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The Amborella vacuolar processing enzyme family.

Poncet V, Scutt C, Tournebize R, Villegente M, Cueff G, Rajjou L, Balliau T, Zivy M, Fogliani B, Job C, de Kochko A, Sarramegna-Burtet V, Job D - Front Plant Sci (2015)

Bottom Line: Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013).Three genes were found to encode VPEs in the Amborella's genome.A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella.

View Article: PubMed Central - PubMed

Affiliation: Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des Plantes Montpellier, France.

ABSTRACT
Most vacuolar proteins are synthesized on rough endoplasmic reticulum as proprotein precursors and then transported to the vacuoles, where they are converted into their respective mature forms by vacuolar processing enzymes (VPEs). In the case of the seed storage proteins, this process is of major importance, as it conditions the establishment of vigorous seedlings. Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013). In the present study, proteomic and genomic approaches were used to characterize the VPE family in this species. Three genes were found to encode VPEs in the Amborella's genome. Phylogenetic analyses showed that the Amborella sequences grouped within two major clades of angiosperm VPEs, indicating that the duplication that generated the ancestors of these clades occurred before the most recent common ancestor of living angiosperms. A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella. An analysis of natural genetic variation for each of the three Amborella VPE genes revealed the absence of selective forces acting on intronic and exonic single-nucleotide polymorphisms among several natural Amborella populations in New Caledonia.

No MeSH data available.


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Mean proportion of exonic and intronic polymorphic SNPs in the four genetic groups (North, Center, Me, and Nak; see Figure 3). The mean minor allele frequencies (MAF) are compared to the mean SSR allelic richness obtained on the same groups by Poncet et al. (2013).
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Figure 4: Mean proportion of exonic and intronic polymorphic SNPs in the four genetic groups (North, Center, Me, and Nak; see Figure 3). The mean minor allele frequencies (MAF) are compared to the mean SSR allelic richness obtained on the same groups by Poncet et al. (2013).

Mentions: We examined the MAF statistics of Amborella VPE genes within the previously described genetic groups North (Tonine, Ponandou, Pwicate, Tchamba), Center (Ba, Aoupinié, Boregaou, Amieu, Dogny), Me (Mé Ori, Mé Fomechawa), and Nak (Nakada). For each of the individuals and genetic groups studied, average MAFs were computed for each Amborella VPE gene (Figures 3, 4; Supplemental Figure S4). For exonic SNPs, higher frequencies were observed for the northern (Ponandou, Pwicate, Tonine, and Tchamba) individuals for genes AmTr_36.100 and AmTr_2.262-2, and for Nakada individual for genes AmTr_2.262-1 and AmTr_2.262-2 (Figure 3). This trend was comparable to the diversity distribution observed with SSR microsatellites (Poncet et al., 2013) with individuals from the north exhibiting higher diversity and clustering in a same group. A similar distribution was also observed for intronic SNPs, with the northern group displaying a high percentage of polymorphic SNPs (71, 68, and 95% for genes AmTr_36.100, AmTr_2.262-1, and AmTr_2.262-2, respectively), the highest percentage of private SNPs (18, 6, and 18% for genes AmTr_36.100, AmTr_2.262-1, and AmTr_2.262-2, respectively) and a mean MAF of 0.43 across all three genes, the highest among all groups (Supplemental Figure S4). In particular, changes in the mean proportion of exonic and intronic polymorphic SNPs across the four genetic groups follow a parallel progression with the mean SSR allelic richness (Figure 4). Levels of naturally occurring genomic variations in the VPE sequences thus appeared to co-vary with divergence and demographic history between populations and in particular with neutrally behaving polymorphisms (SSRs).


The Amborella vacuolar processing enzyme family.

Poncet V, Scutt C, Tournebize R, Villegente M, Cueff G, Rajjou L, Balliau T, Zivy M, Fogliani B, Job C, de Kochko A, Sarramegna-Burtet V, Job D - Front Plant Sci (2015)

Mean proportion of exonic and intronic polymorphic SNPs in the four genetic groups (North, Center, Me, and Nak; see Figure 3). The mean minor allele frequencies (MAF) are compared to the mean SSR allelic richness obtained on the same groups by Poncet et al. (2013).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4544213&req=5

Figure 4: Mean proportion of exonic and intronic polymorphic SNPs in the four genetic groups (North, Center, Me, and Nak; see Figure 3). The mean minor allele frequencies (MAF) are compared to the mean SSR allelic richness obtained on the same groups by Poncet et al. (2013).
Mentions: We examined the MAF statistics of Amborella VPE genes within the previously described genetic groups North (Tonine, Ponandou, Pwicate, Tchamba), Center (Ba, Aoupinié, Boregaou, Amieu, Dogny), Me (Mé Ori, Mé Fomechawa), and Nak (Nakada). For each of the individuals and genetic groups studied, average MAFs were computed for each Amborella VPE gene (Figures 3, 4; Supplemental Figure S4). For exonic SNPs, higher frequencies were observed for the northern (Ponandou, Pwicate, Tonine, and Tchamba) individuals for genes AmTr_36.100 and AmTr_2.262-2, and for Nakada individual for genes AmTr_2.262-1 and AmTr_2.262-2 (Figure 3). This trend was comparable to the diversity distribution observed with SSR microsatellites (Poncet et al., 2013) with individuals from the north exhibiting higher diversity and clustering in a same group. A similar distribution was also observed for intronic SNPs, with the northern group displaying a high percentage of polymorphic SNPs (71, 68, and 95% for genes AmTr_36.100, AmTr_2.262-1, and AmTr_2.262-2, respectively), the highest percentage of private SNPs (18, 6, and 18% for genes AmTr_36.100, AmTr_2.262-1, and AmTr_2.262-2, respectively) and a mean MAF of 0.43 across all three genes, the highest among all groups (Supplemental Figure S4). In particular, changes in the mean proportion of exonic and intronic polymorphic SNPs across the four genetic groups follow a parallel progression with the mean SSR allelic richness (Figure 4). Levels of naturally occurring genomic variations in the VPE sequences thus appeared to co-vary with divergence and demographic history between populations and in particular with neutrally behaving polymorphisms (SSRs).

Bottom Line: Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013).Three genes were found to encode VPEs in the Amborella's genome.A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella.

View Article: PubMed Central - PubMed

Affiliation: Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des Plantes Montpellier, France.

ABSTRACT
Most vacuolar proteins are synthesized on rough endoplasmic reticulum as proprotein precursors and then transported to the vacuoles, where they are converted into their respective mature forms by vacuolar processing enzymes (VPEs). In the case of the seed storage proteins, this process is of major importance, as it conditions the establishment of vigorous seedlings. Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013). In the present study, proteomic and genomic approaches were used to characterize the VPE family in this species. Three genes were found to encode VPEs in the Amborella's genome. Phylogenetic analyses showed that the Amborella sequences grouped within two major clades of angiosperm VPEs, indicating that the duplication that generated the ancestors of these clades occurred before the most recent common ancestor of living angiosperms. A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella. An analysis of natural genetic variation for each of the three Amborella VPE genes revealed the absence of selective forces acting on intronic and exonic single-nucleotide polymorphisms among several natural Amborella populations in New Caledonia.

No MeSH data available.


Related in: MedlinePlus