Journal
JOURNAL OF EXPERIMENTAL BOTANY
Volume 66, Issue 17, Pages 5257-5269Publisher
OXFORD UNIV PRESS
DOI: 10.1093/jxb/erv346
Keywords
Crops; genome annotation; meta-analysis; plant development; signalling peptide
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Funding
- European Commission [LSHG-CT-2006-037704]
- Interuniversity Attraction Poles Programme [IAP P7/29]
- Belgian Science Policy Office
- Ghent University Multidisciplinary Research Partnership 'Bioinformatics: from nucleotides to networks' [01MR0310W]
- Wallenbergs Stiftelse
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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.
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