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

Ghorbani S, Lin YC, Parizot B, Fernandez A, Njo MF, Van de Peer Y, Beeckman T, Hilson P - J. Exp. Bot. (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.

No MeSH data available.


The GLV family identified via de novo global sequence comparison across reference species. (A) Phylogenetic tree of the GLV family across six plants’ genome annotation. Cluster IDs from the first MCL clustering are indicated in the first prefix of each protein sequence and the species ID (data source) corresponds to the second prefix. Known Arabidopsis GLV peptides are highlighted in blue. TAIR10, Arabidopsis TAIR10; RAP2, Oryza sativa RAP-DB, IRGSPbuild5; TIGR6.1, O. sativa MSU 6.1; PORTR: Populus trichocarpa JGI v156; vitis: Vitis vinifera, Genoscope v1; maize: Zea mays ZmB73_5a. (B) GLV/RGF/CLEL cluster relationships. Black lines represent the connectivity between GLV clusters and green numbers indicate the e-value of HMM profile similarity resulting from pairwise cluster comparisons (see Supplementary Table 2 for cluster [c#] and family [f#] content).
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Figure 2: The GLV family identified via de novo global sequence comparison across reference species. (A) Phylogenetic tree of the GLV family across six plants’ genome annotation. Cluster IDs from the first MCL clustering are indicated in the first prefix of each protein sequence and the species ID (data source) corresponds to the second prefix. Known Arabidopsis GLV peptides are highlighted in blue. TAIR10, Arabidopsis TAIR10; RAP2, Oryza sativa RAP-DB, IRGSPbuild5; TIGR6.1, O. sativa MSU 6.1; PORTR: Populus trichocarpa JGI v156; vitis: Vitis vinifera, Genoscope v1; maize: Zea mays ZmB73_5a. (B) GLV/RGF/CLEL cluster relationships. Black lines represent the connectivity between GLV clusters and green numbers indicate the e-value of HMM profile similarity resulting from pairwise cluster comparisons (see Supplementary Table 2 for cluster [c#] and family [f#] content).

Mentions: The MCL clustering based on the protein profiles markedly improved the resolution of known secretory families. For example, the Arabidopsis GLV peptides were all grouped in a single family (Fig. 2A; Supplementary Fig. 2; Table 1; Supplementary Table 2). As expected, the topology of the cluster connectivity network built with the predicted proteins selected from the five reference species resembles the phylogenetic relationships between peptides in the family, as close sequences according to the phylogenetic tree tend to group together in the same cluster or in neighbouring clusters (Fig. 2B).


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

Ghorbani S, Lin YC, Parizot B, Fernandez A, Njo MF, Van de Peer Y, Beeckman T, Hilson P - J. Exp. Bot. (2015)

The GLV family identified via de novo global sequence comparison across reference species. (A) Phylogenetic tree of the GLV family across six plants’ genome annotation. Cluster IDs from the first MCL clustering are indicated in the first prefix of each protein sequence and the species ID (data source) corresponds to the second prefix. Known Arabidopsis GLV peptides are highlighted in blue. TAIR10, Arabidopsis TAIR10; RAP2, Oryza sativa RAP-DB, IRGSPbuild5; TIGR6.1, O. sativa MSU 6.1; PORTR: Populus trichocarpa JGI v156; vitis: Vitis vinifera, Genoscope v1; maize: Zea mays ZmB73_5a. (B) GLV/RGF/CLEL cluster relationships. Black lines represent the connectivity between GLV clusters and green numbers indicate the e-value of HMM profile similarity resulting from pairwise cluster comparisons (see Supplementary Table 2 for cluster [c#] and family [f#] content).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
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getmorefigures.php?uid=PMC4526923&req=5

Figure 2: The GLV family identified via de novo global sequence comparison across reference species. (A) Phylogenetic tree of the GLV family across six plants’ genome annotation. Cluster IDs from the first MCL clustering are indicated in the first prefix of each protein sequence and the species ID (data source) corresponds to the second prefix. Known Arabidopsis GLV peptides are highlighted in blue. TAIR10, Arabidopsis TAIR10; RAP2, Oryza sativa RAP-DB, IRGSPbuild5; TIGR6.1, O. sativa MSU 6.1; PORTR: Populus trichocarpa JGI v156; vitis: Vitis vinifera, Genoscope v1; maize: Zea mays ZmB73_5a. (B) GLV/RGF/CLEL cluster relationships. Black lines represent the connectivity between GLV clusters and green numbers indicate the e-value of HMM profile similarity resulting from pairwise cluster comparisons (see Supplementary Table 2 for cluster [c#] and family [f#] content).
Mentions: The MCL clustering based on the protein profiles markedly improved the resolution of known secretory families. For example, the Arabidopsis GLV peptides were all grouped in a single family (Fig. 2A; Supplementary Fig. 2; Table 1; Supplementary Table 2). As expected, the topology of the cluster connectivity network built with the predicted proteins selected from the five reference species resembles the phylogenetic relationships between peptides in the family, as close sequences according to the phylogenetic tree tend to group together in the same cluster or in neighbouring clusters (Fig. 2B).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.

No MeSH data available.