SUPPORTING_INFORMATION_LEGENDS
Figure S1. Red-fluorescence and side-scatter profiles of Symbiodinium SSB01
generated by the Guava flow cytometer after growth at different light conditions.
Profiles were shown for day 0 and 25 of the growth test experiment of Figure 1a and
b. Both axes are in log scale. The red box gates the cells with high fluorescence.
Figure S2. Schematic diagram of experimental design used for generating the
Symbiodinium cultures used for the RNA-Seq analysis. Features of the Symb6
transcriptome are also summarized. Both IMK and IMK + cas medium were used for
the RNA-Seq analysis. (a) RNA isolation from cultured Symbiodinium SSB01: Precultures were grown in IMK + cas at 27oC, 10 µmol photons m−2 s−1, and then split
equally into eight flasks. The eight cultures were immediately transferred to 0, 10, 100
and 500 µmol photons m−2 s−1 for 1 or 24 h, and at each of these times was sampled
for RNA extraction and deep sequencing (RNA-Seq). An identical RNA-Seq
experiment was performed with cells grown in IMK (no casamino acid
supplementation). All samples generated for RNA-Seq are given in Table S7. (b)
Length distribution and frequency of assembled transcripts. (c) Summary of features
of Symb6. N=number of transcripts; n: 100=number of transcripts longer than 100 bp;
min, medium, mean and max=minimum, medium, mean and maximum lengths of
transcripts; N50=length-weighted, median contig length; sum=total number of
nucleotides generate by transcriptome sequencing.
Figure S3. Nucleotide sequence alignments of 5’ ends of the transcripts with full
length 22-nt SL sequence in Symb6. The alignment was performed using Clustalw
and the graphic view of alignment was generated by BioEdit for multiple sequence
alignment. The consensus nucleotides were in shade and the dots represent gap
regions.
Figure S4. Expression profiling of a select set of RCC1 genes in cells maintained
under various light conditions for 1 or 24 h. Two biological replicates were used for
all treatments. The heat-map shows mRNA abundances of RCC1s isolated from cells
grown in IMK and IMK + cas media, and exposed to different light intensities for 1
and 24 h. The treatment and times are given at the top of the heat-map; the fold
changes in transcript abundance at the given light intensities relative to 10 μmol
photons m-2 s-1 are given in the color scale (scale below the heat maps).
Figure S5. Symbiodinium surface complexity, viewed by SEM, when cells were
maintained in LL conditions. The surface structure patterns of Symbiodinium cells at
mid- to late- log phase were examined using scanning electron microscopy (SEM)
and, based on their appearance (visual); Symbiodinium surface patterns were
categorized as smooth, medium and rough.
Figure S6. qRT-PCR analysis of ACPPC (s6_25516), CRY2 (s6_16929) and RCC1
(s6_19117) after 1 and 24 h of exposure to various light conditions. Total RNA was
isolated from samples exposed to different light intensities for 1 or 24 h in IMK + cas
medium. cDNA synthesis and qPCR analysis to quantify the levels of the three
transcripts were performed with primers given in Table S8, as described in SI
Materials and Methods. Error bars represent one standard deviation around mean of
three biological replicates.
Figure S7. Amino acid alignments of predicted Symbiodinium AcpPC (s6_25516)
with LHCSR2 and LHCSR3 from Chlamydomonas reinhardtii. The alignment was
performed using Clustalw and the graphic view of alignment was generated by
BioEdit for multiple sequence alignment. The consensus residues were in shade and
the dots represent gap regions.
Figure S8. Amino acid alignments of predicted Symbiodinium CRY2 (s6_16929)
with cryptochromes from Emiliania Huxleyi CCMP1516, Phaeodactylum tricornutum
CCAP 1055/1 and Arabidopsis thaliana. The alignment was performed using
Clustalw and the graphic view of alignment was generated by BioEdit for multiple
sequence alignment. The consensus residues were in shade and the dots represent gap
regions.
Table S1. Functional categories and frequencies assigned to transcripts in IMK and
IMK + cas medium that were differentially expressed when the cells were transferred
from LL to 0 L.
Table S2. Extracellular matrix related proteins encoded in Symb6.
Table S3. Photosynthesis genes and their expression levels (TPM1) in Symb6.
Table S4. Photoreceptors encoded in the Symb6 library.
Table S5. Histones and multiple DVNP genes and their expression levels (TPM1) in
Symb6.
Table S6. Expression Levels of collagen-like protein 1-like proteins and selected
transcripts under different conditions.
Table S7. Symbiodinium SSB01 cDNA libraries that were used for RNA-Seq.
Table S8. Primers used for qRT-PCR analysis.
Data S1. RCC1 is encoded by 592 transcripts in Symb6.
Data S2. Transcripts differentially expressed when Symbiodininium cells were
transferred from LL to 0 L, ML and HL in IMK and IMK + cas medium. Data were
shown as Log2 (Fold change).
Data S3. Blastx results and InterPro annotation of transcripts with full-length or
truncated SL sequences.
Appendix S1. Sequences of the transcripts with full-length SL sequences: A22, T22
or G22.
Supporting method S1. Material and Methods.