ABSTRACT
The study of the transcriptome, that is, the complete set of RNAs that are present in an organism, organ, tissue or cell type, has emerged as a highly productive experimental strategy to dissect many aspects of tomato (Solanum lycopersicum L.) biology, including vegetative development, fruit ripening and responses to biotic/abiotic stresses. Indeed, advances in tomato genomics, and transcriptomics in particular, have helped propel the species to its prominence as an experimental model for the study of fl eshy fruit biology, pathogen responses and more general areas of crop breeding and improvement. In this section, we review existing tools and methods that have been applied to characterize the tomato transcriptome, and also the linked and revolutionary changes that the fi eld is experiencing as a consequence of new sequencing technologies and resulting sequencebased resources. The remarkable increase in the rate and accuracy of transcript identifi cation and expression profi ling, together with plummeting sequencing costs and emerging genome sequence of tomato and several of its relatives, which are presenting numerous exciting opportunities for tomato research. We also discuss some potential practical applications, together with some of the challenges associated with the unprecedented and ever-increasing quantity of transcript expression data.
