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

Sarieh Ghorbani, Yao-Cheng Lin, 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
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
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
journal title
JOURNAL OF EXPERIMENTAL BOTANY
J. Exp. Bot.
volume
66
issue
17
pages
5257 - 5269
Web of Science type
Article
Web of Science id
000359688700012
JCR category
PLANT SCIENCES
JCR impact factor
5.677 (2015)
JCR rank
12/209 (2015)
JCR quartile
1 (2015)
ISSN
0022-0957
DOI
10.1093/jxb/erv346
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
additional info
the first two authors contributed equally to this work
copyright statement
I have retained and own the full copyright for this publication
id
6923231
handle
http://hdl.handle.net/1854/LU-6923231
date created
2015-09-07 14:37:19
date last changed
2016-12-19 15:45:53
@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},
}

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.