection generated from tomato contains high quality sequences of 152,635 distinct ESTs from 27 different cDNA libraries. These ESTs were reduced to a total of 31,012 unique genes with 15,925 tentative consensus sequences (TCs) and 15,087 singletons. To better understand tomato gene expression at a global level and to identify differentially expressed and tissue specific genes, we developed and implemented a digital expression analysis protocol. By clustering genes according to their relative abundance in the various EST libraries, expression patterns of genes across various tissues were generated and genes with similar patterns were grouped. Statistical analysis of EST prevalence in the fruit and pathogenesis-related libraries resulted in 333 genes being classified as fruit ripening induced, 185 as fruit ripening repressed, and 169 as pathogenesis related (P < 0.05). By choosing a significance level of P < 0.01, we estimated that approximately 1379 and 370 loci in the tomato genome are differentially expressed during the stages analyzed for fruit and flower development, respectively. Tomato fruit digital expression data was also compared to publicly available grape EST data to gain insight into molecular manifestation of ripening processes governing ripening regulation across species and of climacteric versus non-climacteric fruits.