Additional file 1:

Summary of Putative BAHD Acyltransferases in the Populus trichocarpa Genome. BAHD acyltransferase loci are listed by clade, then by corresponding JGI v2.0 and v1.1 gene models and previously assigned names [3]. Protein length, exon number, and intron number are included along with manual curation notes.

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Additional file 2:

Summary of Putative BAHD Acyltransferases in Arabidopsis thaliana, Medicago truncatula, Oryza sativa, and Vitis vinifera Genomes. BAHD acyltransferase loci are listed alphabetically by genus, then by clade, then by locus number.

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Additional file 3:

Detailed Views of Phylogenetic Relationships Within Clades Ib, II, IIIb, IV, and Vb. Coloration of clades and symbols are as described in Figures 1, 2, 3, 4.

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Additional file 4:

Additional Clade-Specific Motifs Identified by MINER. Motifs are arranged by clade, and bordered with the same color scheme as in Figure 1. The thickly boxed motif in Clade Ia overlaps with the range for the QVTX(F/L)XCGG motif shown in Figure 5. Clade Ib had no additional motifs beyond those shown in Figure 5.

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Additional file 5:

Analysis of BAHD Acyltransferase Protein Subcellular Localization. Each chart indicates the results from a different prediction algorithm, with the number of sequences indicated by the y-axis and clade indicated on the x-axis

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Additional file 6:

Duplications and Retrotransposons Associated With Populus BAHD Acyltransferase Genes. Genes are organized as in Additional file 1.

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Additional file 7:

Pairwise Gene Expression Correlation Across Populus BAHD Acyltransferase Duplication Types. Box plots for Spearman rank correlations of pairwise gene expression by clade across all microarray experiments. Gene pairs are grouped by their association with local duplication, salicoid duplication, or others (all other pairwise combinations). Categories with the same letter had median correlation values that were not significantly different at α = 0.05 according to Dunn's Multiple Comparison test.

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Additional file 8:

QPCR Expression Analysis of Populus CHATL Genes. A: Relative expression of the highly similar CHATL1/2, CHATL3/6 and CHATL4/5 gene pairs in various P. tremuloides tissues. Data represent means ± SE of three biological replicates. Tissues examined included apical bud/leaves (Apex), young leaves (LPI 0/1), mature leaves (LPI 8), internodes 1-4 (IN 1-4) and 7-10 (IN 7-10), root tips (Root), female flowers (F Flwr), and male flowers (M Flwr). Dashed orange line indicates an expression level comparable to the presence vs. absence cutoff used in microarray analysis. B: Relative expression of CHATL genes in young (YL) and expanding (EL) leaves from the nitrogen stress experiment. Data represent means ± SD of two biological replicates. Genotypes are listed as in Figure 7A, with "High N" samples corresponding to non-stressed tissues in Figure 7A.

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Additional file 9:

Manually Curated Populus BAHD Acyltransferase Protein and CDS Sequences. Data provided for sequences noted in Additional File 1.

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Additional file 10:

Biochemically Characterized BAHD Acyltransferases Included in the Phylogenetic Analysis. All biochemically characterized BAHD proteins included in our analysis are listed by clade and by their order of appearance (from top to bottom) in the detailed phylogenies

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Additional file 11:

Correspondences of Populus BAHD Acyltransferase Genes and Affymetrix Probe Identifiers. Coloration for gene name is assigned according to clade membership in Figure 1.

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