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Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

Sarieh Ghorbani (UGent) , Yao-Cheng Lin (UGent) , Boris Parizot (UGent) , Ana Fernandez Salina (UGent) , Maria Njo (UGent) , Yves Van de Peer (UGent) , Tom Beeckman (UGent) and Pierre Hilson (UGent)
(2015) JOURNAL OF EXPERIMENTAL BOTANY. 66(17). p.5257-5269
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
PLANT DEVELOPMENT, SEQUENCE, SHOOT DEVELOPMENT, ARABIDOPSIS ROOT, LATERAL ROOT, SMALL SIGNALING PEPTIDES, signalling peptide, plant development, meta-analysis, genome annotation, Crops, IDENTIFICATION, INITIATION, EXPRESSION, REVEALS

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Citation

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Chicago
Ghorbani, Sarieh, Yao-Cheng Lin, Boris Parizot, Ana Fernandez Salina, Maria Njo, Yves Van de Peer, Tom Beeckman, and Pierre Hilson. 2015. “Expanding the Repertoire of Secretory Peptides Controlling Root Development with Comparative Genome Analysis and Functional Assays.” Journal of Experimental Botany 66 (17): 5257–5269.
APA
Ghorbani, S., Lin, Y.-C., Parizot, B., Fernandez Salina, A., Njo, M., Van de Peer, Y., Beeckman, T., et al. (2015). Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays. JOURNAL OF EXPERIMENTAL BOTANY, 66(17), 5257–5269.
Vancouver
1.
Ghorbani S, Lin Y-C, Parizot B, Fernandez Salina A, Njo M, Van de Peer Y, et al. Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays. JOURNAL OF EXPERIMENTAL BOTANY. 2015;66(17):5257–69.
MLA
Ghorbani, Sarieh, Yao-Cheng Lin, Boris Parizot, et al. “Expanding the Repertoire of Secretory Peptides Controlling Root Development with Comparative Genome Analysis and Functional Assays.” JOURNAL OF EXPERIMENTAL BOTANY 66.17 (2015): 5257–5269. Print.
@article{6923231,
  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.},
  author       = {Ghorbani, Sarieh and Lin, Yao-Cheng and Parizot, Boris and Fernandez Salina, Ana and Njo, Maria and Van de Peer, Yves and Beeckman, Tom and Hilson, Pierre},
  issn         = {0022-0957},
  journal      = {JOURNAL OF EXPERIMENTAL BOTANY},
  keyword      = {PLANT DEVELOPMENT,SEQUENCE,SHOOT DEVELOPMENT,ARABIDOPSIS ROOT,LATERAL ROOT,SMALL SIGNALING PEPTIDES,signalling peptide,plant development,meta-analysis,genome annotation,Crops,IDENTIFICATION,INITIATION,EXPRESSION,REVEALS},
  language     = {eng},
  number       = {17},
  pages        = {5257--5269},
  title        = {Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays},
  url          = {http://dx.doi.org/10.1093/jxb/erv346},
  volume       = {66},
  year         = {2015},
}

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