Transcriptome Analysis of Cytokinin Response in Tomato Leaves

Background: Tomato is one of the most economically and agriculturally important Solanaceous species and vegetable crops. It serves as a model for examination of fruit biology as well as compound leaf development. Cytokinin is a plant hormone linked to the control of leaf development that is known to regulate a wide range of genes including many transcription factors. To date there is little known of the leaf transcriptome in tomato and how it might be regulated by cytokinin. We employ high throughput mRNA sequencing technology bioinformatic methodologies to robustly analyze cytokinin regulated tomato leaf transcriptomes. Methodology: To examine cytokinin regulated gene expression at a transcriptome level in tomato leaves we shotgun sequenced messenger RNA with Illumina technology and assembled de novo the tomato leaf transcriptome. Leaf samples of two ages, 13d and 35d were treated with cytokinin or the solvent vehicle control DMSO for 2h or 24h, after which RNA was extracted for RNA sequencing. To confirm the accuracy of RNA sequencing results, we performed qPCR analysis of select transcripts identified as cytokinin regulated by the RNA sequencing approach. Conclusions: The resulting data provide the first hormone transcriptome analysis of leaves in tomato. Specifically we identified several previously untested tomato orthologs of cytokinin-related genes found in other species as well as numerous novel cytokinin-regulated transcripts in tomato leaves. Principle component analysis of the data indicates that length of cytokinin treatment and plant age are the major factors responsible for changes in transcripts observed in this study. Overall this provides a solid foundation for future study of cytokinin and cytokinin regulated genes involved in compound leaf development or other developmental processes in tomato.