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Genome-wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues of Arabidopsis thaliana.

Hastwell AH, Gresshoff PM, Ferguson BJ - J. Exp. Bot. (2015)

Bottom Line: The soybean CLE pre-propeptide family was further analysed and separated into seven distinct groups based on structure, with groupings strongly associated with the CLE domain sequence and function.Transcriptional evidence was also used to provide further insight into the location and function of all CLE peptide-encoding members currently available in gene atlases for the three species.Taken together, this in-depth analysis helped to identify and categorize the complete CLE peptide families of soybean and common bean, established gene orthologues within the two legume species, and Arabidopsis, and provided a platform to help compare, contrast, and identify the function of critical CLE peptide hormones in plant development.

View Article: PubMed Central - PubMed

Affiliation: Centre for Integrative Legume Research, School of Agricultural and Food Sciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.

No MeSH data available.


Soybean CLE pre-propeptide phylogenetic tree illustrating the seven distinct identity groups. Phylogenetic analysis was performed using the multiple sequence alignment generated with entire pre-propeptide sequences (Fig. 1), including AtCLV3 as an outgroup. Homeologous genes consistently cluster together with high confidence (indicated by high bootstrap values). The seven groups (Group I–VII) were assigned based on clustering in the tree, in addition to sequence similarity. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.
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Figure 5: Soybean CLE pre-propeptide phylogenetic tree illustrating the seven distinct identity groups. Phylogenetic analysis was performed using the multiple sequence alignment generated with entire pre-propeptide sequences (Fig. 1), including AtCLV3 as an outgroup. Homeologous genes consistently cluster together with high confidence (indicated by high bootstrap values). The seven groups (Group I–VII) were assigned based on clustering in the tree, in addition to sequence similarity. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.

Mentions: The function of many CLE peptides can be predicted based on sequence. The Arabidopsis CLE peptides are currently categorized into two groups: type-A affecting root and shoot meristem development, and type-B affecting vasculature development (Matsubayashi, 2014). The soybean CLE peptides were assigned into different categories based on the sequence alignment, phylogenetic grouping of their pre-propeptides, and their functional roles where known. The groups were initially defined based on phylogenetic analysis, and were then further refined following examination of their CLE domain and adjacent residues. In total, seven groups (Groups I–VII) were identified (Fig. 5). Logo alignments (Fig. 6) were subsequently constructed to establish the level of conservation within the 13 amino acid CLE domain of each group, with highly conserved residues probably critical to their function.


Genome-wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues of Arabidopsis thaliana.

Hastwell AH, Gresshoff PM, Ferguson BJ - J. Exp. Bot. (2015)

Soybean CLE pre-propeptide phylogenetic tree illustrating the seven distinct identity groups. Phylogenetic analysis was performed using the multiple sequence alignment generated with entire pre-propeptide sequences (Fig. 1), including AtCLV3 as an outgroup. Homeologous genes consistently cluster together with high confidence (indicated by high bootstrap values). The seven groups (Group I–VII) were assigned based on clustering in the tree, in addition to sequence similarity. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4526924&req=5

Figure 5: Soybean CLE pre-propeptide phylogenetic tree illustrating the seven distinct identity groups. Phylogenetic analysis was performed using the multiple sequence alignment generated with entire pre-propeptide sequences (Fig. 1), including AtCLV3 as an outgroup. Homeologous genes consistently cluster together with high confidence (indicated by high bootstrap values). The seven groups (Group I–VII) were assigned based on clustering in the tree, in addition to sequence similarity. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.
Mentions: The function of many CLE peptides can be predicted based on sequence. The Arabidopsis CLE peptides are currently categorized into two groups: type-A affecting root and shoot meristem development, and type-B affecting vasculature development (Matsubayashi, 2014). The soybean CLE peptides were assigned into different categories based on the sequence alignment, phylogenetic grouping of their pre-propeptides, and their functional roles where known. The groups were initially defined based on phylogenetic analysis, and were then further refined following examination of their CLE domain and adjacent residues. In total, seven groups (Groups I–VII) were identified (Fig. 5). Logo alignments (Fig. 6) were subsequently constructed to establish the level of conservation within the 13 amino acid CLE domain of each group, with highly conserved residues probably critical to their function.

Bottom Line: The soybean CLE pre-propeptide family was further analysed and separated into seven distinct groups based on structure, with groupings strongly associated with the CLE domain sequence and function.Transcriptional evidence was also used to provide further insight into the location and function of all CLE peptide-encoding members currently available in gene atlases for the three species.Taken together, this in-depth analysis helped to identify and categorize the complete CLE peptide families of soybean and common bean, established gene orthologues within the two legume species, and Arabidopsis, and provided a platform to help compare, contrast, and identify the function of critical CLE peptide hormones in plant development.

View Article: PubMed Central - PubMed

Affiliation: Centre for Integrative Legume Research, School of Agricultural and Food Sciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.

No MeSH data available.