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Diversification of the C-TERMINALLY ENCODED PEPTIDE (CEP) gene family in angiosperms, and evolution of plant-family specific CEP genes.

Ogilvie HA, Imin N, Djordjevic MA - BMC Genomics (2014)

Bottom Line: Using a motif-based system developed for this study to identify canonical CEP peptide domains, a total of 916 CEP genes and 1,223 CEP domains were found in angiosperms and for the first time in gymnosperms.Both CEP genes and domains were found to have diversified in angiosperms, particularly in the Poaceae and Solanaceae plant families.Multispecies orthologous relationships were determined for 22% of identified CEP genes, and further analysis of those groups found selective constraints upon residues within the CEP peptide and within the previously little-characterized variable region.

View Article: PubMed Central - PubMed

Affiliation: Research School of Biology, The Australian National University, Canberra ACT 0200, Australia. huw.ogilvie@anu.edu.au.

ABSTRACT

Background: Small, secreted signaling peptides work in parallel with phytohormones to control important aspects of plant growth and development. Genes from the C-TERMINALLY ENCODED PEPTIDE (CEP) family produce such peptides which negatively regulate plant growth, especially under stress, and affect other important developmental processes. To illuminate how the CEP gene family has evolved within the plant kingdom, including its emergence, diversification and variation between lineages, a comprehensive survey was undertaken to identify and characterize CEP genes in 106 plant genomes.

Results: Using a motif-based system developed for this study to identify canonical CEP peptide domains, a total of 916 CEP genes and 1,223 CEP domains were found in angiosperms and for the first time in gymnosperms. This defines a narrow band for the emergence of CEP genes in plants, from the divergence of lycophytes to the angiosperm/gymnosperm split. Both CEP genes and domains were found to have diversified in angiosperms, particularly in the Poaceae and Solanaceae plant families. Multispecies orthologous relationships were determined for 22% of identified CEP genes, and further analysis of those groups found selective constraints upon residues within the CEP peptide and within the previously little-characterized variable region. An examination of public Oryza sativa RNA-Seq datasets revealed an expression pattern that links OsCEP5 and OsCEP6 to panicle development and flowering, and CEP gene trees reveal these emerged from a duplication event associated with the Poaceae plant family.

Conclusions: The characterization of the plant-family specific CEP genes OsCEP5 and OsCEP6, the association of CEP genes with angiosperm-specific development processes like panicle development, and the diversification of CEP genes in angiosperms provides further support for the hypothesis that CEP genes have been integral to the evolution of novel traits within the angiosperm lineage. Beyond these findings, the comprehensive set of CEP genes and their properties reported here will be a resource for future research on CEP genes and peptides.

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Nucleotide and amino acid maximum likelihood trees of all identified CEP genes. Maximum likelihood trees were computed based on aligned, non-redundant CEP gene sequences. Both trees were rooted using the largest cluster of gymnosperm CEP genes. The putative panicle development associated genes OsCEP5 and OsCEP6 (cyan arrows) are part of a single cluster of Poaceae CEP genes.
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Fig8: Nucleotide and amino acid maximum likelihood trees of all identified CEP genes. Maximum likelihood trees were computed based on aligned, non-redundant CEP gene sequences. Both trees were rooted using the largest cluster of gymnosperm CEP genes. The putative panicle development associated genes OsCEP5 and OsCEP6 (cyan arrows) are part of a single cluster of Poaceae CEP genes.

Mentions: To infer when OsCEP5 and OsCEP6 emerged in the evolutionary history of plants, maximum likelihood phylogenetic genes of all CEP genes identified in this study were reconstructed based on both AA and nucleotide sequences. In both AA and nucleotide trees, OsCEP5 and OsCEP6 were located within a single cluster of Poaceae CEP genes (FigureĀ 8). Bootstrap support values were calculated for both trees, and in the AA tree the cluster has a strong support value of 91 (Additional file 4), while in the nucleotide tree it has a weak support value of 49 (Additional file 5).Figure 8


Diversification of the C-TERMINALLY ENCODED PEPTIDE (CEP) gene family in angiosperms, and evolution of plant-family specific CEP genes.

