Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on
structural features that characterize SSP families known to take part in postembryonic development, this comparative
genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication.
Because genome annotation based on short sequence homology is difficult, the criteria for the de novo
identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species.
The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic
pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide
with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.
psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana
SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and
in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized
SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic
peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining
comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors
potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different
species for the study of a wide range of developmental programmes.