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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.


Multiple sequence alignment of common bean (Phaseolus vulgaris) CLE pre-propeptides. Related sequences tend to align closer together. Shading of amino acid residues represents conservation, with the darker the shading the more highly conserved the residues. As with the soybean prepropeptides shown in Fig. 1, the CLE domain and the leucine-rich region of the signal peptide domain exhibit the greatest degree of conservation across the entire pre-propeptide family. (This figure is available in colour at JXB online.)
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Figure 2: Multiple sequence alignment of common bean (Phaseolus vulgaris) CLE pre-propeptides. Related sequences tend to align closer together. Shading of amino acid residues represents conservation, with the darker the shading the more highly conserved the residues. As with the soybean prepropeptides shown in Fig. 1, the CLE domain and the leucine-rich region of the signal peptide domain exhibit the greatest degree of conservation across the entire pre-propeptide family. (This figure is available in colour at JXB online.)

Mentions: To characterize their amino acid sequences, all identified CLE peptide-encoding genes were translated and successive multiple sequence alignments were conducted using entire CLE pre-propeptide sequences. Despite having large variable domains, the pre-propeptides grouped strongly according to their CLE domain sequence in both soybean (Fig. 1) and common bean (Fig. 2). This helped in identifying likely homeologous (duplicate) copies of genes in the palaeopolyploid genome of soybean, with 39 pairs identified compared with only six genes having no duplicate (Fig. 1; Table 1). The six genes lacking a duplicate were re-blasted against the soybean genome to confirm their lack of a duplicate, and their homeologous chromosome region was checked for unannotated genes. The presence of a common bean orthologue confirmed they were not triplicated within the soybean genome.


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)

Multiple sequence alignment of common bean (Phaseolus vulgaris) CLE pre-propeptides. Related sequences tend to align closer together. Shading of amino acid residues represents conservation, with the darker the shading the more highly conserved the residues. As with the soybean prepropeptides shown in Fig. 1, the CLE domain and the leucine-rich region of the signal peptide domain exhibit the greatest degree of conservation across the entire pre-propeptide family. (This figure is available in colour at JXB online.)
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Multiple sequence alignment of common bean (Phaseolus vulgaris) CLE pre-propeptides. Related sequences tend to align closer together. Shading of amino acid residues represents conservation, with the darker the shading the more highly conserved the residues. As with the soybean prepropeptides shown in Fig. 1, the CLE domain and the leucine-rich region of the signal peptide domain exhibit the greatest degree of conservation across the entire pre-propeptide family. (This figure is available in colour at JXB online.)
Mentions: To characterize their amino acid sequences, all identified CLE peptide-encoding genes were translated and successive multiple sequence alignments were conducted using entire CLE pre-propeptide sequences. Despite having large variable domains, the pre-propeptides grouped strongly according to their CLE domain sequence in both soybean (Fig. 1) and common bean (Fig. 2). This helped in identifying likely homeologous (duplicate) copies of genes in the palaeopolyploid genome of soybean, with 39 pairs identified compared with only six genes having no duplicate (Fig. 1; Table 1). The six genes lacking a duplicate were re-blasted against the soybean genome to confirm their lack of a duplicate, and their homeologous chromosome region was checked for unannotated genes. The presence of a common bean orthologue confirmed they were not triplicated within the soybean genome.

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.