In silico identification and in vivo validation of a set of evolutionary conserved plant root-specific cis-regulatory elements.

Abstract Marker genes are specifically expressed in a tissue, organ or time of development. Here we used a computational screen to identify marker genes of the root in Arabidopsis thaliana . We mined the existing transcriptome datasets for genes having high expression in roots while being low in all other organs under a wide range of growth conditions. We show that the root-specificity of these genes is conserved in the sister species Arabidopsis lyrata , indicating that their expression pattern is under selective pressure. We delineated the cis-regulatory elements responsible for root-specific expression and validated two third of those in planta as bona fide root-specific regulatory sequences. We identified three motifs over-represented in these sequences, which mutation resulted in alteration of root-specific expression, demonstrating that these motifs are functionally relevant. In addition, the three motifs are also over-represented in the cis-regulatory regions of the A. lyrata orthologs of our root-specific genes, and this despite an overall low degree of sequence conservation of these regions. Our results provide a resource to assess root-identity in the model genus Arabidopsis and shed light on the evolutionary history of gene regulation in plants.