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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.


Related in: MedlinePlus

SSP evolution in plants. For each genome, the number of proteins in a given secretory peptide family is represented as shown in the bottom bar: species with no SSP are encoded in grey, those with one SSP in white, and those with higher number of SSPs in increasingly deep red. The graph was generated with the MeV software package (Saeed et al., 2003). Blue boxes indicate five reference species. Arlyr: Arabidopsis lyrata; Artha: Arabidopsis thaliana; Brdis: Brachypodium distachyon; Brrap: Brassica rapa; Capap: Carica papaya; Carub: Capsella rubella; Chrei: Chlamydomonas reinhardtii; Cisin: Citrus sinensis; Cosub: Coccomyxa subellipsoidea; Frves: Fragaria vesca; Glmax: Glycine max; Gorai: Gossypium raimondii; Liusi: Linum usitatissimum; Madom: Malus domestica; Maesc: Manihot esculenta; Metru: Medicago truncatula; Mipus1545: Micromonas pusilla CCMP1545; Mipus299: M. pusilla RCC299; Orsat: Oryza sativa; Osluc: Ostreococcus lucimarinus; Phpat: Physcomitrella patens; Potri: Populus trichocarpa; Prper: Prunus persica; Ricom: Ricinus communis; Semoe: Selaginella moellendorffii; Sobic: Sorghum bicolor; Solyc: Solanum lycopersicum; Sotub: Solanum tuberosum; Thcac: Theobroma cacao; Vivin: Vitis vinifera; Vocar: Volvox carteri; Zemay: Zea mays. See Supplementary Table 1 for genome information and Supplementary Table 4 for family content and gene ID.
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Figure 4: SSP evolution in plants. For each genome, the number of proteins in a given secretory peptide family is represented as shown in the bottom bar: species with no SSP are encoded in grey, those with one SSP in white, and those with higher number of SSPs in increasingly deep red. The graph was generated with the MeV software package (Saeed et al., 2003). Blue boxes indicate five reference species. Arlyr: Arabidopsis lyrata; Artha: Arabidopsis thaliana; Brdis: Brachypodium distachyon; Brrap: Brassica rapa; Capap: Carica papaya; Carub: Capsella rubella; Chrei: Chlamydomonas reinhardtii; Cisin: Citrus sinensis; Cosub: Coccomyxa subellipsoidea; Frves: Fragaria vesca; Glmax: Glycine max; Gorai: Gossypium raimondii; Liusi: Linum usitatissimum; Madom: Malus domestica; Maesc: Manihot esculenta; Metru: Medicago truncatula; Mipus1545: Micromonas pusilla CCMP1545; Mipus299: M. pusilla RCC299; Orsat: Oryza sativa; Osluc: Ostreococcus lucimarinus; Phpat: Physcomitrella patens; Potri: Populus trichocarpa; Prper: Prunus persica; Ricom: Ricinus communis; Semoe: Selaginella moellendorffii; Sobic: Sorghum bicolor; Solyc: Solanum lycopersicum; Sotub: Solanum tuberosum; Thcac: Theobroma cacao; Vivin: Vitis vinifera; Vocar: Volvox carteri; Zemay: Zea mays. See Supplementary Table 1 for genome information and Supplementary Table 4 for family content and gene ID.

Mentions: Despite the challenge of short ORF prediction and the unequal quality of genome annotations, a clear trend of SSP expansion can be observed: known SSPs are encoded in large families in land plants but are almost completely absent in Chlorophyta (Fig. 4). This phylogenetic pattern may reflect that unknown sets of intercellular signals, among which secretory peptides, were required for the development of complex architectures characterizing the land plant lineage.


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)

SSP evolution in plants. For each genome, the number of proteins in a given secretory peptide family is represented as shown in the bottom bar: species with no SSP are encoded in grey, those with one SSP in white, and those with higher number of SSPs in increasingly deep red. The graph was generated with the MeV software package (Saeed et al., 2003). Blue boxes indicate five reference species. Arlyr: Arabidopsis lyrata; Artha: Arabidopsis thaliana; Brdis: Brachypodium distachyon; Brrap: Brassica rapa; Capap: Carica papaya; Carub: Capsella rubella; Chrei: Chlamydomonas reinhardtii; Cisin: Citrus sinensis; Cosub: Coccomyxa subellipsoidea; Frves: Fragaria vesca; Glmax: Glycine max; Gorai: Gossypium raimondii; Liusi: Linum usitatissimum; Madom: Malus domestica; Maesc: Manihot esculenta; Metru: Medicago truncatula; Mipus1545: Micromonas pusilla CCMP1545; Mipus299: M. pusilla RCC299; Orsat: Oryza sativa; Osluc: Ostreococcus lucimarinus; Phpat: Physcomitrella patens; Potri: Populus trichocarpa; Prper: Prunus persica; Ricom: Ricinus communis; Semoe: Selaginella moellendorffii; Sobic: Sorghum bicolor; Solyc: Solanum lycopersicum; Sotub: Solanum tuberosum; Thcac: Theobroma cacao; Vivin: Vitis vinifera; Vocar: Volvox carteri; Zemay: Zea mays. See Supplementary Table 1 for genome information and Supplementary Table 4 for family content and gene ID.
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Related In: Results  -  Collection

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Figure 4: SSP evolution in plants. For each genome, the number of proteins in a given secretory peptide family is represented as shown in the bottom bar: species with no SSP are encoded in grey, those with one SSP in white, and those with higher number of SSPs in increasingly deep red. The graph was generated with the MeV software package (Saeed et al., 2003). Blue boxes indicate five reference species. Arlyr: Arabidopsis lyrata; Artha: Arabidopsis thaliana; Brdis: Brachypodium distachyon; Brrap: Brassica rapa; Capap: Carica papaya; Carub: Capsella rubella; Chrei: Chlamydomonas reinhardtii; Cisin: Citrus sinensis; Cosub: Coccomyxa subellipsoidea; Frves: Fragaria vesca; Glmax: Glycine max; Gorai: Gossypium raimondii; Liusi: Linum usitatissimum; Madom: Malus domestica; Maesc: Manihot esculenta; Metru: Medicago truncatula; Mipus1545: Micromonas pusilla CCMP1545; Mipus299: M. pusilla RCC299; Orsat: Oryza sativa; Osluc: Ostreococcus lucimarinus; Phpat: Physcomitrella patens; Potri: Populus trichocarpa; Prper: Prunus persica; Ricom: Ricinus communis; Semoe: Selaginella moellendorffii; Sobic: Sorghum bicolor; Solyc: Solanum lycopersicum; Sotub: Solanum tuberosum; Thcac: Theobroma cacao; Vivin: Vitis vinifera; Vocar: Volvox carteri; Zemay: Zea mays. See Supplementary Table 1 for genome information and Supplementary Table 4 for family content and gene ID.
Mentions: Despite the challenge of short ORF prediction and the unequal quality of genome annotations, a clear trend of SSP expansion can be observed: known SSPs are encoded in large families in land plants but are almost completely absent in Chlorophyta (Fig. 4). This phylogenetic pattern may reflect that unknown sets of intercellular signals, among which secretory peptides, were required for the development of complex architectures characterizing the land plant lineage.

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.


Related in: MedlinePlus