Abstract
Plant organs are made from multiple cell types, and defining the expression level of a gene in any one cell or group of cells from a complex mixture is difficult. Dicotyledonous plants normally have three distinct layers of cells, L1, L2 and L3. Layer L1 is the single layer of cells making up the epidermis, layer L2 the single cell sub-epidermal layer and layer L3 constitutes the rest of the internal cells. Here we show how it is possible to harvest an organ and characterise the level of layer-specific expression by using a periclinal chimera that has its L1 layer from Solanum pennellii and its L2 and L3 layers from Solanum lycopersicum. This is possible by measuring the level of the frequency of species-specific transcripts. RNA-seq analysis enabled the genome-wide assessment of whether a gene is expressed in the L1 or L2/L3 layers. From 13 277 genes that are expressed in both the chimera and the parental lines and with at least one polymorphism between the parental alleles, we identified 382 genes that are preferentially expressed in L1 in contrast to 1159 genes in L2/L3. Gene ontology analysis shows that many genes preferentially expressed in L1 are involved in cutin and wax biosynthesis, whereas numerous genes that are preferentially expressed in L2/L3 tissue are associated with chloroplastic processes. These data indicate the use of such chimeras and provide detailed information on the level of layer-specific expression of genes.
Highlights
Ever since Hooke’s seminal observations that organisms are made from cells a fundamental question has existed as to what defines the components that make each cell unique
RNA-seq analysis and the availability of the tomato genome sequence and annotation enabled the genome-wide assessment of whether a gene is expressed in the L1 or L2/ L3 layers
To generate the periclinal chimera about 120 ‘V’ grafts were made between the tomato lines Heinz 1706 (Solanum lycopersicum) and LA716 (Solanum pennellii)
Summary
Ever since Hooke’s seminal observations that organisms are made from cells a fundamental question has existed as to what defines the components that make each cell unique. The second source constitutes samples collected from specific cell types or groups of cells These cells can be identified either by staining or cell-specific reporter gene expression and subsequent dissection and cell sorting, e.g. guard cells, by the isolation of specific cells or groups of cells, for example epidermal peels, or by the mechanical removal of trichomes (Birnbaum et al, 2005; Day et al, 2005; Bargmann and Birnbaum, 2010; Matas et al, 2010, 2011; Hu et al, 2011). In both scenarios the transcriptome can be analysed using either arrays or high-throughput sequencing
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