Global transcriptome profiling uncovers footprints of root and shoot development in crop models barley and tomato

Land plants establish their forms at two development hotspots- root and shoots apices. In this study, we dissected and compared the global transcriptome of these developmental zones in crop models barley and tomato. We employed a state of the art transcriptome analysis technique for deep profiling of expressed genes. This analysis resulted in highly reproducible quantitative expression profiles of 19,441 and 23,388 genes in barley and tomato, respectively. In barley, 16,834 genes were expressed both in root and shoot apices, whereas 1,081 genes were specific to root apex and 1,526 genes were active in shoot apex. With significant variations 20,154 genes were expressed in root and shoot apices of tomato of which 1,858 and 1,376 genes showed root and shoot specificities. Systematic analyses of these genes revealed distinct commonalties and divergence among the active genes for root and shoot development. A deeper insight in these data uncover tissue- and species specific genes, unique footprints of gene ontologies and divergence of auxins pathway genes in root and shoot apices of barley and tomato. These data provide a primary resource to understand intra- and inter-species genetic networks of root and shoot development as well as the evolution of genes in crop plants.