Supplementary Figure 1, Postnikova et al. Mol Gen Genom

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Supplementary Figure 1, Postnikova et al. Mol Gen Genom

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Supplementary Figure 1, Postnikova et al. Mol Gen Genom

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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).

VIIIc

XIV

IX

XI

X

Va

XII

VIIa+b

IVa

Ib

XV

II

Vb

IVc

IIIa+b

IVd

IIb

Ia

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.

IIa

IIb

Ib

IXc

IVa,b

VI

Ia,b

VIIa

VIIa

Xa,b

IIIe

IXa,c

11

IIa

VIIIb

Xa,b

Xa,b

Vb

IIIb,c,d

VIa

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 highlightedin yellow.

V

VI-2

IV-2

VIII-1

VI-1

III-2

VII-1

III-1

VII-2

III-3

IX-1

I-1

I-4

IV-2

II-1

1,2

II-3

I-2

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.

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

III

IIb

IId

IIe

ICT

INT

IIc

IIa

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.