title: Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays.
abstract: 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.
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Sarieh
authors.initials: S
authors.lastname: Ghorbani
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Yao-Cheng
authors.identifier: http://orcid.org/0000-0002-9390-795X
authors.initials: YC
authors.lastname: Lin
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Boris
authors.identifier: http://orcid.org/0000-0003-1445-6925
authors.initials: B
authors.lastname: Parizot
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Ana
authors.initials: A
authors.lastname: Fernandez
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Maria Fransiska
authors.initials: MF
authors.lastname: Njo
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa.
authors.forename: Yves
authors.identifier: http://orcid.org/0000-0003-4327-3730
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
authors.forename: Tom
authors.initials: T
authors.lastname: Beeckman
authors.affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Saclay Plant Sciences, INRA, route de Saint-Cyr, 78026 Versailles, France pierre.hilson@versailles.inra.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Hilson
mesh_terms: D017124:Conserved Sequence; D020869:Gene Expression Profiling; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D018895:Microsatellite Repeats; D010455:Peptides / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D063245:Plant Development / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development
chemical_list: D010455:Peptides; D010940:Plant Proteins
keywords: Crops; genome annotation; meta-analysis; plant development; signalling peptide.