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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.


TDIF genes in soybean, common bean, Arabidopsis, Zinnia elegans, and M. truncatula. (A) Genomic environments of the TDIF-encoding genes highlight the genetic synteny between the genes identified here in soybean, common bean, and M. truncatula with previously characterized TDIF genes of A. thaliana, AtCLE41, AtCLE42, and AtCLE44. TDIF-encoding genes are shown positioned centrally and shaded in grey. Species and chromosome number are indicated to the left of each genomic segment. Surrounding genes similar in putative function are indicated by the same colour and genes with unrelated putative functions are uncoloured. The direction of the arrow represents the orientation of the gene compared with that of the CLE gene. A high level of genetic synteny is shown here for each of the predicted TDIF-encoding genes, but was not found for AtCLE46 and GmCLE13 (data not shown), whose CLE domain begins with a histidine residue but is not a TDIF peptide. (B) Phylogenetic tree of TDIF-encoding pre-propeptides, including ZeTDIF, and also AtCLV3 as an outgroup. Two pre-propeptides, AtCLE46 and GmCLE13, are also included that have CLE domains beginning with a histidine residue, but are not true TDIF CLE peptides and did not group with the TDIF pre-propeptides. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.
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Figure 7: TDIF genes in soybean, common bean, Arabidopsis, Zinnia elegans, and M. truncatula. (A) Genomic environments of the TDIF-encoding genes highlight the genetic synteny between the genes identified here in soybean, common bean, and M. truncatula with previously characterized TDIF genes of A. thaliana, AtCLE41, AtCLE42, and AtCLE44. TDIF-encoding genes are shown positioned centrally and shaded in grey. Species and chromosome number are indicated to the left of each genomic segment. Surrounding genes similar in putative function are indicated by the same colour and genes with unrelated putative functions are uncoloured. The direction of the arrow represents the orientation of the gene compared with that of the CLE gene. A high level of genetic synteny is shown here for each of the predicted TDIF-encoding genes, but was not found for AtCLE46 and GmCLE13 (data not shown), whose CLE domain begins with a histidine residue but is not a TDIF peptide. (B) Phylogenetic tree of TDIF-encoding pre-propeptides, including ZeTDIF, and also AtCLV3 as an outgroup. Two pre-propeptides, AtCLE46 and GmCLE13, are also included that have CLE domains beginning with a histidine residue, but are not true TDIF CLE peptides and did not group with the TDIF pre-propeptides. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.

Mentions: The groupings described here could help in elucidating the function of CLE peptides where a function is yet to be assigned. Indeed, these groupings, together with genomic environment analyses, were used to identify previously unknown soybean and/or common bean orthologues of AtCLV3-, AtCLE40-, and TDIF-encoding genes, as well as likely M. truncatula orthologues. AtCLV3 was the first CLE gene to be identified in any species (Fletcher et al., 1999) and has since been identified in soybean and M. truncatula (GmCLV3a, GmCLV3b, and MtCLV3; Chen et al., 2009; Wong et al., 2013). Investigations into the genomic environment and pre-propeptide sequence similarity (Fig. 3B) led to the identification of a CLV3 orthologue in common bean. Similar approaches were used to identify AtCLE40 orthologues (Fig. 3C) in common bean and M. truncatula, in addition to GmCLE40b, the homeologue of GmCLE40a. Moreover, all TDIF orthologues in soybean, common bean, and M. truncatula were established (Fig. 7). In contrast, despite AtCLE46 and GmCLE13 sharing a high level of sequence similarity in the CLE domain, they do not show synteny to the TDIF genes, or to each other, and cluster separately (Fig. 7). Thus, these genes are unlikely to be true TDIF peptides.


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)

TDIF genes in soybean, common bean, Arabidopsis, Zinnia elegans, and M. truncatula. (A) Genomic environments of the TDIF-encoding genes highlight the genetic synteny between the genes identified here in soybean, common bean, and M. truncatula with previously characterized TDIF genes of A. thaliana, AtCLE41, AtCLE42, and AtCLE44. TDIF-encoding genes are shown positioned centrally and shaded in grey. Species and chromosome number are indicated to the left of each genomic segment. Surrounding genes similar in putative function are indicated by the same colour and genes with unrelated putative functions are uncoloured. The direction of the arrow represents the orientation of the gene compared with that of the CLE gene. A high level of genetic synteny is shown here for each of the predicted TDIF-encoding genes, but was not found for AtCLE46 and GmCLE13 (data not shown), whose CLE domain begins with a histidine residue but is not a TDIF peptide. (B) Phylogenetic tree of TDIF-encoding pre-propeptides, including ZeTDIF, and also AtCLV3 as an outgroup. Two pre-propeptides, AtCLE46 and GmCLE13, are also included that have CLE domains beginning with a histidine residue, but are not true TDIF CLE peptides and did not group with the TDIF pre-propeptides. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 7: TDIF genes in soybean, common bean, Arabidopsis, Zinnia elegans, and M. truncatula. (A) Genomic environments of the TDIF-encoding genes highlight the genetic synteny between the genes identified here in soybean, common bean, and M. truncatula with previously characterized TDIF genes of A. thaliana, AtCLE41, AtCLE42, and AtCLE44. TDIF-encoding genes are shown positioned centrally and shaded in grey. Species and chromosome number are indicated to the left of each genomic segment. Surrounding genes similar in putative function are indicated by the same colour and genes with unrelated putative functions are uncoloured. The direction of the arrow represents the orientation of the gene compared with that of the CLE gene. A high level of genetic synteny is shown here for each of the predicted TDIF-encoding genes, but was not found for AtCLE46 and GmCLE13 (data not shown), whose CLE domain begins with a histidine residue but is not a TDIF peptide. (B) Phylogenetic tree of TDIF-encoding pre-propeptides, including ZeTDIF, and also AtCLV3 as an outgroup. Two pre-propeptides, AtCLE46 and GmCLE13, are also included that have CLE domains beginning with a histidine residue, but are not true TDIF CLE peptides and did not group with the TDIF pre-propeptides. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.
Mentions: The groupings described here could help in elucidating the function of CLE peptides where a function is yet to be assigned. Indeed, these groupings, together with genomic environment analyses, were used to identify previously unknown soybean and/or common bean orthologues of AtCLV3-, AtCLE40-, and TDIF-encoding genes, as well as likely M. truncatula orthologues. AtCLV3 was the first CLE gene to be identified in any species (Fletcher et al., 1999) and has since been identified in soybean and M. truncatula (GmCLV3a, GmCLV3b, and MtCLV3; Chen et al., 2009; Wong et al., 2013). Investigations into the genomic environment and pre-propeptide sequence similarity (Fig. 3B) led to the identification of a CLV3 orthologue in common bean. Similar approaches were used to identify AtCLE40 orthologues (Fig. 3C) in common bean and M. truncatula, in addition to GmCLE40b, the homeologue of GmCLE40a. Moreover, all TDIF orthologues in soybean, common bean, and M. truncatula were established (Fig. 7). In contrast, despite AtCLE46 and GmCLE13 sharing a high level of sequence similarity in the CLE domain, they do not show synteny to the TDIF genes, or to each other, and cluster separately (Fig. 7). Thus, these genes are unlikely to be true TDIF peptides.

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.