Volume 12, Issue 3, Pages 298-320 (March 2019) Auxin EvoDevo: Conservation and Diversification of Genes Regulating Auxin Biosynthesis, Transport, and Signaling  Michaela Sylvia Matthes, Norman Bradley Best, Janlo M. Robil, Simon Malcomber, Andrea Gallavotti, Paula McSteen  Molecular Plant  Volume 12, Issue 3, Pages 298-320 (March 2019) DOI: 10.1016/j.molp.2018.12.012 Copyright © 2019 The Author Terms and Conditions

Figure 1 Phylogenetic Trees and Transcript Expression across Tissues of TRYPTOPHAN AMINOTRANSFERASE (TAA) and YUCCA (YUC) Flavin-Containing Monooxygenase Enzyme Family Members. Approximately maximum-likelihood phylogenetic trees of (A) TAA and (B) YUC protein sequences from maize (green), rice (orange), and Arabidopsis (blue) with Physcomitrella (black) as an outgroup. The relative expression of each gene, mined from publicly available data, is depicted as a heatmap. To normalize for the different experiments, FPKM (maize and rice) and microarray data (Arabidopsis) values were converted to a percentage across tissues, so the heatmap indicates the highest (yellow) to lowest (blue) expression for each gene. To enable comparison of gene expression within a species, the average expression column was calculated for each gene by averaging the expression across all tissues, and then dividing by the average expression of all gene family members within a given species. Missing data or unrelated tissues across species are left blank. See Supplemental Table 2 and Supplemental Materials and Methods for detailed descriptions of tissue types and expression data (Schmid et al., 2005; Wang et al., 2009b; Davidson et al., 2011, 2012). Molecular Plant 2019 12, 298-320DOI: (10.1016/j.molp.2018.12.012) Copyright © 2019 The Author Terms and Conditions

Figure 2 Phylogenetic Tree of PINFORMED (PIN) Auxin Exporter Family Members and Transcript Expression across Tissues. Approximately maximum-likelihood phylogenetic tree of PIN protein sequences from maize (green), rice (orange), and Arabidopsis (blue) with Physcomitrella (black) as an outgroup. The heatmap for gene expression comparison was generated as described in the legends of Figure 1. Molecular Plant 2019 12, 298-320DOI: (10.1016/j.molp.2018.12.012) Copyright © 2019 The Author Terms and Conditions

Figure 3 Phylogenetic Tree of Known Auxin Transporter ATP-BINDING CASSETTE-B (ABCB) and Related Proteins with Transcript Expression across Tissues. Approximately maximum-likelihood phylogenetic tree of selected ABCB protein sequences from maize (green), rice (orange), Arabidopsis (blue), and Physcomitrella (black). Due to high sequence diversity among the ABCBs, not all members of the family were included in the final tree (see Supplemental Materials and Methods). The heatmap for gene expression comparison was generated as described in the legends of Figure 1. Molecular Plant 2019 12, 298-320DOI: (10.1016/j.molp.2018.12.012) Copyright © 2019 The Author Terms and Conditions

Figure 4 Phylogenetic Tree of AUXIN1/LIKE-AUX (AUX/LAX) Auxin Importer Family Members and Transcript Expression across Tissues. Approximately maximum-likelihood phylogenetic tree of AUX/LAX protein sequences from maize (green), rice (orange), and Arabidopsis (blue) with Physcomitrella (black) as an outgroup. The relative expression of each gene, mined from publicly available data, is depicted as a heatmap. To normalize for the different experiments, FPKM (maize and rice) and microarray data (Arabidopsis) values were converted to a percentage across tissues, so the heatmap indicates the highest (yellow) to lowest (blue) expression for each gene. To enable comparison of gene expression within a species, the average expression column was calculated for each gene by averaging the expression across all tissues, and then dividing by the average expression of all gene family members within a given species. Missing data or unrelated tissues across species are left blank. See Supplemental Table 2 and Supplemental Materials and Methods for detailed descriptions of tissue types and expression data (Schmid et al., 2005; Wang et al., 2009b; Davidson et al., 2011, 2012). Molecular Plant 2019 12, 298-320DOI: (10.1016/j.molp.2018.12.012) Copyright © 2019 The Author Terms and Conditions

Figure 5 Phylogenetic Tree of TRANSPORT INHIBITOR RESPONSE1/AUXIN F-BOX (TIR1/AFB) Auxin Receptor Family Members and Transcript Expression across Tissues. Approximately maximum-likelihood phylogenetic tree of TIR1/AFB protein sequences from maize (green), rice (orange), and Arabidopsis (blue) with Physcomitrella (black) as an outgroup. The heatmap for gene expression comparison was generated as described in the legends of Figure 1. Molecular Plant 2019 12, 298-320DOI: (10.1016/j.molp.2018.12.012) Copyright © 2019 The Author Terms and Conditions

Figure 6 Phylogenetic Tree of AUXIN RESPONSE FACTOR (ARF) Family Members and Transcript Expression across Tissues. Approximately maximum-likelihood phylogenetic tree of ARF protein sequences from maize (green), rice (orange), and Arabidopsis (blue) with Physcomitrella (black) as an outgroup. Clade A (orange), clade B (blue), and clade C (gray) are color shaded and depicted on the left side of the phylogenetic tree. The heatmap for gene expression comparison was generated as described in the legends of Figure 1. Molecular Plant 2019 12, 298-320DOI: (10.1016/j.molp.2018.12.012) Copyright © 2019 The Author Terms and Conditions

Figure 7 Phylogenetic Tree of AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) Transcription Repression Factor Family Members and Transcript Expression across Tissues. Approximately maximum-likelihood phylogenetic tree of Aux/IAA protein sequences from maize (green), rice (orange), and Arabidopsis (blue) with Physcomitrella (black) as an outgroup. Respective clades are named and color shaded on the left side of the phylogenetic tree to facilitate description for this article. Clade I (shaded in blue), clade II (dark orange), clade III (green), clade IV (red), clade V (gray), clade VI (light orange), clade VII (purple), clade VIII (dark blue), and clade IX (yellow) are shown. The heatmap for gene expression comparison was generated as described in the legends of Figure 1. Molecular Plant 2019 12, 298-320DOI: (10.1016/j.molp.2018.12.012) Copyright © 2019 The Author Terms and Conditions