Ogilvie HA, Imin N, Djordjevic MA - BMC Genomics (2014)

Nucleotide and amino acid maximum likelihood trees of all identified CEP genes. Maximum likelihood trees were computed based on aligned, non-redundant CEP gene sequences. Both trees were rooted using the largest cluster of gymnosperm CEP genes. The putative panicle development associated genes OsCEP5 and OsCEP6 (cyan arrows) are part of a single cluster of Poaceae CEP genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4197245&req=5

Fig8: Nucleotide and amino acid maximum likelihood trees of all identified CEP genes. Maximum likelihood trees were computed based on aligned, non-redundant CEP gene sequences. Both trees were rooted using the largest cluster of gymnosperm CEP genes. The putative panicle development associated genes OsCEP5 and OsCEP6 (cyan arrows) are part of a single cluster of Poaceae CEP genes.
Mentions: To infer when OsCEP5 and OsCEP6 emerged in the evolutionary history of plants, maximum likelihood phylogenetic genes of all CEP genes identified in this study were reconstructed based on both AA and nucleotide sequences. In both AA and nucleotide trees, OsCEP5 and OsCEP6 were located within a single cluster of Poaceae CEP genes (FigureĀ 8). Bootstrap support values were calculated for both trees, and in the AA tree the cluster has a strong support value of 91 (Additional file 4), while in the nucleotide tree it has a weak support value of 49 (Additional file 5).Figure 8

Bottom Line: Using a motif-based system developed for this study to identify canonical CEP peptide domains, a total of 916 CEP genes and 1,223 CEP domains were found in angiosperms and for the first time in gymnosperms.Both CEP genes and domains were found to have diversified in angiosperms, particularly in the Poaceae and Solanaceae plant families.Multispecies orthologous relationships were determined for 22% of identified CEP genes, and further analysis of those groups found selective constraints upon residues within the CEP peptide and within the previously little-characterized variable region.

View Article: PubMed Central - PubMed

Affiliation: Research School of Biology, The Australian National University, Canberra ACT 0200, Australia. huw.ogilvie@anu.edu.au.

ABSTRACT

Background: Small, secreted signaling peptides work in parallel with phytohormones to control important aspects of plant growth and development. Genes from the C-TERMINALLY ENCODED PEPTIDE (CEP) family produce such peptides which negatively regulate plant growth, especially under stress, and affect other important developmental processes. To illuminate how the CEP gene family has evolved within the plant kingdom, including its emergence, diversification and variation between lineages, a comprehensive survey was undertaken to identify and characterize CEP genes in 106 plant genomes.

Results: Using a motif-based system developed for this study to identify canonical CEP peptide domains, a total of 916 CEP genes and 1,223 CEP domains were found in angiosperms and for the first time in gymnosperms. This defines a narrow band for the emergence of CEP genes in plants, from the divergence of lycophytes to the angiosperm/gymnosperm split. Both CEP genes and domains were found to have diversified in angiosperms, particularly in the Poaceae and Solanaceae plant families. Multispecies orthologous relationships were determined for 22% of identified CEP genes, and further analysis of those groups found selective constraints upon residues within the CEP peptide and within the previously little-characterized variable region. An examination of public Oryza sativa RNA-Seq datasets revealed an expression pattern that links OsCEP5 and OsCEP6 to panicle development and flowering, and CEP gene trees reveal these emerged from a duplication event associated with the Poaceae plant family.

Conclusions: The characterization of the plant-family specific CEP genes OsCEP5 and OsCEP6, the association of CEP genes with angiosperm-specific development processes like panicle development, and the diversification of CEP genes in angiosperms provides further support for the hypothesis that CEP genes have been integral to the evolution of novel traits within the angiosperm lineage. Beyond these findings, the comprehensive set of CEP genes and their properties reported here will be a resource for future research on CEP genes and peptides.

Show MeSH