1. Supplementary Figure 1, Postnikova et al. Mol Gen Genom Alignment of the alfalfa bHLH domain. Aromatic amino acids (aa) FYW (blue), basic aa KRH (red), aliphatic aa ILMV (green), hydrophilic aa GPST (yellow).

2. Ib XV Vb IVd IaIIb IIIa+b II IVc IVa VIIa+b X Va XI XIVVIIIc IX XII Supplementary Figure 2, Postnikova et al. Mol Gen Genom Phylogenetic analysis of the bHLH proteins from A. thaliana (green circles), M. truncatula (blue circles) and M. sativa (red circles). Tentative locations of the previously described A. thaliana subfamilies are indicated above the tree in Roman numerals.

3. Xa,b VIIa VI IXc Xa,b IIIb,c,d Vb VIIIb IIa IXa,c IIIe VIIa Ia,b IVa,b Ib IIbIIa VIa 11 Supplementary Figure 3, Postnikova et al., Mol Gen Genom. Phylogenetic analysis of the ERF proteins from A. thaliana (green circles), M. truncatula (blue circles) and M. sativa (red circles). Tentative locations of the previously described A. thaliana ERF subfamilies (Roman numerals) indicated in squire brackets. Novel alfalfa clade numbered as in Fig. 2 is highlighted in yellow.

4. II-1 III-3 III-1 III-2 IV-2 VVI-2 VIII-1 VII-2 IX-1 I-1 I-4 IV-2 I-2 II-3 VII-1 VI-1 Supplementary Figure 4, Postnikova et al., Mol Gen Genom. Phylogenetic analysis of the NAC proteins from A. thaliana (green circles), M. truncatula (blue circles) and M. sativa (red circles). Tentative locations of the previously described A. thaliana NAC subfamilies (Roman numerals) indicated in squire brackets. Novel alfalfa clade numbered as in Figure 4 is highlighted in yellow. 1,2

5. Supplementary Figure 5, Postnikova et al., Mol Gen Genom Alignment of alfalfa and M. truncatula NAC proteins from the novel clade with representative TFs of A. thaliana NAC

6. IIc III IIb ICT INT IIa IId IIe Supplementary Figure 6, Postnikova et al., Mol Gen Genom. Phylogenetic analysis of the WRKY proteins from A. thaliana (green circles), M. truncatula (blue circles) and M. sativa (red circles). Tentative locations of the previously described A. thaliana subfamilies are indicated above the tree in Roman numerals. INT and IC represent the N-terminal and C-terminal domains from the Group I.