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Figure S1.  Phylogenetic tree showing the relationships between B and Bsister proteins. Proteins from gymnosperms are indicated by boxes, all other proteins are from angiosperms. The numbers next to some nodes give bootstrap percentages, shown only for relevant nodes. Some clade names are given at the right.

Figure S2.  Comparison of domain structures of B proteins with those of other MADS-domain proteins from gymnosperms and angiosperms. Conceptual amino acid sequences of MADS-box genes were aligned by the GCG computer program. Asterisks at the sequence ends mark stop codons. Shaded boxes indicate MADS- and K-domains. In between these two domains is the I-region, in which a sequence indel which is specific for B and Bsister proteins is highlighted by a shaded bold line. A double head arrow highlights the sequence insertions specific for PRDGL from Pinus and GGM15 from Gnetum.

Figure S3.  B and Bsister proteins share conserved sequence motifs in their C-terminal regions. An alignment of C-terminal regions of some B and Bsister proteins from angiosperms and gymnosperms is shown. I) DEF-like proteins from higher eudicotyledonous flowering plants (from top to bottom: AP3 from Arabidopsis thaliana, DEF from Antirrhinum majus, PMADS1 from Petunia hybrida). II) DEF-like proteins from lower eudicots (PtAP3 from Pachysandra terminalis; RbAP3-1 from Ranunculus bulbosus) or a basal angiosperm/magnoliid dicot (PhAP3 from Peperomia hirta). III) Bsister proteins, from a gymnosperm (GGM13 from Gnetum gnemon) and a basal angiosperm (AeAP3-2 from Asarum europaeum). IV) B proteins from gymnosperms (GGMn from Gnetum gnemon; DALn from Picea abies; PrDGL from Pinus radiata). V) GLO-like proteins from higher eudicots (GLOBOSA from Antirrhinum majus; FBP1 from Petunia hybrida, PI from Arabidopsis thaliana) or lower eudicots, respectively (CpPI from Caltha palustris, RbPI-1from Ranunculus bulbosus). Gene names are according to Kramer and Irish (2000). Regions defining motifs identified by Kramer et al. (1998) have been boxed. Within boxes of the alignment the most frequent amino acids at any position are highlighted in boldface.

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