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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.


Genomic environment of PvCLE15 tandemly duplicate genes of common bean, and the CLV3 and CLE40 genes of different species. The genes of interest are 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 uncolored. The direction of the arrow represents the orientation of the gene compared with that of the CLE gene. (A) Common bean chromosome 7 containing a tandem gene duplication not found on the orthologous region of soybean on chromosome 10. Orthologues of (B) CLV3 and (C) CLE40 in soybean, common bean, Arabidopsis, and M. truncatula. A high level of genetic synteny is shown here for each of these CLE genes.
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Figure 3: Genomic environment of PvCLE15 tandemly duplicate genes of common bean, and the CLV3 and CLE40 genes of different species. The genes of interest are 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 uncolored. The direction of the arrow represents the orientation of the gene compared with that of the CLE gene. (A) Common bean chromosome 7 containing a tandem gene duplication not found on the orthologous region of soybean on chromosome 10. Orthologues of (B) CLV3 and (C) CLE40 in soybean, common bean, Arabidopsis, and M. truncatula. A high level of genetic synteny is shown here for each of these CLE genes.

Mentions: When identifying gene orthologues, it was noticed that three of the 44 genes identified in common bean did not have an apparent orthologue in soybean (Table 1; Supplementary Fig. S1 at JXB online). These genes are all part of a group of four tandemly duplicated genes located on chromosome 7, called PvCLE15a, b, c, and d, and thus can all be considered orthologous to the same genes in soybean, GmCLE15a and b. This indicates that the tandem duplication occurred in common bean after it diverged ~19 MYA from soybean. Directly upstream of these tandemly duplicated genes and adjacent to PvCLE15d is another CLE peptide-encoding gene, PvCLE14 (Fig. 3A). This tandem duplication also occurs in soybean (GmCLE14 and GmCLE15a) and thus must have occurred prior to the two species diverging.


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)

Genomic environment of PvCLE15 tandemly duplicate genes of common bean, and the CLV3 and CLE40 genes of different species. The genes of interest are 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 uncolored. The direction of the arrow represents the orientation of the gene compared with that of the CLE gene. (A) Common bean chromosome 7 containing a tandem gene duplication not found on the orthologous region of soybean on chromosome 10. Orthologues of (B) CLV3 and (C) CLE40 in soybean, common bean, Arabidopsis, and M. truncatula. A high level of genetic synteny is shown here for each of these CLE genes.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: Genomic environment of PvCLE15 tandemly duplicate genes of common bean, and the CLV3 and CLE40 genes of different species. The genes of interest are 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 uncolored. The direction of the arrow represents the orientation of the gene compared with that of the CLE gene. (A) Common bean chromosome 7 containing a tandem gene duplication not found on the orthologous region of soybean on chromosome 10. Orthologues of (B) CLV3 and (C) CLE40 in soybean, common bean, Arabidopsis, and M. truncatula. A high level of genetic synteny is shown here for each of these CLE genes.
Mentions: When identifying gene orthologues, it was noticed that three of the 44 genes identified in common bean did not have an apparent orthologue in soybean (Table 1; Supplementary Fig. S1 at JXB online). These genes are all part of a group of four tandemly duplicated genes located on chromosome 7, called PvCLE15a, b, c, and d, and thus can all be considered orthologous to the same genes in soybean, GmCLE15a and b. This indicates that the tandem duplication occurred in common bean after it diverged ~19 MYA from soybean. Directly upstream of these tandemly duplicated genes and adjacent to PvCLE15d is another CLE peptide-encoding gene, PvCLE14 (Fig. 3A). This tandem duplication also occurs in soybean (GmCLE14 and GmCLE15a) and thus must have occurred prior to the two species diverging.

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.