Duplications and functional divergence of ADP-glucose pyrophosphorylase genes in plants

Additional file 1:

Alignment of large and small subunits AGPases from angiosperms with protein domains highlighted. The blue domain indicates the hypervariable N terminus of the large and the small subunit. The pink and green domains indicate the catalytic domain and the β-helix domain respectively. The yellow domain indicates the loop that connects the catalytic to the β-helix domain.

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Additional file 2:

Species tree. Times of divergence are indicated in million of years (MY) at nodes [83-92]. All divergence times were examined for consistency with the fossil record [93].

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Additional file 3:

Reconciled large and small subunit trees. A) Angiosperm large subunit reconciled tree. B) Angiosperm small subunit reconciled tree. The topology of the trees shown in A) and B) was determined by ML using aligned cDNA sequences analyzed by GARLI. Nodes with bootstrap values < 70% (Figure 1) were then rearranged to minimize the number of duplications (to increase congruence with the species tree). Branch lengths reflect numbers of amino acid substitutions per site, estimated AAML (with the scale bar showing the number of amino acid substitutions per site). Reconciled tree analyses were conducted using GENETREE and the species tree in Additional file 1. Black boxes indicate duplication events. The trees in A) and B) were rooted with the AGPase large and small subunit from Chlamydomonas reinhardtii respectively. Thicker lines indicate branches with K_S < 0.1 following duplication events (using ML estimates of synonymous branch lengths).

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Additional file 4:

Phylogenetic trees of the large and the small subunits from angiosperms after rate-smoothing. The trees in parts A) and B) of this figure are rate-smoothed versions of the gene trees shown in Additional file 3A and 3B that were rearranged to increase congruence with the species tree. Rate-smoothing was done by using the PL method implemented in the r8s software. Black boxes indicate duplication events.

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Additional file 5:

Average number of synonymous substitutions per site per year. The trees in A) and B) have the topology of the trees shown in Figure 1B and 1C respectively. The length of the branches represents the number of synonymous substitutions per site as estimated by the free model of CODEML. The bars correspond to the number of synonymous substitutions per site. The numbers of synonymous substitutions per site per year, shown in C), were estimated from the most recent dated speciation events to present sequences of the trees shown in A) and B). The error bars represent 2× standard error.

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Additional file 6:

Amino acid sites in the large and the small subunit of AGPase from angiosperms under positive selection. Large subunit site numbers correspond to the amino acid sequence encoded by Shrunken-2 (NCBI accession number: P55241). Small subunit site numbers correspond to the amino acid sequence encoded by Brittle-2 (NCBI accession number: AAQ14870).

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Additional file 7:

Distribution of type I sites along the large (A) and the small (B) subunit. The cut-off value of posterior probability is empirical and it was set to 0.5 for all group comparisons except for group 1-group 3b and group 2-group 3b where the cut-off value was set to 0.6, since theta was greater for these pairs. The Y-axis corresponds to posterior probability. The X-axis corresponds to the number of the amino acid site based on the subunits encoded by Shrunken-2 (A) (NCBI accession number: P55241) and Brittle-2 (B) (NCBI accession number: AAQ14870).

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Additional file 8:

Type-I sites in the large and the small subunit of AGPase from angiosperms. Type-I functional divergence between large and small subunit groups was estimated by DIVERGE. Large subunit site numbers correspond to the amino acid sequence encoded by Shrunken-2 (NCBI accession number: P55241). Small subunit site numbers correspond to the amino acid sequence encoded by Brittle-2 (NCBI accession number: AAQ14870).

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Additional file 9:

Type-II sites in the large and the small subunit of AGPase from angiosperms. Type-II functional divergence between large and small subunit groups was estimated by DIVERGE. Large subunit site numbers correspond to the amino acid sequence encoded by Shrunken-2 (NCBI accession number: P55241). Small subunit site numbers correspond to the amino acid sequence encoded by Brittle-2 (NCBI accession number: AAQ14870).

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Additional file 10:

AGPase subunit accession numbers

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