Computational-Based Analysis to Associate the Function of Plant Signaling Peptides with Distinct Biological Processes

Over 1,000 putative secreted peptides have been identified in the Arabidopsis genome, but little is known about their functional roles. Here we demonstrate, using PROPEP2 in a worked example, how a computational-based co-expression analysis can be used to associate the function of a specific plant peptide with a specific biological process. The analysis reveals that PROPEP2 is, highly co-expressed with pathogen defense genes including, the PROPEP3 paralog and the extracellular Pep1 and Pep2 receptors. It additionally reveals that the co-expressed genes are induced in response to a broad range of pathogens and their associated elicitors. The results are completely supportive of previously known functional roles of this peptide and thus clearly demonstrate that the computational-based analysis presented can be used to associate the function of a specific plant peptide with a specific biological process and can also accurately identify functionally related genes.