Using a perclinal chimera to determine layer-specific gene expression

The aim of this study was to identify the layer specific transcriptome in a mixture of tomato cell types. A tomato L1 periclinal chimera was generated that has an epidermal L1 layer from Solanum pennellii and internal L2 and L3 layers from Solanum lycopersicum. SOLiD RNA-seq data was generated from the chimera and the parental lines using different tissue samples (leaf, leaf under water deficit conditions and mature green fruit). Mapping the transcriptomic reads of the parental lines to the S. lycopersicum genome sequence enabled the identification of polymorphisms within each species. Reads from the chimera were assessed as coming from one or other of the parental species based upon the single nucleotide polymorphisms detected and the species specific gene expression was defined. By comparing the S. pennellii and S. lycopersicum specific expression in the chimera with the related expression in the parental lines, genes with layer-specific expression were identified.