1 Dr. Julia Weiss Genetics Institute of Plant ... - Plant Physiology

contigs and singletons, respectively, identified from the EST database. Clones labeled
as ‘O. ficus indica contig used’ were chosen for expression analysis.
Figure 4. Phylogenetic analysis of (A) TOC and PRR genes and (B). Bootstrapping and
clone labelling as described for Figure 3.
Figure 5. Gene expression chronograms of CAM and circadian rhythm pathways during
the day/night cycle in cladodes of O. ficus-indica. Three normalized, relative gene
expression quantities corresponding to three biological replicates were collected every
four hours (dots). Oscillation (represented as a continuous curve) was modelled, via
Fourier analysis, decomposing it in two harmonics or sinusoidal components; one
circadian (24 h harmonic) and one ultradian (12 h). Dotted curves indicate harmonic
adjustment. The straight line indicates the proposed model including all the significant
harmonics.
SUPPLEMENTAL DATA LEGENDS
Table S1 Primer information and amplicon characteristics for CAM metabolism,
circadian clock and reference genes.
Table S2. Characteristics of the Opuntia db sequences. Opuntia's EST characteristics
determined before and after assembly. Each contig was compared with the NCBI's nr
database with the blastx software (see material and methods); contigs matching CAM or
Arabidopsis are defined as those with their highest blastx hit scoring an accession of
that species.
Table S3. Optimal genes for expression quantification in individual and mixed organs.
M values computed by geNorm ,and M and CV values calculated by qBasePlus allow
for ranking of optimal reference genes. The number of genes required for a reliable
quantification is established using a Pairwise Variation (PV) cut-off of 0.15; data below
that threshold are shown as NA. Gene and organ combinations are highlighted if they
are above the following limits: 0.5 for M values and 0.2 for CV values.
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