Additional file 1:

Amino acid sequence alignment of Aux/IAA proteins of A. thaliana, S. moellendorffii and P. patens across conserved domain I. An LxLxL motif is encoded by Aux/IAAs of A. thaliana and S. moellendorffii, but not of P. patens.

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Additional file 2:

Phylogenetic relationship of A. thaliana and P. patens TOPLESS-like transcriptional co-repressors (Neighbor Joining (NJ) method). The P. patens genome encodes two TOPLESS-like transcriptional co-repressors. Bootstrap values greater than 49 are recorded.

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Additional file 3:

Amino acid sequence alignment of Aux/IAA proteins of A. thaliana, S. moellendorffii and P. patens domain II. The core motif of domain II of Aux/IAA proteins was present in all plant species tested. Bootstrap values greater than 49 are recorded.

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Additional file 4:

Phylogenetic relationship of A. thaliana and P. patens TIR1-like F-box proteins (Neighbor Joining (NJ) method). Four paralogs of the TIR1-family of F-box proteins are present in P. patens. Bootstrap values greater than 49 are presented.

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Additional file 5:

Phylogenetic relationship of A. thaliana, S. moellendorffii and P. patens ARF and Aux/IAA proteins (Bayesian inference). To infer the history of duplication and losses among the species tested, the CTD+ phylogeny was reconciled with Notung using the species tree (Phypa, (Selmo, Arath)).

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Additional file 6:

Phylogeny of A. thaliana and P. trichocarpa Aux/IAA (A) and ARF (B) proteins. Boxes identify nodes tested for positive selection.

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Additional file 7:

Expression pattern of paralogous pairs of A. thaliana Aux/IAA genes (A-J). gcRMA normalized data were used. Three biological replications were used to generate the data set. The two-way ANOVA was used to partition the gene (G), sample (S) and GxS interaction effects.

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Additional file 8:

Phylogenetic relationship of A. thaliana, S. moellendorffii and P. patens ARF proteins. Reconciled tree based on Bayesian inference. Length of middle region was normalized and transformed into a continuous character matrix.

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Additional file 9:

Detailed comparison of A. thaliana, P. patens and S. moellendorffii ARFs. Here we present details of the middle region of ARFs, the presence of domain III and IV, amino acid frequency for Q, S, G, P, L, M, the total length of proteins, and the presence of amino acid-rich domains using ScanProsite.

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Additional file 10:

Phylogenetic relationship of A. thaliana, S. moellendorffii and P. patens ARF proteins. Reconciled tree based on Bayesian inference. Q-rich regions are represented by the amino acid frequency normalized with the length of the MR.

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Additional file 11:

ARF protein sequence alignment of the middle regions in the ARF7 node of A. thaliana and P. trichocarpa. Arrows indicate sites at which positive selection was detected. Boxed amino acids indicate putative phosphorylation motifs.

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Additional file 12:

Phylogenetic relationship (neighbor-joining (NJ) method) of A. thaliana, S. moellendorffii and P. patens GH3 proteins. PpGH3s are indicated in light blue. SmGH3s are indicated in light green.

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Additional file 13:

Phylogenetic relationship (neighbor-joining (NJ) method) of A. thaliana and P. patens SAUR proteins. The P. patens SAURs are indicated in light blue.A. thaliana SAURs transcriptionally up-regulated by auxin are indicated in purple.

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Additional file 14:

Phylogenetic relationship (neighbor-joining (NJ) method) of A. thaliana and P. patens LBD proteins. LBD proteins of P. patens are indicated in light green. A. thaliana LBDs transcriptionally up-regulated by auxin are indicated in purple.

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