1. Plants and algae Fungi Metazoa Protist Supplementary Figure 1. Phylogenetic analysis of GlsA1/ZRF orthologs in different organisms. Coloured background indicates different groups of organisms: blue-plants and algae, pink-fungi and green- metazoa. A. thaliana GlsA sequences are indicated by red boxes and the A. tequilana GlsA sequence by a green box. Accession numbers of sequences used in phylogenetic analysis are listed in Supplementary Table 1.

2. (a) (b) Supplementary Figure 2. Expression levels of AtglsA1 and AtGlsA2 under stress conditions. (a) AtglsA1 and AtGlsA2 absolute mRNA expression levels in heat stressed shoots (b) AtglsA1 and AtGlsA2 absolute mRNA expression levels in cold stressed shoots Data were extracted from public expression arrays: (http://bar.utoronto.ca/efp/cgibin/efpWeb.cgi).

3. 100pb ZUO1 DNAJ SANT AtGlsA1 (At3G11450) AtGlsA2 (At5G06110) atglsa1-3 atglsa 2-1 atglsa1-1 atglsa1-2 atglsa2-2 ba cd Act2 c d a b atglsa1-2atglsa1-3atglsa2-1atglsa2-2atglsa1-1Wild type A B Supplementary Figure 3. Characterization of A. thaliana GlsA insertion mutants. A. Representation of the structure of AtGlsA1 and AtGlsA2 loci. Known protein domains are color coded as indicated in the key. Triangles indicate T-DNA insertion sites. B. Semiquantitative RT-PCR analysis of 9-day-old A. thaliana seedlings. Genotypes are shown above each lane and amplified regions denoted a-d as shown in Figure 4A are indicated to the left of each gel fragment. Act2-Actin control.

4. Wild type atglsa1-3 atglsa2-1 atglsa1-3 atglsa2-1 7 week old plants g e f h a b c d Supplementary Figure 4. Morphologies of atglsa1-3 atglsa2-1 in aerial tissues. a. Wild type (left) and atglsa1-3 atglsa2-1 (right) Scale bar: 5cm. b. Detail of atglsa1-3 atglsa2-1 showing multiple ectopic rosettes c. 7 week old atglsa1-3 atglsa2-1 showing short inflorescences. Scale bars: 1cm. d. Wild type (left) and atglsa1-3 atglsa2-1 (right) inflorescences of 7 week old plants, scale bar 2cm. e, f wild type siliques, g, h atglsa1-3 atglsa2-1 siliques, scale bars are 0.5 mm.

5. (c) (d) (e) (f) (g) (h) (a) (b) Supplementary Figure 5. Phenotype confirmation of atglsa1 atglsa2 double mutants. a-d-12 day old plants, e-h-7 week old plants, a and e-wild type, b and f-atglsa1-2 atglsa2-2, c and g-atglsa1-1 atglsa2-2, d and h-atglsa1-3 atglsa2-1. Scale bars in b and c are 0.5mm, in a and d, 1mm.

6. WT atglsa1-3 atglsa2-1 Supplementary Figure 6. qRT-PCR analysis of stem cell identity and differentiation marker genes in 6 day old plants of the atglas1-3 atglsa2-1 mutant relative to the Wild type (WT). WUS-WUSCHEL, CLV3- CLAVATA3, AS1-ASYMETRIC LEAVES1, RBR-RETINOBLASTOMA, SCR-SCARECROW, STM- SHOOTMERISTEMLESS, BP-BREVIPEDICELLUS. The data represent the average of two biological replicates and three technical replicates, error bars represent standard deviation.