Legends of supplemental figures
Figure S1. CiFL1 protein has the same domain structure as FLC-like proteins from
Brassicaceae. (a) Pairwise alignment of CiFL1 deduced amino acid sequence (CCO61905.1)
and AtFLC protein sequence (NP_196576). Conserved domains of MIKC-type MADSdomain proteins are shown below sequences. (b) Alignment of I-, K- and C- domains from
CiFL1 protein against the respective consensus sequences (≥ 70% conservation) from
Brassicaceae. Protein sequence logos and consensus sequences were obtained from the
alignment of annotated FLC- and MAF-like proteins from Brassicaceae(see Experimental
procedures). Bars indicate identical amino acids while colons indicate amino acids with
similar functions; the arrow points to a 1-amino acid insertion present in 5 out of the 25
aligned proteins.
Figure S2. Analysis of CiMFL1 and CiMFL2 sequences from Locascio et al. (2009). (a)
Schematic representation of AtFLC (NM_121052; NP_196576), CiMFL1 (FJ347968;
ACL54965) and CiMFL2 (JF347969; ACL54966) domains. A 540-bp fragment (180 AA) is
conserved across the three sequences, corresponding to the MADS-box, the I-, K- and Cdomains. 45 bp are missing at the 5’-end of the MADS-box in CiMFL1 and CiMFL2.
(b) Percentage of identity in the 540-bp conserved sequence between AtFLC, CiMFL1 and
CiMFL2. Arabidopsis lyrata FLC (XM_002873395; XP_002873441) and Capsella rubella
FLC (JQ993009; AFV28312) were further considered as closely related Brassicaceae
sequences (see Figure 3d). Alignments showed a 6-bp insertion in Capsella rubella FLC.
CiMFL1/2 display higher similarity with AtFLC than A. lyrata FLC and C. rubella FLC do.
(c) Best BLASTN hits of non-conserved regions of CiMFL1 and CiMFL2. α and  regions
display similarities with, respectively, vector sequences and transposon insertion while β
region is an antisense fragment of a C. intybus cDNA closely related to a component of
photosystem II from Nicotiana tabacum. (d) Arbitrarily rooted FLC-like ML tree (GTR+Γ4
model) based on conserved MADS-box nucleotide sequences found in NCBI cDNA (black)
and EST (red) databases. Numbers on each branch correspond to statistical support values (≥
50 %) obtained from the analysis of 500 bootstrap replicates. CiMFL1 and CiMFL2 sequences
(red arrows) fall in the AtFLC subtree (highlighted in orange), whereas CiFL1 isolated in this
paper (black arrow) clusters with Asterales ESTs.
Reference
Locascio, A., Lucchin, M. and Varotto, S. (2009) Characterization of a MADS
FLOWERING LOCUS C-LIKE (MFL) sequence in Cichorium intybus: a comparative study
of CiMFL and AtFLC reveals homologies and divergences in gene function. New Phytol.,
182, 630-643.
Figure S3. Steady-state levels of CiFL1 transcripts in aerial parts of Cichorium intybus var.
sativum (cv.Fredonia): (a) during vernalization of 7-day plantlets at 4°C; (b) after 4 weeks of
vernalization (black) and transfer to 17-20°C (white) or 25°C (grey) in 16-h LD. TUBULINE
(TUB) was used as a constitutive control gene.